Preprints
Available on bioRxiv.
Publications
1.
Li, Yuhao; Harris, Bradley S.; Li, Zhongwu; Shi, Chenyang; Abdullah, Jobaer; Majumder, Sagardip; Berhanu, Samuel; Vorobieva, Anastassia A.; Myers, Sydney K.; Hettige, Jeevapani; Baer, Marcel D.; Yoreo, James J. De; Baker, David; Noy, Aleksandr
Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels Journal Article
In: ACS Nano, 2025.
@article{Li2024,
title = {Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels},
author = {Yuhao Li and Bradley S. Harris and Zhongwu Li and Chenyang Shi and Jobaer Abdullah and Sagardip Majumder and Samuel Berhanu and Anastassia A. Vorobieva and Sydney K. Myers and Jeevapani Hettige and Marcel D. Baer and James J. De Yoreo and David Baker and Aleksandr Noy},
url = {https://pubs.acs.org/doi/10.1021/acsnano.4c11317, ACS Nano
https://www.bakerlab.org/wp-content/uploads/2025/02/li-et-al-2024-water-solute-and-ion-transport-in-de-novo-designed-membrane-protein-channels.pdf, PDF},
doi = {10.1021/acsnano.4c11317},
year = {2025},
date = {2025-01-21},
urldate = {2025-01-21},
journal = {ACS Nano},
publisher = {American Chemical Society (ACS)},
abstract = {Biological organisms engineer peptide sequences to fold into membrane pore proteins capable of performing a wide variety of transport functions. Synthetic de novo-designed membrane pores can mimic this approach to achieve a potentially even larger set of functions. Here we explore water, solute, and ion transport in three de novo designed β-barrel membrane channels in the 5–10 Å pore size range. We show that these proteins form passive membrane pores with high water transport efficiencies and size rejection characteristics consistent with the pore size encoded in the protein structure. Ion conductance and ion selectivity measurements also show trends consistent with the pore size, with the two larger pores showing weak cation selectivity. MD simulations of water and ion transport and solute size exclusion are consistent with the experimental trends and provide further insights into structure–function correlations in these membrane pores.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Biological organisms engineer peptide sequences to fold into membrane pore proteins capable of performing a wide variety of transport functions. Synthetic de novo-designed membrane pores can mimic this approach to achieve a potentially even larger set of functions. Here we explore water, solute, and ion transport in three de novo designed β-barrel membrane channels in the 5–10 Å pore size range. We show that these proteins form passive membrane pores with high water transport efficiencies and size rejection characteristics consistent with the pore size encoded in the protein structure. Ion conductance and ion selectivity measurements also show trends consistent with the pore size, with the two larger pores showing weak cation selectivity. MD simulations of water and ion transport and solute size exclusion are consistent with the experimental trends and provide further insights into structure–function correlations in these membrane pores.
2.
Piraner, Dan I.; Abedi, Mohamad H.; Gonzalez, Maria J. Duran; Chazin-Gray, Adam; Lin, Annie; Zhu, Iowis; Ravindran, Pavithran T.; Schlichthaerle, Thomas; Huang, Buwei; Bearchild, Tyler H.; Lee, David; Wyman, Sarah; Jun, Young-wook; Baker, David; Roybal, Kole T.
Engineered receptors for soluble cellular communication and disease sensing Journal Article
In: Nature, 2024.
@article{Piraner2024,
title = {Engineered receptors for soluble cellular communication and disease sensing},
author = {Dan I. Piraner and Mohamad H. Abedi and Maria J. Duran Gonzalez and Adam Chazin-Gray and Annie Lin and Iowis Zhu and Pavithran T. Ravindran and Thomas Schlichthaerle and Buwei Huang and Tyler H. Bearchild and David Lee and Sarah Wyman and Young-wook Jun and David Baker and Kole T. Roybal},
url = {https://www.nature.com/articles/s41586-024-08366-0, Nature},
doi = {10.1038/s41586-024-08366-0},
year = {2024},
date = {2024-11-14},
urldate = {2024-11-14},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
abstract = {Despite recent advances in mammalian synthetic biology, there remains a lack of modular synthetic receptors that can robustly respond to soluble ligands and in turn activate bespoke cellular functions. Such receptors would have extensive clinical potential to regulate the activity of engineered therapeutic cells, but to date only receptors against cell surface targets have approached clinical translation1. To address this gap, we developed a receptor architecture called synthetic intramembrane proteolysis receptor (SNIPR), that has the added ability to be activated by soluble ligands, both natural and synthetic, with remarkably low baseline activity and high fold activation, through an endocytic, pH-dependent cleavage mechanism. We demonstrate the therapeutic capabilities of the receptor platform by localizing the activity of CAR T cells to solid tumors where soluble disease-associated factors are expressed, bypassing the major hurdle of on-target off-tumor toxicity in bystander organs. We further applied the SNIPR platform to engineer fully synthetic signaling networks between cells orthogonal to natural signaling pathways, expanding the scope of synthetic biology. Our design framework enables cellular communication and environmental interactions, extending the capabilities of synthetic cellular networking in clinical and research contexts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Despite recent advances in mammalian synthetic biology, there remains a lack of modular synthetic receptors that can robustly respond to soluble ligands and in turn activate bespoke cellular functions. Such receptors would have extensive clinical potential to regulate the activity of engineered therapeutic cells, but to date only receptors against cell surface targets have approached clinical translation1. To address this gap, we developed a receptor architecture called synthetic intramembrane proteolysis receptor (SNIPR), that has the added ability to be activated by soluble ligands, both natural and synthetic, with remarkably low baseline activity and high fold activation, through an endocytic, pH-dependent cleavage mechanism. We demonstrate the therapeutic capabilities of the receptor platform by localizing the activity of CAR T cells to solid tumors where soluble disease-associated factors are expressed, bypassing the major hurdle of on-target off-tumor toxicity in bystander organs. We further applied the SNIPR platform to engineer fully synthetic signaling networks between cells orthogonal to natural signaling pathways, expanding the scope of synthetic biology. Our design framework enables cellular communication and environmental interactions, extending the capabilities of synthetic cellular networking in clinical and research contexts.
3.
Huang, Buwei; Abedi, Mohamad; Ahn, Green; Coventry, Brian; Sappington, Isaac; Tang, Cong; Wang, Rong; Schlichthaerle, Thomas; Zhang, Jason Z.; Wang, Yujia; Goreshnik, Inna; Chiu, Ching Wen; Chazin-Gray, Adam; Chan, Sidney; Gerben, Stacey; Murray, Analisa; Wang, Shunzhi; O’Neill, Jason; Yi, Li; Yeh, Ronald; Misquith, Ayesha; Wolf, Anitra; Tomasovic, Luke M.; Piraner, Dan I.; Gonzalez, Maria J. Duran; Bennett, Nathaniel R.; Venkatesh, Preetham; Ahlrichs, Maggie; Dobbins, Craig; Yang, Wei; Wang, Xinru; Sahtoe, Danny D.; Vafeados, Dionne; Mout, Rubul; Shivaei, Shirin; Cao, Longxing; Carter, Lauren; Stewart, Lance; Spangler, Jamie B.; Roybal, Kole T.; Greisen, Per Jr; Li, Xiaochun; Bernardes, Gonçalo J. L.; Bertozzi, Carolyn R.; Baker, David
Designed endocytosis-inducing proteins degrade targets and amplify signals Journal Article
In: Nature, 2024.
@article{Huang2024b,
title = {Designed endocytosis-inducing proteins degrade targets and amplify signals},
author = {Buwei Huang and Mohamad Abedi and Green Ahn and Brian Coventry and Isaac Sappington and Cong Tang and Rong Wang and Thomas Schlichthaerle and Jason Z. Zhang and Yujia Wang and Inna Goreshnik and Ching Wen Chiu and Adam Chazin-Gray and Sidney Chan and Stacey Gerben and Analisa Murray and Shunzhi Wang and Jason O’Neill and Li Yi and Ronald Yeh and Ayesha Misquith and Anitra Wolf and Luke M. Tomasovic and Dan I. Piraner and Maria J. Duran Gonzalez and Nathaniel R. Bennett and Preetham Venkatesh and Maggie Ahlrichs and Craig Dobbins and Wei Yang and Xinru Wang and Danny D. Sahtoe and Dionne Vafeados and Rubul Mout and Shirin Shivaei and Longxing Cao and Lauren Carter and Lance Stewart and Jamie B. Spangler and Kole T. Roybal and Per Jr Greisen and Xiaochun Li and Gonçalo J. L. Bernardes and Carolyn R. Bertozzi and David Baker},
url = {https://www.nature.com/articles/s41586-024-07948-2, Nature [Open Access]
https://www.bakerlab.org/wp-content/uploads/2025/03/Huang-et-al-EndoTags-Nature-25Sep2024.pdf, PDF},
doi = {10.1038/s41586-024-07948-2},
year = {2024},
date = {2024-09-25},
urldate = {2024-09-25},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
abstract = {Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by endogenous ligands. Therapeutic approaches such as lysosome-targeting chimaeras1,2 (LYTACs) and cytokine receptor-targeting chimeras3 (KineTACs) have used this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. Although powerful, these approaches can be limited by competition with native ligands and requirements for chemical modification that limit genetic encodability and can complicate manufacturing, and, more generally, there may be no native ligands that stimulate endocytosis through a given receptor. Here we describe computational design approaches for endocytosis-triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for insulin-like growth factor 2 receptor (IGF2R) and asialoglycoprotein receptor (ASGPR), sortilin and transferrin receptors, and show that fusing these tags to soluble or transmembrane target protein binders leads to lysosomal trafficking and target degradation. As these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. EndoTag fusion to a PD-L1 antibody considerably increases efficacy in a mouse tumour model compared to antibody alone. The modularity and genetic encodability of EndoTags enables AND gate control for higher-specificity targeted degradation, and the localized secretion of degraders from engineered cells. By promoting endocytosis, EndoTag fusion increases signalling through an engineered ligand–receptor system by nearly 100-fold. EndoTags have considerable therapeutic potential as targeted degradation inducers, signalling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody–drug and antibody–RNA conjugates.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by endogenous ligands. Therapeutic approaches such as lysosome-targeting chimaeras1,2 (LYTACs) and cytokine receptor-targeting chimeras3 (KineTACs) have used this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. Although powerful, these approaches can be limited by competition with native ligands and requirements for chemical modification that limit genetic encodability and can complicate manufacturing, and, more generally, there may be no native ligands that stimulate endocytosis through a given receptor. Here we describe computational design approaches for endocytosis-triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for insulin-like growth factor 2 receptor (IGF2R) and asialoglycoprotein receptor (ASGPR), sortilin and transferrin receptors, and show that fusing these tags to soluble or transmembrane target protein binders leads to lysosomal trafficking and target degradation. As these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. EndoTag fusion to a PD-L1 antibody considerably increases efficacy in a mouse tumour model compared to antibody alone. The modularity and genetic encodability of EndoTags enables AND gate control for higher-specificity targeted degradation, and the localized secretion of degraders from engineered cells. By promoting endocytosis, EndoTag fusion increases signalling through an engineered ligand–receptor system by nearly 100-fold. EndoTags have considerable therapeutic potential as targeted degradation inducers, signalling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody–drug and antibody–RNA conjugates.
4.
Humphreys, Ian R.; Zhang, Jing; Baek, Minkyung; Wang, Yaxi; Krishnakumar, Aditya; Pei, Jimin; Anishchenko, Ivan; Tower, Catherine A.; Jackson, Blake A.; Warrier, Thulasi; Hung, Deborah T.; Peterson, S. Brook; Mougous, Joseph D.; Cong, Qian; Baker, David
Protein interactions in human pathogens revealed through deep learning Journal Article
In: Nature Microbiology, 2024, ISSN: 2058-5276.
@article{Humphreys2024,
title = {Protein interactions in human pathogens revealed through deep learning},
author = {Ian R. Humphreys and Jing Zhang and Minkyung Baek and Yaxi Wang and Aditya Krishnakumar and Jimin Pei and Ivan Anishchenko and Catherine A. Tower and Blake A. Jackson and Thulasi Warrier and Deborah T. Hung and S. Brook Peterson and Joseph D. Mougous and Qian Cong and David Baker},
url = {https://www.nature.com/articles/s41564-024-01791-x, Nature Microbiology [Open Access]},
doi = {10.1038/s41564-024-01791-x},
issn = {2058-5276},
year = {2024},
date = {2024-09-18},
urldate = {2024-09-18},
journal = {Nature Microbiology},
publisher = {Springer Science and Business Media LLC},
abstract = {Identification of bacterial protein–protein interactions and predicting the structures of these complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here we developed RoseTTAFold2-Lite, a rapid deep learning model that leverages residue–residue coevolution and protein structure prediction to systematically identify and structurally characterize protein–protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1,923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer-membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Identification of bacterial protein–protein interactions and predicting the structures of these complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here we developed RoseTTAFold2-Lite, a rapid deep learning model that leverages residue–residue coevolution and protein structure prediction to systematically identify and structurally characterize protein–protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1,923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer-membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
5.
Berhanu, Samuel; Majumder, Sagardip; Müntener, Thomas; Whitehouse, James; Berner, Carolin; Bera, Asim K.; Kang, Alex; Liang, Binyong; Khan, Nasir; Sankaran, Banumathi; Tamm, Lukas K.; Brockwell, David J.; Hiller, Sebastian; Radford, Sheena E.; Baker, David; Vorobieva, Anastassia A.
Sculpting conducting nanopore size and shape through de novo protein design Journal Article
In: Science, 2024.
@article{Berhanu2024,
title = {Sculpting conducting nanopore size and shape through de novo protein design},
author = {Samuel Berhanu and Sagardip Majumder and Thomas Müntener and James Whitehouse and Carolin Berner and Asim K. Bera and Alex Kang and Binyong Liang and Nasir Khan and Banumathi Sankaran and Lukas K. Tamm and David J. Brockwell and Sebastian Hiller and Sheena E. Radford and David Baker and Anastassia A. Vorobieva},
url = {https://www.science.org/doi/10.1126/science.adn3796, Science},
doi = {10.1126/science.adn3796},
year = {2024},
date = {2024-07-19},
urldate = {2024-07-19},
journal = {Science},
publisher = {American Association for the Advancement of Science (AAAS)},
abstract = {Transmembrane β-barrels have considerable potential for a broad range of sensing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels, which provide suboptimal starting points. By contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to designing transmembrane β-barrel pores with different diameters and pore geometries. Nuclear magnetic resonance and crystallographic characterization show that the designs are stably folded with structures resembling those of the design models. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 picosiemens (~0.5 nanometer pore diameter) to 430 picosiemens (~1.1 nanometer pore diameter). Our approach opens the door to the custom design of transmembrane nanopores for sensing and sequencing applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Transmembrane β-barrels have considerable potential for a broad range of sensing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels, which provide suboptimal starting points. By contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to designing transmembrane β-barrel pores with different diameters and pore geometries. Nuclear magnetic resonance and crystallographic characterization show that the designs are stably folded with structures resembling those of the design models. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 picosiemens (~0.5 nanometer pore diameter) to 430 picosiemens (~1.1 nanometer pore diameter). Our approach opens the door to the custom design of transmembrane nanopores for sensing and sequencing applications.
6.
Peruzzi, Justin A.; Gunnels, Taylor F.; Edelstein, Hailey I.; Lu, Peilong; Baker, David; Leonard, Joshua N.; Kamat, Neha P.
Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions Journal Article
In: Nature Communications, 2024.
@article{Peruzzi2024b,
title = {Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions},
author = {Justin A. Peruzzi and Taylor F. Gunnels and Hailey I. Edelstein and Peilong Lu and David Baker and Joshua N. Leonard and Neha P. Kamat},
url = {https://www.nature.com/articles/s41467-024-49678-z [Nature Communications, Open Access]},
doi = {10.1038/s41467-024-49678-z},
year = {2024},
date = {2024-07-04},
urldate = {2024-12-00},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
abstract = {Naturally generated lipid nanoparticles termed extracellular vesicles (EVs) hold significant promise as engineerable therapeutic delivery vehicles. However, active loading of protein cargo into EVs in a manner that is useful for delivery remains a challenge. Here, we demonstrate that by rationally designing proteins to traffic to the plasma membrane and associate with lipid rafts, we can enhance loading of protein cargo into EVs for a set of structurally diverse transmembrane and peripheral membrane proteins. We then demonstrate the capacity of select lipid tags to mediate increased EV loading and functional delivery of an engineered transcription factor to modulate gene expression in target cells. We envision that this technology could be leveraged to develop new EV-based therapeutics that deliver a wide array of macromolecular cargo.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Naturally generated lipid nanoparticles termed extracellular vesicles (EVs) hold significant promise as engineerable therapeutic delivery vehicles. However, active loading of protein cargo into EVs in a manner that is useful for delivery remains a challenge. Here, we demonstrate that by rationally designing proteins to traffic to the plasma membrane and associate with lipid rafts, we can enhance loading of protein cargo into EVs for a set of structurally diverse transmembrane and peripheral membrane proteins. We then demonstrate the capacity of select lipid tags to mediate increased EV loading and functional delivery of an engineered transcription factor to modulate gene expression in target cells. We envision that this technology could be leveraged to develop new EV-based therapeutics that deliver a wide array of macromolecular cargo.
7.
Goverde, Casper A.; Pacesa, Martin; Goldbach, Nicolas; Dornfeld, Lars J.; Balbi, Petra E. M.; Georgeon, Sandrine; Rosset, Stéphane; Kapoor, Srajan; Choudhury, Jagrity; Dauparas, Justas; Schellhaas, Christian; Kozlov, Simon; Baker, David; Ovchinnikov, Sergey; Vecchio, Alex J.; Correia, Bruno E.
Computational design of soluble and functional membrane protein analogues Journal Article
In: Nature, 2024, ISSN: 1476-4687.
@article{Goverde2024,
title = {Computational design of soluble and functional membrane protein analogues},
author = {Casper A. Goverde and Martin Pacesa and Nicolas Goldbach and Lars J. Dornfeld and Petra E. M. Balbi and Sandrine Georgeon and Stéphane Rosset and Srajan Kapoor and Jagrity Choudhury and Justas Dauparas and Christian Schellhaas and Simon Kozlov and David Baker and Sergey Ovchinnikov and Alex J. Vecchio and Bruno E. Correia},
url = {https://www.nature.com/articles/s41586-024-07601-y, Nature [Open Access]
},
doi = {10.1038/s41586-024-07601-y},
issn = {1476-4687},
year = {2024},
date = {2024-06-19},
urldate = {2024-06-19},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
abstract = {De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses demonstrate the high thermal stability of the designs, and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, as a proof of concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we have designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses demonstrate the high thermal stability of the designs, and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, as a proof of concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we have designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.
8.
Craven, Timothy W.; Nolan, Mark D.; Bailey, Jonathan; Olatunji, Samir; Bann, Samantha J.; Bowen, Katherine; Ostrovitsa, Nikita; Costa, Thaina M. Da; Ballantine, Ross D.; Weichert, Dietmar; Levine, Paul M.; Stewart, Lance J.; Bhardwaj, Gaurav; Geoghegan, Joan A.; Cochrane, Stephen A.; Scanlan, Eoin M.; Caffrey, Martin; Baker, David
Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase Journal Article
In: ACS Chemical Biology, 2024.
@article{Craven2024,
title = {Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase},
author = {Timothy W. Craven and Mark D. Nolan and Jonathan Bailey and Samir Olatunji and Samantha J. Bann and Katherine Bowen and Nikita Ostrovitsa and Thaina M. Da Costa and Ross D. Ballantine and Dietmar Weichert and Paul M. Levine and Lance J. Stewart and Gaurav Bhardwaj and Joan A. Geoghegan and Stephen A. Cochrane and Eoin M. Scanlan and Martin Caffrey and David Baker},
url = {https://pubs.acs.org/doi/10.1021/acschembio.4c00076, ACS Chem. Bio. [Open Access]
https://www.bakerlab.org/wp-content/uploads/2024/05/craven-et-al-2024-computational-design-of-cyclic-peptide-inhibitors-of-a-bacterial-membrane-lipoprotein-peptidase.pdf, PDF},
doi = {10.1021/acschembio.4c00076},
year = {2024},
date = {2024-05-07},
urldate = {2024-05-07},
journal = {ACS Chemical Biology},
publisher = {American Chemical Society (ACS)},
abstract = {There remains a critical need for new antibiotics against multi-drug-resistant Gram-negative bacteria, a major global threat that continues to impact mortality rates. Lipoprotein signal peptidase II is an essential enzyme in the lipoprotein biosynthetic pathway of Gram-negative bacteria, making it an attractive target for antibacterial drug discovery. Although natural inhibitors of LspA have been identified, such as the cyclic depsipeptide globomycin, poor stability and production difficulties limit their use in a clinical setting. We harness computational design to generate stable de novo cyclic peptide analogues of globomycin. Only 12 peptides needed to be synthesized and tested to yield potent inhibitors, avoiding costly preparation of large libraries and screening campaigns. The most potent analogues showed comparable or better antimicrobial activity than globomycin in microdilution assays against ESKAPE-E pathogens. This work highlights computational design as a general strategy to combat antibiotic resistance.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
There remains a critical need for new antibiotics against multi-drug-resistant Gram-negative bacteria, a major global threat that continues to impact mortality rates. Lipoprotein signal peptidase II is an essential enzyme in the lipoprotein biosynthetic pathway of Gram-negative bacteria, making it an attractive target for antibacterial drug discovery. Although natural inhibitors of LspA have been identified, such as the cyclic depsipeptide globomycin, poor stability and production difficulties limit their use in a clinical setting. We harness computational design to generate stable de novo cyclic peptide analogues of globomycin. Only 12 peptides needed to be synthesized and tested to yield potent inhibitors, avoiding costly preparation of large libraries and screening campaigns. The most potent analogues showed comparable or better antimicrobial activity than globomycin in microdilution assays against ESKAPE-E pathogens. This work highlights computational design as a general strategy to combat antibiotic resistance.
9.
Hicks DR An L, Zorine D
Hallucination of closed repeat proteins containing central pockets Journal Article
In: Nature Structural & Molecular Biology, 2023.
@article{An2023,
title = {Hallucination of closed repeat proteins containing central pockets},
author = {An L, Hicks DR, Zorine D, Dauparas J, Wicky BIM, Milles LF, Courbet A, Bera AK, Nguyen H, Kang A, Carter L, Baker D},
url = {https://www.nature.com/articles/s41594-023-01112-6, Nature Structural & Molecular Biology [Open Access] },
doi = {10.1038/s41594-023-01112-6},
year = {2023},
date = {2023-09-28},
urldate = {2023-09-28},
journal = {Nature Structural & Molecular Biology},
abstract = {In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.
10.
Goldbach, Nicolas; Benna, Issa; Wicky, Basile I. M.; Croft, Jacob T.; Carter, Lauren; Bera, Asim K.; Nguyen, Hannah; Kang, Alex; Sankaran, Banumathi; Yang, Erin C.; Lee, Kelly K.; Baker, David
De novo design of monomeric helical bundles for pH-controlled membrane lysis Journal Article
In: Protein Science, 2023.
@article{Goldbach2023,
title = {De novo design of monomeric helical bundles for pH-controlled membrane lysis},
author = {Nicolas Goldbach and Issa Benna and Basile I. M. Wicky and Jacob T. Croft and Lauren Carter and Asim K. Bera and Hannah Nguyen and Alex Kang and Banumathi Sankaran and Erin C. Yang and Kelly K. Lee and David Baker},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4769, Protein Science
https://www.bakerlab.org/wp-content/uploads/2023/08/Protein-Science-2023-Goldbach.pdf, PDF},
doi = {https://doi.org/10.1002/pro.4769},
year = {2023},
date = {2023-08-26},
urldate = {2023-08-26},
journal = {Protein Science},
abstract = {Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of 30 designs that were experimentally tested, all expressed in E. coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0 - 5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of 30 designs that were experimentally tested, all expressed in E. coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0 – 5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.
11.
Wang, Jing Yang (John); Khmelinskaia, Alena; Sheffler, William; Miranda, Marcos C.; Antanasijevic, Aleksandar; Borst, Andrew J.; Torres, Susana V.; Shu, Chelsea; Hsia, Yang; Nattermann, Una; Ellis, Daniel; Walkey, Carl; Ahlrichs, Maggie; Chan, Sidney; Kang, Alex; Nguyen, Hannah; Sydeman, Claire; Sankaran, Banumathi; Wu, Mengyu; Bera, Asim K.; Carter, Lauren; Fiala, Brooke; Murphy, Michael; Baker, David; Ward, Andrew B.; King, Neil P.
Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains Journal Article
In: Proceedings of the National Academy of Sciences, 2023.
@article{Wang2023,
title = {Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains},
author = {Wang, Jing Yang (John)
and Khmelinskaia, Alena
and Sheffler, William
and Miranda, Marcos C.
and Antanasijevic, Aleksandar
and Borst, Andrew J.
and Torres, Susana V.
and Shu, Chelsea
and Hsia, Yang
and Nattermann, Una
and Ellis, Daniel
and Walkey, Carl
and Ahlrichs, Maggie
and Chan, Sidney
and Kang, Alex
and Nguyen, Hannah
and Sydeman, Claire
and Sankaran, Banumathi
and Wu, Mengyu
and Bera, Asim K.
and Carter, Lauren
and Fiala, Brooke
and Murphy, Michael
and Baker, David
and Ward, Andrew B.
and King, Neil P.},
url = {https://www.pnas.org/doi/10.1073/pnas.2214556120, PNAS (Open Access)},
doi = {10.1073/pnas.2214556120},
year = {2023},
date = {2023-03-08},
urldate = {2023-03-08},
journal = {Proceedings of the National Academy of Sciences},
abstract = {Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.
12.
Bhardwaj, Gaurav; O’Connor, Jacob; Rettie, Stephen; Huang, Yen-Hua; Ramelot, Theresa A.; Mulligan, Vikram Khipple; Alpkilic, Gizem Gokce; Palmer, Jonathan; Bera, Asim K.; Bick, Matthew J.; Piazza, Maddalena Di; Li, Xinting; Hosseinzadeh, Parisa; Craven, Timothy W.; Tejero, Roberto; Lauko, Anna; Choi, Ryan; Glynn, Calina; Dong, Linlin; Griffin, Robert; van Voorhis, Wesley C.; Rodriguez, Jose; Stewart, Lance; Montelione, Gaetano T.; Craik, David; Baker, David
Accurate de novo design of membrane-traversing macrocycles Journal Article
In: Cell, 2022.
@article{Bhardwaj2022,
title = {Accurate de novo design of membrane-traversing macrocycles},
author = {Gaurav Bhardwaj and Jacob O’Connor and Stephen Rettie and Yen-Hua Huang and Theresa A. Ramelot and Vikram Khipple Mulligan and Gizem Gokce Alpkilic and Jonathan Palmer and Asim K. Bera and Matthew J. Bick and Maddalena {Di Piazza} and Xinting Li and Parisa Hosseinzadeh and Timothy W. Craven and Roberto Tejero and Anna Lauko and Ryan Choi and Calina Glynn and Linlin Dong and Robert Griffin and Wesley C. {van Voorhis} and Jose Rodriguez and Lance Stewart and Gaetano T. Montelione and David Craik and David Baker},
url = {https://www.sciencedirect.com/science/article/pii/S0092867422009229?via%3Dihub, Cell
https://www.bakerlab.org/wp-content/uploads/2022/08/1-s2.0-S0092867422009229-main.pdf, PDF},
doi = {10.1016/j.cell.2022.07.019},
year = {2022},
date = {2022-08-29},
urldate = {2022-08-29},
journal = {Cell},
abstract = {We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6–12 residue macrocycles with a wide range of predicted structures containing noncanonical backbone modifications and experimentally determined structures of 35; 29 are very close to the computational models. With such control, we show that membrane permeability can be systematically achieved by ensuring all amide (NH) groups are engaged in internal hydrogen bonding interactions. 84 designs over the 6–12 residue size range cross membranes with an apparent permeability greater than 1 × 10−6 cm/s. Designs with exposed NH groups can be made membrane permeable through the design of an alternative isoenergetic fully hydrogen-bonded state favored in the lipid membrane. The ability to robustly design membrane-permeable and orally bioavailable peptides with high structural accuracy should contribute to the next generation of designed macrocycle therapeutics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6–12 residue macrocycles with a wide range of predicted structures containing noncanonical backbone modifications and experimentally determined structures of 35; 29 are very close to the computational models. With such control, we show that membrane permeability can be systematically achieved by ensuring all amide (NH) groups are engaged in internal hydrogen bonding interactions. 84 designs over the 6–12 residue size range cross membranes with an apparent permeability greater than 1 × 10−6 cm/s. Designs with exposed NH groups can be made membrane permeable through the design of an alternative isoenergetic fully hydrogen-bonded state favored in the lipid membrane. The ability to robustly design membrane-permeable and orally bioavailable peptides with high structural accuracy should contribute to the next generation of designed macrocycle therapeutics.
13.
Macé, Kévin; Vadakkepat, Abhinav K.; Redzej, Adam; Lukoyanova, Natalya; Oomen, Clasien; Braun, Nathalie; Ukleja, Marta; Lu, Fang; Costa, Tiago R. D.; Orlova, Elena V.; Baker, David; Cong, Qian; Waksman, Gabriel
Cryo-EM structure of a type IV secretion system Journal Article
In: Nature, 2022.
@article{Macé2022,
title = {Cryo-EM structure of a type IV secretion system},
author = {Macé, Kévin
and Vadakkepat, Abhinav K.
and Redzej, Adam
and Lukoyanova, Natalya
and Oomen, Clasien
and Braun, Nathalie
and Ukleja, Marta
and Lu, Fang
and Costa, Tiago R. D.
and Orlova, Elena V.
and Baker, David
and Cong, Qian
and Waksman, Gabriel},
url = {https://www.nature.com/articles/s41586-022-04859-y, Nature
https://www.bakerlab.org/wp-content/uploads/2022/08/Mace2022s41586-022-04859-y.pdf, PDF},
doi = {10.1038/s41586-022-04859-y},
year = {2022},
date = {2022-07-01},
urldate = {2022-07-01},
journal = {Nature},
abstract = {Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell1. It is the primary means by which antibiotic resistance genes spread among bacterial populations2,3. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus—the conjugative type IV secretion system (T4SS)—produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament—the conjugative pilus—that is essential for DNA transfer4,5. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein–protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell1. It is the primary means by which antibiotic resistance genes spread among bacterial populations2,3. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus—the conjugative type IV secretion system (T4SS)—produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament—the conjugative pilus—that is essential for DNA transfer4,5. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein–protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.
14.
Vorobieva, Anastassia A.; White, Paul; Liang, Binyong; Horne, Jim E.; Bera, Asim K.; Chow, Cameron M.; Gerben, Stacey; Marx, Sinduja; Kang, Alex; Stiving, Alyssa Q.; Harvey, Sophie R.; Marx, Dagan C.; Khan, G. Nasir; Fleming, Karen G.; Wysocki, Vicki H.; Brockwell, David J.; Tamm, Lukas K.; Radford, Sheena E.; Baker, David
De novo design of transmembrane beta barrels Journal Article
In: Science, vol. 371, no. 6531, 2021.
@article{Vorobieva2021,
title = {De novo design of transmembrane beta barrels},
author = {Vorobieva, Anastassia A. and White, Paul and Liang, Binyong and Horne, Jim E. and Bera, Asim K. and Chow, Cameron M. and Gerben, Stacey and Marx, Sinduja and Kang, Alex and Stiving, Alyssa Q. and Harvey, Sophie R. and Marx, Dagan C. and Khan, G. Nasir and Fleming, Karen G. and Wysocki, Vicki H. and Brockwell, David J. and Tamm, Lukas K. and Radford, Sheena E. and Baker, David},
url = {https://science.sciencemag.org/content/371/6531/eabc8182, Science
https://www.bakerlab.org/wp-content/uploads/2021/02/Vorobieva_etal_Science2021_De_Novo_Transmembrane_beta_barrels.pdf, Download PDF},
doi = {10.1126/science.abc8182},
year = {2021},
date = {2021-02-19},
urldate = {2021-02-19},
journal = {Science},
volume = {371},
number = {6531},
abstract = {Computational design offers the possibility of making proteins with customized structures and functions. The range of accessible protein scaffolds has expanded with the design of increasingly complex cytoplasmic proteins and, recently, helical membrane proteins. Vorobieva et al. describe the successful computational design of eight-stranded transmembrane β-barrel proteins (TMBs). Using an iterative approach, they show the importance of negative design to prevent off-target structures and gain insight into the sequence determinants of TMB folding. Twenty-three designs satisfied biochemical screens for a TMB structure, and two structures were experimentally validated by nuclear magnetic resonance spectroscopy or x-ray crystallography. This is a step toward the custom design of pores for applications such as single-molecule sequencing.Science, this issue p. eabc8182INTRODUCTIONDespite their key biological roles, only a few proteins that fold into lipid membranes have been designed de novo. A class of membrane proteins{textemdash}transmembrane β barrels (TMBs){textemdash}forms a continuous sheet that closes on itself in lipid membranes. In addition to the challenge of designing β-sheet proteins, which are prone to misfolding and aggregation if folding is not properly controlled, the computational design of TMBs is complicated by limited understanding of TMB folding. As a result, no TMB has been designed de novo to date.Although the folding of TMBs in vivo is catalyzed by the β-barrel assembly machinery (BAM), many TMBs can also fold spontaneously in synthetic membranes to form stable pores, making them attractive for biotechnology and single-molecule analytical applications. Hence, de novo design of TMBs has potential both for understanding the determinants of TMB folding and membrane insertion and for the custom engineering of TMB nanopores.RATIONALEWe used de novo protein design to distill key principles of TMB folding through several design-build-test cycles. We iterated between hypothesis formulation, its implementation into computational design methods, and experimental characterization of the resulting proteins. To focus on the fundamental principles of TMB folding in the absence of complications due to interactions with chaperones and BAM in vivo, we focused on the challenge of de novo design of eight-stranded TMBs, which can fold and assemble into synthetic lipid membranes.RESULTSWe used a combination of purely geometric models and explicit Rosetta protein structure simulations to determine the constraints that β-strand connectivity and membrane embedding place on the TMB architecture. Through a series of design-build-test cycles, we found that, unlike almost all other classes of proteins, locally destabilizing sequences are critical for expression and folding of TMBs, and that the β-turns that translocate through the bilayer during folding have to be destabilized to enable correct assembly in the membrane. Our results suggest that premature formation of β hairpins may result in off-target β-sheet structures that compete with proper membrane insertion and folding, and hence the β hairpins of TMBs must be designed such that they are only transiently formed prior to membrane insertion, when the protein is in an aqueous environment. In the hydrophobic environment of the lipid bilayer, the full TMB can assemble because the membrane-facing nonpolar residues, which would tend to cluster nonspecifically in an aqueous environment, instead make favorable interactions with the lipids. As the TMB assembles, the β hairpins are stabilized by interactions with the neighboring β strands.Using computational methods that incorporate the above insights, we designed TMB sequences that successfully fold and assemble into both detergent micelles and lipid bilayers. Two of the designs were highly stable and could fold into liposomes more rapidly and reversibly than the transmembrane domain of the model outer membrane protein A (tOmpA) of Escherichia coli. A nuclear magnetic resonance solution structure and a high-resolution crystal structure for two different designs closely match the design models, showing that the TMB design method developed here can generate new structures with atomic-level accuracy.CONCLUSIONThis study elucidates key principles for de novo design of transmembrane β barrels, ranging from constraints on β-barrel architecture and β-hairpin design, as well as local and global sequence features. Our designs provide starting points for the bottom-up elucidation of the molecular mechanisms underlying TMB folding and interactions with the cellular outer membrane folding and insertion machinery. More generally, our work demonstrates that TMBs can be designed with atomic-level accuracy and opens the door to custom design of nanopores tailored for applications such as single-molecule sensing and sequencing.De novo{textendash}designed eight-stranded transmembrane β barrels fold spontaneously and reversibly into synthetic lipid membranes.The illustration shows the crystal structure of the protein TMB2.17 designed in this study, which adopts a structure identical to the design model.Credit: Ian Haydon.Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a {textquotedblleft}hypothesis, design, and test{textquotedblright} approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Computational design offers the possibility of making proteins with customized structures and functions. The range of accessible protein scaffolds has expanded with the design of increasingly complex cytoplasmic proteins and, recently, helical membrane proteins. Vorobieva et al. describe the successful computational design of eight-stranded transmembrane β-barrel proteins (TMBs). Using an iterative approach, they show the importance of negative design to prevent off-target structures and gain insight into the sequence determinants of TMB folding. Twenty-three designs satisfied biochemical screens for a TMB structure, and two structures were experimentally validated by nuclear magnetic resonance spectroscopy or x-ray crystallography. This is a step toward the custom design of pores for applications such as single-molecule sequencing.Science, this issue p. eabc8182INTRODUCTIONDespite their key biological roles, only a few proteins that fold into lipid membranes have been designed de novo. A class of membrane proteins{textemdash}transmembrane β barrels (TMBs){textemdash}forms a continuous sheet that closes on itself in lipid membranes. In addition to the challenge of designing β-sheet proteins, which are prone to misfolding and aggregation if folding is not properly controlled, the computational design of TMBs is complicated by limited understanding of TMB folding. As a result, no TMB has been designed de novo to date.Although the folding of TMBs in vivo is catalyzed by the β-barrel assembly machinery (BAM), many TMBs can also fold spontaneously in synthetic membranes to form stable pores, making them attractive for biotechnology and single-molecule analytical applications. Hence, de novo design of TMBs has potential both for understanding the determinants of TMB folding and membrane insertion and for the custom engineering of TMB nanopores.RATIONALEWe used de novo protein design to distill key principles of TMB folding through several design-build-test cycles. We iterated between hypothesis formulation, its implementation into computational design methods, and experimental characterization of the resulting proteins. To focus on the fundamental principles of TMB folding in the absence of complications due to interactions with chaperones and BAM in vivo, we focused on the challenge of de novo design of eight-stranded TMBs, which can fold and assemble into synthetic lipid membranes.RESULTSWe used a combination of purely geometric models and explicit Rosetta protein structure simulations to determine the constraints that β-strand connectivity and membrane embedding place on the TMB architecture. Through a series of design-build-test cycles, we found that, unlike almost all other classes of proteins, locally destabilizing sequences are critical for expression and folding of TMBs, and that the β-turns that translocate through the bilayer during folding have to be destabilized to enable correct assembly in the membrane. Our results suggest that premature formation of β hairpins may result in off-target β-sheet structures that compete with proper membrane insertion and folding, and hence the β hairpins of TMBs must be designed such that they are only transiently formed prior to membrane insertion, when the protein is in an aqueous environment. In the hydrophobic environment of the lipid bilayer, the full TMB can assemble because the membrane-facing nonpolar residues, which would tend to cluster nonspecifically in an aqueous environment, instead make favorable interactions with the lipids. As the TMB assembles, the β hairpins are stabilized by interactions with the neighboring β strands.Using computational methods that incorporate the above insights, we designed TMB sequences that successfully fold and assemble into both detergent micelles and lipid bilayers. Two of the designs were highly stable and could fold into liposomes more rapidly and reversibly than the transmembrane domain of the model outer membrane protein A (tOmpA) of Escherichia coli. A nuclear magnetic resonance solution structure and a high-resolution crystal structure for two different designs closely match the design models, showing that the TMB design method developed here can generate new structures with atomic-level accuracy.CONCLUSIONThis study elucidates key principles for de novo design of transmembrane β barrels, ranging from constraints on β-barrel architecture and β-hairpin design, as well as local and global sequence features. Our designs provide starting points for the bottom-up elucidation of the molecular mechanisms underlying TMB folding and interactions with the cellular outer membrane folding and insertion machinery. More generally, our work demonstrates that TMBs can be designed with atomic-level accuracy and opens the door to custom design of nanopores tailored for applications such as single-molecule sensing and sequencing.De novo{textendash}designed eight-stranded transmembrane β barrels fold spontaneously and reversibly into synthetic lipid membranes.The illustration shows the crystal structure of the protein TMB2.17 designed in this study, which adopts a structure identical to the design model.Credit: Ian Haydon.Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a {textquotedblleft}hypothesis, design, and test{textquotedblright} approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.
15.
Ben-Sasson, Ariel J.; Watson, Joseph L.; Sheffler, William; Johnson, Matthew Camp; Bittleston, Alice; Somasundaram, Logeshwaran; Decarreau, Justin; Jiao, Fang; Chen, Jiajun; Mela, Ioanna; Drabek, Andrew A.; Jarrett, Sanchez M.; Blacklow, Stephen C.; Kaminski, Clemens F.; Hura, Greg L.; De Yoreo, James J.; Kollman, Justin M.; Ruohola-Baker, Hannele; Derivery, Emmanuel; Baker, David
Design of biologically active binary protein 2D materials Journal Article
In: Nature, 2021.
@article{Ben-Sasson2020,
title = {Design of biologically active binary protein 2D materials},
author = {Ben-Sasson, Ariel J. and Watson, Joseph L. and Sheffler, William and Johnson, Matthew Camp and Bittleston, Alice and Somasundaram, Logeshwaran and Decarreau, Justin and Jiao, Fang and Chen, Jiajun and Mela, Ioanna and Drabek, Andrew A. and Jarrett, Sanchez M. and Blacklow, Stephen C. and Kaminski, Clemens F. and Hura, Greg L. and De Yoreo, James J. and Kollman, Justin M. and Ruohola-Baker, Hannele and Derivery, Emmanuel and Baker, David},
url = {https://www.nature.com/articles/s41586-020-03120-8, Nature
https://www.bakerlab.org/wp-content/uploads/2021/02/Ben-Sasson_Nature2021_Binary_2D_arrays.pdf, Download PDF},
doi = {10.1038/s41586-020-03120-8},
year = {2021},
date = {2021-01-06},
urldate = {2021-01-06},
journal = {Nature},
abstract = {Ordered two-dimensional arrays such as S-layers1,2 and designed analogues3–5 have intrigued bioengineers6,7, but with the exception of a single lattice formed with flexible linkers8, they are constituted from just one protein component. Materials composed of two components have considerable potential advantages for modulating assembly dynamics and incorporating more complex functionality9–12. Here we describe a computational method to generate co-assembling binary layers by designing rigid interfaces between pairs of dihedral protein building blocks, and use it to design a p6m lattice. The designed array components are soluble at millimolar concentrations, but when combined at nanomolar concentrations, they rapidly assemble into nearly crystalline micrometre-scale arrays nearly identical to the computational design model in vitro and in cells without the need for a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces, which we demonstrate can drive extensive receptor clustering, downstream protein recruitment and signalling. Using atomic force microscopy on supported bilayers and quantitative microscopy on living cells, we show that arrays assembled on membranes have component stoichiometry and structure similar to arrays formed in vitro, and that our material can therefore impose order onto fundamentally disordered substrates such as cell membranes. In contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, we find that large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work provides a foundation for a synthetic cell biology in which multi-protein macroscale materials are designed to modulate cell responses and reshape synthetic and living systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ordered two-dimensional arrays such as S-layers1,2 and designed analogues3–5 have intrigued bioengineers6,7, but with the exception of a single lattice formed with flexible linkers8, they are constituted from just one protein component. Materials composed of two components have considerable potential advantages for modulating assembly dynamics and incorporating more complex functionality9–12. Here we describe a computational method to generate co-assembling binary layers by designing rigid interfaces between pairs of dihedral protein building blocks, and use it to design a p6m lattice. The designed array components are soluble at millimolar concentrations, but when combined at nanomolar concentrations, they rapidly assemble into nearly crystalline micrometre-scale arrays nearly identical to the computational design model in vitro and in cells without the need for a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces, which we demonstrate can drive extensive receptor clustering, downstream protein recruitment and signalling. Using atomic force microscopy on supported bilayers and quantitative microscopy on living cells, we show that arrays assembled on membranes have component stoichiometry and structure similar to arrays formed in vitro, and that our material can therefore impose order onto fundamentally disordered substrates such as cell membranes. In contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, we find that large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work provides a foundation for a synthetic cell biology in which multi-protein macroscale materials are designed to modulate cell responses and reshape synthetic and living systems.
16.
Xu, Chunfu; Lu, Peilong; El-Din, Tamer M. Gamal; Pei, Xue Y.; Johnson, Matthew C.; Uyeda, Atsuko; Bick, Matthew J.; Xu, Qi; Jiang, Daohua; Bai, Hua; Reggiano, Gabriella; Hsia, Yang; Brunette, T J; Dou, Jiayi; Ma, Dan; Lynch, Eric M.; Boyken, Scott E.; Huang, Po-Ssu; Stewart, Lance; DiMaio, Frank; Kollman, Justin M.; Luisi, Ben F.; Matsuura, Tomoaki; Catterall, William A.; Baker, David
Computational design of transmembrane pores Journal Article
In: Nature, vol. 585, pp. 129–134, 2020.
@article{Xu2020,
title = {Computational design of transmembrane pores},
author = {Chunfu Xu and Peilong Lu and Tamer M. Gamal El-Din and Xue Y. Pei and Matthew C. Johnson and Atsuko Uyeda and Matthew J. Bick and Qi Xu and Daohua Jiang and Hua Bai and Gabriella Reggiano and Yang Hsia and T J Brunette and Jiayi Dou and Dan Ma and Eric M. Lynch and Scott E. Boyken and Po-Ssu Huang and Lance Stewart and Frank DiMaio and Justin M. Kollman and Ben F. Luisi and Tomoaki Matsuura and William A. Catterall and David Baker },
url = {https://www.bakerlab.org/wp-content/uploads/2020/08/Xuetal_Nature2020_DeNovoPores.pdf
https://www.nature.com/articles/s41586-020-2646-5},
doi = {10.1038/s41586-020-2646-5},
year = {2020},
date = {2020-08-26},
journal = {Nature},
volume = {585},
pages = {129–134},
abstract = {Transmembrane channels and pores have key roles in fundamental biological processes and in biotechnological applications such as DNA nanopore sequencing, resulting in considerable interest in the design of pore-containing proteins. Synthetic amphiphilic peptides have been found to form ion channels, and there have been recent advances in de novo membrane protein design and in redesigning naturally occurring channel-containing proteins. However, the de novo design of stable, well-defined transmembrane protein pores that are capable of conducting ions selectively or are large enough to enable the passage of small-molecule fluorophores remains an outstanding challenge. Here we report the computational design of protein pores formed by two concentric rings of α-helices that are stable and monodisperse in both their water-soluble and their transmembrane forms. Crystal structures of the water-soluble forms of a 12-helical pore and a 16-helical pore closely match the computational design models. Patch-clamp electrophysiology experiments show that, when expressed in insect cells, the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium; ion passage is blocked by specific chemical modification at the pore entrance. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore—but not the 12-helix pore—enables the passage of biotinylated Alexa Fluor 488. A cryo-electron microscopy structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer channels and pores for a wide variety of applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Transmembrane channels and pores have key roles in fundamental biological processes and in biotechnological applications such as DNA nanopore sequencing, resulting in considerable interest in the design of pore-containing proteins. Synthetic amphiphilic peptides have been found to form ion channels, and there have been recent advances in de novo membrane protein design and in redesigning naturally occurring channel-containing proteins. However, the de novo design of stable, well-defined transmembrane protein pores that are capable of conducting ions selectively or are large enough to enable the passage of small-molecule fluorophores remains an outstanding challenge. Here we report the computational design of protein pores formed by two concentric rings of α-helices that are stable and monodisperse in both their water-soluble and their transmembrane forms. Crystal structures of the water-soluble forms of a 12-helical pore and a 16-helical pore closely match the computational design models. Patch-clamp electrophysiology experiments show that, when expressed in insect cells, the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium; ion passage is blocked by specific chemical modification at the pore entrance. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore—but not the 12-helix pore—enables the passage of biotinylated Alexa Fluor 488. A cryo-electron microscopy structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer channels and pores for a wide variety of applications.
17.
Boyken, Scott E.; Benhaim, Mark A.; Busch, Florian; Jia, Mengxuan; Bick, Matthew J.; Choi, Heejun; Klima, Jason C.; Chen, Zibo; Walkey, Carl; Mileant, Alexander; Sahasrabuddhe, Aniruddha; Wei, Kathy Y.; Hodge, Edgar A.; Byron, Sarah; Quijano-Rubio, Alfredo; Sankaran, Banumathi; King, Neil P.; Lippincott-Schwartz, Jennifer; Wysocki, Vicki H.; Lee, Kelly K.; Baker, David
De novo design of tunable, pH-driven conformational changes Journal Article
In: Science, vol. 364, no. 6441, pp. 658-664, 2019.
@article{Boyken2019,
title = {De novo design of tunable, pH-driven conformational changes},
author = {Boyken, Scott E. and Benhaim, Mark A. and Busch, Florian and Jia, Mengxuan and Bick, Matthew J. and Choi, Heejun and Klima, Jason C. and Chen, Zibo and Walkey, Carl and Mileant, Alexander and Sahasrabuddhe, Aniruddha and Wei, Kathy Y. and Hodge, Edgar A. and Byron, Sarah and Quijano-Rubio, Alfredo and Sankaran, Banumathi and King, Neil P. and Lippincott-Schwartz, Jennifer and Wysocki, Vicki H. and Lee, Kelly K. and Baker, David
},
url = {https://science.sciencemag.org/content/364/6441/658
https://www.bakerlab.org/wp-content/uploads/2019/06/Boyken_etal2019_pH_conformational_changes.pdf},
doi = {10.1126/science.aav7897},
year = {2019},
date = {2019-05-17},
journal = {Science},
volume = {364},
number = {6441},
pages = {658-664},
abstract = {The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.
18.
Lu, Peilong; Min, Duyoung; DiMaio, Frank; Wei, Kathy Y.; Vahey, Michael D.; Boyken, Scott E.; Chen, Zibo; Fallas, Jorge A.; Ueda, George; Sheffler, William; Mulligan, Vikram Khipple; Xu, Wenqing; Bowie, James U.; Baker, David
Accurate computational design of multipass transmembrane proteins Journal Article
In: Science, vol. 359, no. 6379, pp. 1042–1046, 2018, ISSN: 0036-8075.
@article{Lu1042,
title = {Accurate computational design of multipass transmembrane proteins},
author = {Lu, Peilong and Min, Duyoung and DiMaio, Frank and Wei, Kathy Y. and Vahey, Michael D. and Boyken, Scott E. and Chen, Zibo and Fallas, Jorge A. and Ueda, George and Sheffler, William and Mulligan, Vikram Khipple and Xu, Wenqing and Bowie, James U. and Baker, David},
url = {http://science.sciencemag.org/content/359/6379/1042
https://www.bakerlab.org/wp-content/uploads/2018/03/Lu_Science_2018.pdf},
doi = {10.1126/science.aaq1739},
issn = {0036-8075},
year = {2018},
date = {2018-03-02},
journal = {Science},
volume = {359},
number = {6379},
pages = {1042--1046},
abstract = {In recent years, soluble protein design has achieved successes such as artificial enzymes and large protein cages. Membrane proteins present a considerable design challenge, but here too there have been advances, including the design of a zinc-transporting tetramer. Lu et al. report the design of stable transmembrane monomers, homodimers, trimers, and tetramers with up to eight membrane-spanning regions in an oligomer. The designed proteins adopted the target oligomerization state and localized to the predicted cellular membranes, and crystal structures of the designed dimer and tetramer reflected the design models.Science, this issue p. 1042The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer{textemdash}a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices{textemdash}are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In recent years, soluble protein design has achieved successes such as artificial enzymes and large protein cages. Membrane proteins present a considerable design challenge, but here too there have been advances, including the design of a zinc-transporting tetramer. Lu et al. report the design of stable transmembrane monomers, homodimers, trimers, and tetramers with up to eight membrane-spanning regions in an oligomer. The designed proteins adopted the target oligomerization state and localized to the predicted cellular membranes, and crystal structures of the designed dimer and tetramer reflected the design models.Science, this issue p. 1042The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer{textemdash}a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices{textemdash}are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions.
19.
Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A.; Kim, David E.; Kamisetty, Hetunandan; Kyrpides, Nikos C.; Baker, David
Protein structure determination using metagenome sequence data Journal Article
In: Science, vol. 355, no. 6322, pp. 294–298, 2017, ISSN: 0036-8075.
@article{Ovchinnikov294,
title = {Protein structure determination using metagenome sequence data},
author = { Sergey Ovchinnikov and Hahnbeom Park and Neha Varghese and Po-Ssu Huang and Georgios A. Pavlopoulos and David E. Kim and Hetunandan Kamisetty and Nikos C. Kyrpides and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2017/01/ovchinnikov_science_2017.pdf
http://science.sciencemag.org/content/355/6322/294},
doi = {10.1126/science.aah4043},
issn = {0036-8075},
year = {2017},
date = {2017-01-01},
journal = {Science},
volume = {355},
number = {6322},
pages = {294--298},
publisher = {American Association for the Advancement of Science},
abstract = {Fewer than a third of the 14,849 known protein families have at least one member with an experimentally determined structure. This leaves more than 5000 protein families with no structural information. Protein modeling using residue-residue contacts inferred from evolutionary data has been successful in modeling unknown structures, but it requires large numbers of aligned sequences. Ovchinnikov et al. augmented such sequence alignments with metagenome sequence data (see the Perspective by S"oding). They determined the number of sequences required to allow modeling, developed criteria for model quality, and, where possible, improved modeling by matching predicted contacts to known structures. Their method predicted quality structural models for 614 protein families, of which about 140 represent newly discovered protein folds.Science, this issue p. 294; see also p. 248Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fewer than a third of the 14,849 known protein families have at least one member with an experimentally determined structure. This leaves more than 5000 protein families with no structural information. Protein modeling using residue-residue contacts inferred from evolutionary data has been successful in modeling unknown structures, but it requires large numbers of aligned sequences. Ovchinnikov et al. augmented such sequence alignments with metagenome sequence data (see the Perspective by S"oding). They determined the number of sequences required to allow modeling, developed criteria for model quality, and, where possible, improved modeling by matching predicted contacts to known structures. Their method predicted quality structural models for 614 protein families, of which about 140 represent newly discovered protein folds.Science, this issue p. 294; see also p. 248Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost.
20.
Holstein, Carly A; Chevalier, Aaron; Bennett, Steven; Anderson, Caitlin E; Keniston, Karen; Olsen, Cathryn; Li, Bing; Bales, Brian; Moore, David R; Fu, Elain; Baker, David; Yager, Paul
Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers. Journal Article
In: Analytical and bioanalytical chemistry, 2015, ISSN: 1618-2650.
@article{626,
title = {Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers.},
author = { Carly A Holstein and Aaron Chevalier and Steven Bennett and Caitlin E Anderson and Karen Keniston and Cathryn Olsen and Bing Li and Brian Bales and David R Moore and Elain Fu and David Baker and Paul Yager},
url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Holstien_Anal_Bioanal_Chem_2015.pdf},
doi = {10.1007/s00216-015-9052-0},
issn = {1618-2650},
year = {2015},
date = {2015-10-01},
journal = {Analytical and bioanalytical chemistry},
abstract = {To enable enhanced paper-based diagnostics with improved detection capabilities, new methods are needed to immobilize affinity reagents to porous substrates, especially for capture molecules other than IgG. To this end, we have developed and characterized three novel methods for immobilizing protein-based affinity reagents to nitrocellulose membranes. We have demonstrated these methods using recombinant affinity proteins for the influenza surface protein hemagglutinin, leveraging the customizability of these recombinant "flu binders" for the design of features for immobilization. The three approaches shown are: (1) covalent attachment of thiolated affinity protein to an epoxide-functionalized nitrocellulose membrane, (2) attachment of biotinylated affinity protein through a nitrocellulose-binding streptavidin anchor protein, and (3) fusion of affinity protein to a novel nitrocellulose-binding anchor protein for direct coupling and immobilization. We also characterized the use of direct adsorption for the flu binders, as a point of comparison and motivation for these novel methods. Finally, we demonstrated that these novel methods can provide improved performance to an influenza hemagglutinin assay, compared to a traditional antibody-based capture system. Taken together, this work advances the toolkit available for the development of next-generation paper-based diagnostics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
To enable enhanced paper-based diagnostics with improved detection capabilities, new methods are needed to immobilize affinity reagents to porous substrates, especially for capture molecules other than IgG. To this end, we have developed and characterized three novel methods for immobilizing protein-based affinity reagents to nitrocellulose membranes. We have demonstrated these methods using recombinant affinity proteins for the influenza surface protein hemagglutinin, leveraging the customizability of these recombinant "flu binders" for the design of features for immobilization. The three approaches shown are: (1) covalent attachment of thiolated affinity protein to an epoxide-functionalized nitrocellulose membrane, (2) attachment of biotinylated affinity protein through a nitrocellulose-binding streptavidin anchor protein, and (3) fusion of affinity protein to a novel nitrocellulose-binding anchor protein for direct coupling and immobilization. We also characterized the use of direct adsorption for the flu binders, as a point of comparison and motivation for these novel methods. Finally, we demonstrated that these novel methods can provide improved performance to an influenza hemagglutinin assay, compared to a traditional antibody-based capture system. Taken together, this work advances the toolkit available for the development of next-generation paper-based diagnostics.
2025
FROM THE LAB
Sorry, no publications matched your criteria.
COLLABORATOR LED
Yuhao Li, Bradley S. Harris, Zhongwu Li, Chenyang Shi, Jobaer Abdullah, Sagardip Majumder, Samuel Berhanu, Anastassia A. Vorobieva, Sydney K. Myers, Jeevapani Hettige, Marcel D. Baer, James J. De Yoreo, David Baker, Aleksandr Noy
Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels Journal Article
In: ACS Nano, 2025.
@article{Li2024,
title = {Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels},
author = {Yuhao Li and Bradley S. Harris and Zhongwu Li and Chenyang Shi and Jobaer Abdullah and Sagardip Majumder and Samuel Berhanu and Anastassia A. Vorobieva and Sydney K. Myers and Jeevapani Hettige and Marcel D. Baer and James J. De Yoreo and David Baker and Aleksandr Noy},
url = {https://pubs.acs.org/doi/10.1021/acsnano.4c11317, ACS Nano
https://www.bakerlab.org/wp-content/uploads/2025/02/li-et-al-2024-water-solute-and-ion-transport-in-de-novo-designed-membrane-protein-channels.pdf, PDF},
doi = {10.1021/acsnano.4c11317},
year = {2025},
date = {2025-01-21},
urldate = {2025-01-21},
journal = {ACS Nano},
publisher = {American Chemical Society (ACS)},
abstract = {Biological organisms engineer peptide sequences to fold into membrane pore proteins capable of performing a wide variety of transport functions. Synthetic de novo-designed membrane pores can mimic this approach to achieve a potentially even larger set of functions. Here we explore water, solute, and ion transport in three de novo designed β-barrel membrane channels in the 5–10 Å pore size range. We show that these proteins form passive membrane pores with high water transport efficiencies and size rejection characteristics consistent with the pore size encoded in the protein structure. Ion conductance and ion selectivity measurements also show trends consistent with the pore size, with the two larger pores showing weak cation selectivity. MD simulations of water and ion transport and solute size exclusion are consistent with the experimental trends and provide further insights into structure–function correlations in these membrane pores.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Biological organisms engineer peptide sequences to fold into membrane pore proteins capable of performing a wide variety of transport functions. Synthetic de novo-designed membrane pores can mimic this approach to achieve a potentially even larger set of functions. Here we explore water, solute, and ion transport in three de novo designed β-barrel membrane channels in the 5–10 Å pore size range. We show that these proteins form passive membrane pores with high water transport efficiencies and size rejection characteristics consistent with the pore size encoded in the protein structure. Ion conductance and ion selectivity measurements also show trends consistent with the pore size, with the two larger pores showing weak cation selectivity. MD simulations of water and ion transport and solute size exclusion are consistent with the experimental trends and provide further insights into structure–function correlations in these membrane pores.
2024
FROM THE LAB
Dan I. Piraner, Mohamad H. Abedi, Maria J. Duran Gonzalez, Adam Chazin-Gray, Annie Lin, Iowis Zhu, Pavithran T. Ravindran, Thomas Schlichthaerle, Buwei Huang, Tyler H. Bearchild, David Lee, Sarah Wyman, Young-wook Jun, David Baker, Kole T. Roybal
Engineered receptors for soluble cellular communication and disease sensing Journal Article
In: Nature, 2024.
@article{Piraner2024,
title = {Engineered receptors for soluble cellular communication and disease sensing},
author = {Dan I. Piraner and Mohamad H. Abedi and Maria J. Duran Gonzalez and Adam Chazin-Gray and Annie Lin and Iowis Zhu and Pavithran T. Ravindran and Thomas Schlichthaerle and Buwei Huang and Tyler H. Bearchild and David Lee and Sarah Wyman and Young-wook Jun and David Baker and Kole T. Roybal},
url = {https://www.nature.com/articles/s41586-024-08366-0, Nature},
doi = {10.1038/s41586-024-08366-0},
year = {2024},
date = {2024-11-14},
urldate = {2024-11-14},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
abstract = {Despite recent advances in mammalian synthetic biology, there remains a lack of modular synthetic receptors that can robustly respond to soluble ligands and in turn activate bespoke cellular functions. Such receptors would have extensive clinical potential to regulate the activity of engineered therapeutic cells, but to date only receptors against cell surface targets have approached clinical translation1. To address this gap, we developed a receptor architecture called synthetic intramembrane proteolysis receptor (SNIPR), that has the added ability to be activated by soluble ligands, both natural and synthetic, with remarkably low baseline activity and high fold activation, through an endocytic, pH-dependent cleavage mechanism. We demonstrate the therapeutic capabilities of the receptor platform by localizing the activity of CAR T cells to solid tumors where soluble disease-associated factors are expressed, bypassing the major hurdle of on-target off-tumor toxicity in bystander organs. We further applied the SNIPR platform to engineer fully synthetic signaling networks between cells orthogonal to natural signaling pathways, expanding the scope of synthetic biology. Our design framework enables cellular communication and environmental interactions, extending the capabilities of synthetic cellular networking in clinical and research contexts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Despite recent advances in mammalian synthetic biology, there remains a lack of modular synthetic receptors that can robustly respond to soluble ligands and in turn activate bespoke cellular functions. Such receptors would have extensive clinical potential to regulate the activity of engineered therapeutic cells, but to date only receptors against cell surface targets have approached clinical translation1. To address this gap, we developed a receptor architecture called synthetic intramembrane proteolysis receptor (SNIPR), that has the added ability to be activated by soluble ligands, both natural and synthetic, with remarkably low baseline activity and high fold activation, through an endocytic, pH-dependent cleavage mechanism. We demonstrate the therapeutic capabilities of the receptor platform by localizing the activity of CAR T cells to solid tumors where soluble disease-associated factors are expressed, bypassing the major hurdle of on-target off-tumor toxicity in bystander organs. We further applied the SNIPR platform to engineer fully synthetic signaling networks between cells orthogonal to natural signaling pathways, expanding the scope of synthetic biology. Our design framework enables cellular communication and environmental interactions, extending the capabilities of synthetic cellular networking in clinical and research contexts.
Buwei Huang, Mohamad Abedi, Green Ahn, Brian Coventry, Isaac Sappington, Cong Tang, Rong Wang, Thomas Schlichthaerle, Jason Z. Zhang, Yujia Wang, Inna Goreshnik, Ching Wen Chiu, Adam Chazin-Gray, Sidney Chan, Stacey Gerben, Analisa Murray, Shunzhi Wang, Jason O’Neill, Li Yi, Ronald Yeh, Ayesha Misquith, Anitra Wolf, Luke M. Tomasovic, Dan I. Piraner, Maria J. Duran Gonzalez, Nathaniel R. Bennett, Preetham Venkatesh, Maggie Ahlrichs, Craig Dobbins, Wei Yang, Xinru Wang, Danny D. Sahtoe, Dionne Vafeados, Rubul Mout, Shirin Shivaei, Longxing Cao, Lauren Carter, Lance Stewart, Jamie B. Spangler, Kole T. Roybal, Per Jr Greisen, Xiaochun Li, Gonçalo J. L. Bernardes, Carolyn R. Bertozzi, David Baker
Designed endocytosis-inducing proteins degrade targets and amplify signals Journal Article
In: Nature, 2024.
@article{Huang2024b,
title = {Designed endocytosis-inducing proteins degrade targets and amplify signals},
author = {Buwei Huang and Mohamad Abedi and Green Ahn and Brian Coventry and Isaac Sappington and Cong Tang and Rong Wang and Thomas Schlichthaerle and Jason Z. Zhang and Yujia Wang and Inna Goreshnik and Ching Wen Chiu and Adam Chazin-Gray and Sidney Chan and Stacey Gerben and Analisa Murray and Shunzhi Wang and Jason O’Neill and Li Yi and Ronald Yeh and Ayesha Misquith and Anitra Wolf and Luke M. Tomasovic and Dan I. Piraner and Maria J. Duran Gonzalez and Nathaniel R. Bennett and Preetham Venkatesh and Maggie Ahlrichs and Craig Dobbins and Wei Yang and Xinru Wang and Danny D. Sahtoe and Dionne Vafeados and Rubul Mout and Shirin Shivaei and Longxing Cao and Lauren Carter and Lance Stewart and Jamie B. Spangler and Kole T. Roybal and Per Jr Greisen and Xiaochun Li and Gonçalo J. L. Bernardes and Carolyn R. Bertozzi and David Baker},
url = {https://www.nature.com/articles/s41586-024-07948-2, Nature [Open Access]
https://www.bakerlab.org/wp-content/uploads/2025/03/Huang-et-al-EndoTags-Nature-25Sep2024.pdf, PDF},
doi = {10.1038/s41586-024-07948-2},
year = {2024},
date = {2024-09-25},
urldate = {2024-09-25},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
abstract = {Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by endogenous ligands. Therapeutic approaches such as lysosome-targeting chimaeras1,2 (LYTACs) and cytokine receptor-targeting chimeras3 (KineTACs) have used this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. Although powerful, these approaches can be limited by competition with native ligands and requirements for chemical modification that limit genetic encodability and can complicate manufacturing, and, more generally, there may be no native ligands that stimulate endocytosis through a given receptor. Here we describe computational design approaches for endocytosis-triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for insulin-like growth factor 2 receptor (IGF2R) and asialoglycoprotein receptor (ASGPR), sortilin and transferrin receptors, and show that fusing these tags to soluble or transmembrane target protein binders leads to lysosomal trafficking and target degradation. As these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. EndoTag fusion to a PD-L1 antibody considerably increases efficacy in a mouse tumour model compared to antibody alone. The modularity and genetic encodability of EndoTags enables AND gate control for higher-specificity targeted degradation, and the localized secretion of degraders from engineered cells. By promoting endocytosis, EndoTag fusion increases signalling through an engineered ligand–receptor system by nearly 100-fold. EndoTags have considerable therapeutic potential as targeted degradation inducers, signalling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody–drug and antibody–RNA conjugates.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by endogenous ligands. Therapeutic approaches such as lysosome-targeting chimaeras1,2 (LYTACs) and cytokine receptor-targeting chimeras3 (KineTACs) have used this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. Although powerful, these approaches can be limited by competition with native ligands and requirements for chemical modification that limit genetic encodability and can complicate manufacturing, and, more generally, there may be no native ligands that stimulate endocytosis through a given receptor. Here we describe computational design approaches for endocytosis-triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for insulin-like growth factor 2 receptor (IGF2R) and asialoglycoprotein receptor (ASGPR), sortilin and transferrin receptors, and show that fusing these tags to soluble or transmembrane target protein binders leads to lysosomal trafficking and target degradation. As these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. EndoTag fusion to a PD-L1 antibody considerably increases efficacy in a mouse tumour model compared to antibody alone. The modularity and genetic encodability of EndoTags enables AND gate control for higher-specificity targeted degradation, and the localized secretion of degraders from engineered cells. By promoting endocytosis, EndoTag fusion increases signalling through an engineered ligand–receptor system by nearly 100-fold. EndoTags have considerable therapeutic potential as targeted degradation inducers, signalling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody–drug and antibody–RNA conjugates.
Ian R. Humphreys, Jing Zhang, Minkyung Baek, Yaxi Wang, Aditya Krishnakumar, Jimin Pei, Ivan Anishchenko, Catherine A. Tower, Blake A. Jackson, Thulasi Warrier, Deborah T. Hung, S. Brook Peterson, Joseph D. Mougous, Qian Cong, David Baker
Protein interactions in human pathogens revealed through deep learning Journal Article
In: Nature Microbiology, 2024, ISSN: 2058-5276.
@article{Humphreys2024,
title = {Protein interactions in human pathogens revealed through deep learning},
author = {Ian R. Humphreys and Jing Zhang and Minkyung Baek and Yaxi Wang and Aditya Krishnakumar and Jimin Pei and Ivan Anishchenko and Catherine A. Tower and Blake A. Jackson and Thulasi Warrier and Deborah T. Hung and S. Brook Peterson and Joseph D. Mougous and Qian Cong and David Baker},
url = {https://www.nature.com/articles/s41564-024-01791-x, Nature Microbiology [Open Access]},
doi = {10.1038/s41564-024-01791-x},
issn = {2058-5276},
year = {2024},
date = {2024-09-18},
urldate = {2024-09-18},
journal = {Nature Microbiology},
publisher = {Springer Science and Business Media LLC},
abstract = {Identification of bacterial protein–protein interactions and predicting the structures of these complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here we developed RoseTTAFold2-Lite, a rapid deep learning model that leverages residue–residue coevolution and protein structure prediction to systematically identify and structurally characterize protein–protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1,923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer-membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Identification of bacterial protein–protein interactions and predicting the structures of these complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here we developed RoseTTAFold2-Lite, a rapid deep learning model that leverages residue–residue coevolution and protein structure prediction to systematically identify and structurally characterize protein–protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1,923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer-membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
Samuel Berhanu, Sagardip Majumder, Thomas Müntener, James Whitehouse, Carolin Berner, Asim K. Bera, Alex Kang, Binyong Liang, Nasir Khan, Banumathi Sankaran, Lukas K. Tamm, David J. Brockwell, Sebastian Hiller, Sheena E. Radford, David Baker, Anastassia A. Vorobieva
Sculpting conducting nanopore size and shape through de novo protein design Journal Article
In: Science, 2024.
@article{Berhanu2024,
title = {Sculpting conducting nanopore size and shape through de novo protein design},
author = {Samuel Berhanu and Sagardip Majumder and Thomas Müntener and James Whitehouse and Carolin Berner and Asim K. Bera and Alex Kang and Binyong Liang and Nasir Khan and Banumathi Sankaran and Lukas K. Tamm and David J. Brockwell and Sebastian Hiller and Sheena E. Radford and David Baker and Anastassia A. Vorobieva},
url = {https://www.science.org/doi/10.1126/science.adn3796, Science},
doi = {10.1126/science.adn3796},
year = {2024},
date = {2024-07-19},
urldate = {2024-07-19},
journal = {Science},
publisher = {American Association for the Advancement of Science (AAAS)},
abstract = {Transmembrane β-barrels have considerable potential for a broad range of sensing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels, which provide suboptimal starting points. By contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to designing transmembrane β-barrel pores with different diameters and pore geometries. Nuclear magnetic resonance and crystallographic characterization show that the designs are stably folded with structures resembling those of the design models. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 picosiemens (~0.5 nanometer pore diameter) to 430 picosiemens (~1.1 nanometer pore diameter). Our approach opens the door to the custom design of transmembrane nanopores for sensing and sequencing applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Transmembrane β-barrels have considerable potential for a broad range of sensing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels, which provide suboptimal starting points. By contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to designing transmembrane β-barrel pores with different diameters and pore geometries. Nuclear magnetic resonance and crystallographic characterization show that the designs are stably folded with structures resembling those of the design models. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 picosiemens (~0.5 nanometer pore diameter) to 430 picosiemens (~1.1 nanometer pore diameter). Our approach opens the door to the custom design of transmembrane nanopores for sensing and sequencing applications.
Timothy W. Craven, Mark D. Nolan, Jonathan Bailey, Samir Olatunji, Samantha J. Bann, Katherine Bowen, Nikita Ostrovitsa, Thaina M. Da Costa, Ross D. Ballantine, Dietmar Weichert, Paul M. Levine, Lance J. Stewart, Gaurav Bhardwaj, Joan A. Geoghegan, Stephen A. Cochrane, Eoin M. Scanlan, Martin Caffrey, David Baker
Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase Journal Article
In: ACS Chemical Biology, 2024.
@article{Craven2024,
title = {Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase},
author = {Timothy W. Craven and Mark D. Nolan and Jonathan Bailey and Samir Olatunji and Samantha J. Bann and Katherine Bowen and Nikita Ostrovitsa and Thaina M. Da Costa and Ross D. Ballantine and Dietmar Weichert and Paul M. Levine and Lance J. Stewart and Gaurav Bhardwaj and Joan A. Geoghegan and Stephen A. Cochrane and Eoin M. Scanlan and Martin Caffrey and David Baker},
url = {https://pubs.acs.org/doi/10.1021/acschembio.4c00076, ACS Chem. Bio. [Open Access]
https://www.bakerlab.org/wp-content/uploads/2024/05/craven-et-al-2024-computational-design-of-cyclic-peptide-inhibitors-of-a-bacterial-membrane-lipoprotein-peptidase.pdf, PDF},
doi = {10.1021/acschembio.4c00076},
year = {2024},
date = {2024-05-07},
urldate = {2024-05-07},
journal = {ACS Chemical Biology},
publisher = {American Chemical Society (ACS)},
abstract = {There remains a critical need for new antibiotics against multi-drug-resistant Gram-negative bacteria, a major global threat that continues to impact mortality rates. Lipoprotein signal peptidase II is an essential enzyme in the lipoprotein biosynthetic pathway of Gram-negative bacteria, making it an attractive target for antibacterial drug discovery. Although natural inhibitors of LspA have been identified, such as the cyclic depsipeptide globomycin, poor stability and production difficulties limit their use in a clinical setting. We harness computational design to generate stable de novo cyclic peptide analogues of globomycin. Only 12 peptides needed to be synthesized and tested to yield potent inhibitors, avoiding costly preparation of large libraries and screening campaigns. The most potent analogues showed comparable or better antimicrobial activity than globomycin in microdilution assays against ESKAPE-E pathogens. This work highlights computational design as a general strategy to combat antibiotic resistance.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
There remains a critical need for new antibiotics against multi-drug-resistant Gram-negative bacteria, a major global threat that continues to impact mortality rates. Lipoprotein signal peptidase II is an essential enzyme in the lipoprotein biosynthetic pathway of Gram-negative bacteria, making it an attractive target for antibacterial drug discovery. Although natural inhibitors of LspA have been identified, such as the cyclic depsipeptide globomycin, poor stability and production difficulties limit their use in a clinical setting. We harness computational design to generate stable de novo cyclic peptide analogues of globomycin. Only 12 peptides needed to be synthesized and tested to yield potent inhibitors, avoiding costly preparation of large libraries and screening campaigns. The most potent analogues showed comparable or better antimicrobial activity than globomycin in microdilution assays against ESKAPE-E pathogens. This work highlights computational design as a general strategy to combat antibiotic resistance.
COLLABORATOR LED
Justin A. Peruzzi, Taylor F. Gunnels, Hailey I. Edelstein, Peilong Lu, David Baker, Joshua N. Leonard, Neha P. Kamat
Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions Journal Article
In: Nature Communications, 2024.
@article{Peruzzi2024b,
title = {Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions},
author = {Justin A. Peruzzi and Taylor F. Gunnels and Hailey I. Edelstein and Peilong Lu and David Baker and Joshua N. Leonard and Neha P. Kamat},
url = {https://www.nature.com/articles/s41467-024-49678-z [Nature Communications, Open Access]},
doi = {10.1038/s41467-024-49678-z},
year = {2024},
date = {2024-07-04},
urldate = {2024-12-00},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
abstract = {Naturally generated lipid nanoparticles termed extracellular vesicles (EVs) hold significant promise as engineerable therapeutic delivery vehicles. However, active loading of protein cargo into EVs in a manner that is useful for delivery remains a challenge. Here, we demonstrate that by rationally designing proteins to traffic to the plasma membrane and associate with lipid rafts, we can enhance loading of protein cargo into EVs for a set of structurally diverse transmembrane and peripheral membrane proteins. We then demonstrate the capacity of select lipid tags to mediate increased EV loading and functional delivery of an engineered transcription factor to modulate gene expression in target cells. We envision that this technology could be leveraged to develop new EV-based therapeutics that deliver a wide array of macromolecular cargo.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Naturally generated lipid nanoparticles termed extracellular vesicles (EVs) hold significant promise as engineerable therapeutic delivery vehicles. However, active loading of protein cargo into EVs in a manner that is useful for delivery remains a challenge. Here, we demonstrate that by rationally designing proteins to traffic to the plasma membrane and associate with lipid rafts, we can enhance loading of protein cargo into EVs for a set of structurally diverse transmembrane and peripheral membrane proteins. We then demonstrate the capacity of select lipid tags to mediate increased EV loading and functional delivery of an engineered transcription factor to modulate gene expression in target cells. We envision that this technology could be leveraged to develop new EV-based therapeutics that deliver a wide array of macromolecular cargo.
Casper A. Goverde, Martin Pacesa, Nicolas Goldbach, Lars J. Dornfeld, Petra E. M. Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, Christian Schellhaas, Simon Kozlov, David Baker, Sergey Ovchinnikov, Alex J. Vecchio, Bruno E. Correia
Computational design of soluble and functional membrane protein analogues Journal Article
In: Nature, 2024, ISSN: 1476-4687.
@article{Goverde2024,
title = {Computational design of soluble and functional membrane protein analogues},
author = {Casper A. Goverde and Martin Pacesa and Nicolas Goldbach and Lars J. Dornfeld and Petra E. M. Balbi and Sandrine Georgeon and Stéphane Rosset and Srajan Kapoor and Jagrity Choudhury and Justas Dauparas and Christian Schellhaas and Simon Kozlov and David Baker and Sergey Ovchinnikov and Alex J. Vecchio and Bruno E. Correia},
url = {https://www.nature.com/articles/s41586-024-07601-y, Nature [Open Access]
},
doi = {10.1038/s41586-024-07601-y},
issn = {1476-4687},
year = {2024},
date = {2024-06-19},
urldate = {2024-06-19},
journal = {Nature},
publisher = {Springer Science and Business Media LLC},
abstract = {De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses demonstrate the high thermal stability of the designs, and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, as a proof of concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we have designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
De novo design of complex protein folds using solely computational means remains a substantial challenge. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses demonstrate the high thermal stability of the designs, and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, as a proof of concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we have designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.
2023
FROM THE LAB
An L, Hicks DR, Zorine D, Dauparas J, Wicky BIM, Milles LF, Courbet A, Bera AK, Nguyen H, Kang A, Carter L, Baker D
Hallucination of closed repeat proteins containing central pockets Journal Article
In: Nature Structural & Molecular Biology, 2023.
@article{An2023,
title = {Hallucination of closed repeat proteins containing central pockets},
author = {An L, Hicks DR, Zorine D, Dauparas J, Wicky BIM, Milles LF, Courbet A, Bera AK, Nguyen H, Kang A, Carter L, Baker D},
url = {https://www.nature.com/articles/s41594-023-01112-6, Nature Structural & Molecular Biology [Open Access] },
doi = {10.1038/s41594-023-01112-6},
year = {2023},
date = {2023-09-28},
urldate = {2023-09-28},
journal = {Nature Structural & Molecular Biology},
abstract = {In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.
Nicolas Goldbach, Issa Benna, Basile I. M. Wicky, Jacob T. Croft, Lauren Carter, Asim K. Bera, Hannah Nguyen, Alex Kang, Banumathi Sankaran, Erin C. Yang, Kelly K. Lee, David Baker
De novo design of monomeric helical bundles for pH-controlled membrane lysis Journal Article
In: Protein Science, 2023.
@article{Goldbach2023,
title = {De novo design of monomeric helical bundles for pH-controlled membrane lysis},
author = {Nicolas Goldbach and Issa Benna and Basile I. M. Wicky and Jacob T. Croft and Lauren Carter and Asim K. Bera and Hannah Nguyen and Alex Kang and Banumathi Sankaran and Erin C. Yang and Kelly K. Lee and David Baker},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.4769, Protein Science
https://www.bakerlab.org/wp-content/uploads/2023/08/Protein-Science-2023-Goldbach.pdf, PDF},
doi = {https://doi.org/10.1002/pro.4769},
year = {2023},
date = {2023-08-26},
urldate = {2023-08-26},
journal = {Protein Science},
abstract = {Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of 30 designs that were experimentally tested, all expressed in E. coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0 - 5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of 30 designs that were experimentally tested, all expressed in E. coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0 – 5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.
COLLABORATOR LED
Wang, Jing Yang (John) and Khmelinskaia, Alena and Sheffler, William and Miranda, Marcos C. and Antanasijevic, Aleksandar and Borst, Andrew J. and Torres, Susana V. and Shu, Chelsea and Hsia, Yang and Nattermann, Una and Ellis, Daniel and Walkey, Carl and Ahlrichs, Maggie and Chan, Sidney and Kang, Alex and Nguyen, Hannah and Sydeman, Claire and Sankaran, Banumathi and Wu, Mengyu and Bera, Asim K. and Carter, Lauren and Fiala, Brooke and Murphy, Michael and Baker, David and Ward, Andrew B. and King, Neil P.
Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains Journal Article
In: Proceedings of the National Academy of Sciences, 2023.
@article{Wang2023,
title = {Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains},
author = {Wang, Jing Yang (John)
and Khmelinskaia, Alena
and Sheffler, William
and Miranda, Marcos C.
and Antanasijevic, Aleksandar
and Borst, Andrew J.
and Torres, Susana V.
and Shu, Chelsea
and Hsia, Yang
and Nattermann, Una
and Ellis, Daniel
and Walkey, Carl
and Ahlrichs, Maggie
and Chan, Sidney
and Kang, Alex
and Nguyen, Hannah
and Sydeman, Claire
and Sankaran, Banumathi
and Wu, Mengyu
and Bera, Asim K.
and Carter, Lauren
and Fiala, Brooke
and Murphy, Michael
and Baker, David
and Ward, Andrew B.
and King, Neil P.},
url = {https://www.pnas.org/doi/10.1073/pnas.2214556120, PNAS (Open Access)},
doi = {10.1073/pnas.2214556120},
year = {2023},
date = {2023-03-08},
urldate = {2023-03-08},
journal = {Proceedings of the National Academy of Sciences},
abstract = {Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.
2022
FROM THE LAB
Gaurav Bhardwaj, Jacob O’Connor, Stephen Rettie, Yen-Hua Huang, Theresa A. Ramelot, Vikram Khipple Mulligan, Gizem Gokce Alpkilic, Jonathan Palmer, Asim K. Bera, Matthew J. Bick, Maddalena Di Piazza, Xinting Li, Parisa Hosseinzadeh, Timothy W. Craven, Roberto Tejero, Anna Lauko, Ryan Choi, Calina Glynn, Linlin Dong, Robert Griffin, Wesley C. van Voorhis, Jose Rodriguez, Lance Stewart, Gaetano T. Montelione, David Craik, David Baker
Accurate de novo design of membrane-traversing macrocycles Journal Article
In: Cell, 2022.
@article{Bhardwaj2022,
title = {Accurate de novo design of membrane-traversing macrocycles},
author = {Gaurav Bhardwaj and Jacob O’Connor and Stephen Rettie and Yen-Hua Huang and Theresa A. Ramelot and Vikram Khipple Mulligan and Gizem Gokce Alpkilic and Jonathan Palmer and Asim K. Bera and Matthew J. Bick and Maddalena {Di Piazza} and Xinting Li and Parisa Hosseinzadeh and Timothy W. Craven and Roberto Tejero and Anna Lauko and Ryan Choi and Calina Glynn and Linlin Dong and Robert Griffin and Wesley C. {van Voorhis} and Jose Rodriguez and Lance Stewart and Gaetano T. Montelione and David Craik and David Baker},
url = {https://www.sciencedirect.com/science/article/pii/S0092867422009229?via%3Dihub, Cell
https://www.bakerlab.org/wp-content/uploads/2022/08/1-s2.0-S0092867422009229-main.pdf, PDF},
doi = {10.1016/j.cell.2022.07.019},
year = {2022},
date = {2022-08-29},
urldate = {2022-08-29},
journal = {Cell},
abstract = {We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6–12 residue macrocycles with a wide range of predicted structures containing noncanonical backbone modifications and experimentally determined structures of 35; 29 are very close to the computational models. With such control, we show that membrane permeability can be systematically achieved by ensuring all amide (NH) groups are engaged in internal hydrogen bonding interactions. 84 designs over the 6–12 residue size range cross membranes with an apparent permeability greater than 1 × 10−6 cm/s. Designs with exposed NH groups can be made membrane permeable through the design of an alternative isoenergetic fully hydrogen-bonded state favored in the lipid membrane. The ability to robustly design membrane-permeable and orally bioavailable peptides with high structural accuracy should contribute to the next generation of designed macrocycle therapeutics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6–12 residue macrocycles with a wide range of predicted structures containing noncanonical backbone modifications and experimentally determined structures of 35; 29 are very close to the computational models. With such control, we show that membrane permeability can be systematically achieved by ensuring all amide (NH) groups are engaged in internal hydrogen bonding interactions. 84 designs over the 6–12 residue size range cross membranes with an apparent permeability greater than 1 × 10−6 cm/s. Designs with exposed NH groups can be made membrane permeable through the design of an alternative isoenergetic fully hydrogen-bonded state favored in the lipid membrane. The ability to robustly design membrane-permeable and orally bioavailable peptides with high structural accuracy should contribute to the next generation of designed macrocycle therapeutics.
COLLABORATOR LED
Macé, Kévin and Vadakkepat, Abhinav K. and Redzej, Adam and Lukoyanova, Natalya and Oomen, Clasien and Braun, Nathalie and Ukleja, Marta and Lu, Fang and Costa, Tiago R. D. and Orlova, Elena V. and Baker, David and Cong, Qian and Waksman, Gabriel
Cryo-EM structure of a type IV secretion system Journal Article
In: Nature, 2022.
@article{Macé2022,
title = {Cryo-EM structure of a type IV secretion system},
author = {Macé, Kévin
and Vadakkepat, Abhinav K.
and Redzej, Adam
and Lukoyanova, Natalya
and Oomen, Clasien
and Braun, Nathalie
and Ukleja, Marta
and Lu, Fang
and Costa, Tiago R. D.
and Orlova, Elena V.
and Baker, David
and Cong, Qian
and Waksman, Gabriel},
url = {https://www.nature.com/articles/s41586-022-04859-y, Nature
https://www.bakerlab.org/wp-content/uploads/2022/08/Mace2022s41586-022-04859-y.pdf, PDF},
doi = {10.1038/s41586-022-04859-y},
year = {2022},
date = {2022-07-01},
urldate = {2022-07-01},
journal = {Nature},
abstract = {Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell1. It is the primary means by which antibiotic resistance genes spread among bacterial populations2,3. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus—the conjugative type IV secretion system (T4SS)—produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament—the conjugative pilus—that is essential for DNA transfer4,5. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein–protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell1. It is the primary means by which antibiotic resistance genes spread among bacterial populations2,3. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus—the conjugative type IV secretion system (T4SS)—produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament—the conjugative pilus—that is essential for DNA transfer4,5. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein–protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.
2021
FROM THE LAB
Vorobieva, Anastassia A., White, Paul, Liang, Binyong, Horne, Jim E., Bera, Asim K., Chow, Cameron M., Gerben, Stacey, Marx, Sinduja, Kang, Alex, Stiving, Alyssa Q., Harvey, Sophie R., Marx, Dagan C., Khan, G. Nasir, Fleming, Karen G., Wysocki, Vicki H., Brockwell, David J., Tamm, Lukas K., Radford, Sheena E., Baker, David
De novo design of transmembrane beta barrels Journal Article
In: Science, vol. 371, no. 6531, 2021.
@article{Vorobieva2021,
title = {De novo design of transmembrane beta barrels},
author = {Vorobieva, Anastassia A. and White, Paul and Liang, Binyong and Horne, Jim E. and Bera, Asim K. and Chow, Cameron M. and Gerben, Stacey and Marx, Sinduja and Kang, Alex and Stiving, Alyssa Q. and Harvey, Sophie R. and Marx, Dagan C. and Khan, G. Nasir and Fleming, Karen G. and Wysocki, Vicki H. and Brockwell, David J. and Tamm, Lukas K. and Radford, Sheena E. and Baker, David},
url = {https://science.sciencemag.org/content/371/6531/eabc8182, Science
https://www.bakerlab.org/wp-content/uploads/2021/02/Vorobieva_etal_Science2021_De_Novo_Transmembrane_beta_barrels.pdf, Download PDF},
doi = {10.1126/science.abc8182},
year = {2021},
date = {2021-02-19},
urldate = {2021-02-19},
journal = {Science},
volume = {371},
number = {6531},
abstract = {Computational design offers the possibility of making proteins with customized structures and functions. The range of accessible protein scaffolds has expanded with the design of increasingly complex cytoplasmic proteins and, recently, helical membrane proteins. Vorobieva et al. describe the successful computational design of eight-stranded transmembrane β-barrel proteins (TMBs). Using an iterative approach, they show the importance of negative design to prevent off-target structures and gain insight into the sequence determinants of TMB folding. Twenty-three designs satisfied biochemical screens for a TMB structure, and two structures were experimentally validated by nuclear magnetic resonance spectroscopy or x-ray crystallography. This is a step toward the custom design of pores for applications such as single-molecule sequencing.Science, this issue p. eabc8182INTRODUCTIONDespite their key biological roles, only a few proteins that fold into lipid membranes have been designed de novo. A class of membrane proteins{textemdash}transmembrane β barrels (TMBs){textemdash}forms a continuous sheet that closes on itself in lipid membranes. In addition to the challenge of designing β-sheet proteins, which are prone to misfolding and aggregation if folding is not properly controlled, the computational design of TMBs is complicated by limited understanding of TMB folding. As a result, no TMB has been designed de novo to date.Although the folding of TMBs in vivo is catalyzed by the β-barrel assembly machinery (BAM), many TMBs can also fold spontaneously in synthetic membranes to form stable pores, making them attractive for biotechnology and single-molecule analytical applications. Hence, de novo design of TMBs has potential both for understanding the determinants of TMB folding and membrane insertion and for the custom engineering of TMB nanopores.RATIONALEWe used de novo protein design to distill key principles of TMB folding through several design-build-test cycles. We iterated between hypothesis formulation, its implementation into computational design methods, and experimental characterization of the resulting proteins. To focus on the fundamental principles of TMB folding in the absence of complications due to interactions with chaperones and BAM in vivo, we focused on the challenge of de novo design of eight-stranded TMBs, which can fold and assemble into synthetic lipid membranes.RESULTSWe used a combination of purely geometric models and explicit Rosetta protein structure simulations to determine the constraints that β-strand connectivity and membrane embedding place on the TMB architecture. Through a series of design-build-test cycles, we found that, unlike almost all other classes of proteins, locally destabilizing sequences are critical for expression and folding of TMBs, and that the β-turns that translocate through the bilayer during folding have to be destabilized to enable correct assembly in the membrane. Our results suggest that premature formation of β hairpins may result in off-target β-sheet structures that compete with proper membrane insertion and folding, and hence the β hairpins of TMBs must be designed such that they are only transiently formed prior to membrane insertion, when the protein is in an aqueous environment. In the hydrophobic environment of the lipid bilayer, the full TMB can assemble because the membrane-facing nonpolar residues, which would tend to cluster nonspecifically in an aqueous environment, instead make favorable interactions with the lipids. As the TMB assembles, the β hairpins are stabilized by interactions with the neighboring β strands.Using computational methods that incorporate the above insights, we designed TMB sequences that successfully fold and assemble into both detergent micelles and lipid bilayers. Two of the designs were highly stable and could fold into liposomes more rapidly and reversibly than the transmembrane domain of the model outer membrane protein A (tOmpA) of Escherichia coli. A nuclear magnetic resonance solution structure and a high-resolution crystal structure for two different designs closely match the design models, showing that the TMB design method developed here can generate new structures with atomic-level accuracy.CONCLUSIONThis study elucidates key principles for de novo design of transmembrane β barrels, ranging from constraints on β-barrel architecture and β-hairpin design, as well as local and global sequence features. Our designs provide starting points for the bottom-up elucidation of the molecular mechanisms underlying TMB folding and interactions with the cellular outer membrane folding and insertion machinery. More generally, our work demonstrates that TMBs can be designed with atomic-level accuracy and opens the door to custom design of nanopores tailored for applications such as single-molecule sensing and sequencing.De novo{textendash}designed eight-stranded transmembrane β barrels fold spontaneously and reversibly into synthetic lipid membranes.The illustration shows the crystal structure of the protein TMB2.17 designed in this study, which adopts a structure identical to the design model.Credit: Ian Haydon.Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a {textquotedblleft}hypothesis, design, and test{textquotedblright} approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Computational design offers the possibility of making proteins with customized structures and functions. The range of accessible protein scaffolds has expanded with the design of increasingly complex cytoplasmic proteins and, recently, helical membrane proteins. Vorobieva et al. describe the successful computational design of eight-stranded transmembrane β-barrel proteins (TMBs). Using an iterative approach, they show the importance of negative design to prevent off-target structures and gain insight into the sequence determinants of TMB folding. Twenty-three designs satisfied biochemical screens for a TMB structure, and two structures were experimentally validated by nuclear magnetic resonance spectroscopy or x-ray crystallography. This is a step toward the custom design of pores for applications such as single-molecule sequencing.Science, this issue p. eabc8182INTRODUCTIONDespite their key biological roles, only a few proteins that fold into lipid membranes have been designed de novo. A class of membrane proteins{textemdash}transmembrane β barrels (TMBs){textemdash}forms a continuous sheet that closes on itself in lipid membranes. In addition to the challenge of designing β-sheet proteins, which are prone to misfolding and aggregation if folding is not properly controlled, the computational design of TMBs is complicated by limited understanding of TMB folding. As a result, no TMB has been designed de novo to date.Although the folding of TMBs in vivo is catalyzed by the β-barrel assembly machinery (BAM), many TMBs can also fold spontaneously in synthetic membranes to form stable pores, making them attractive for biotechnology and single-molecule analytical applications. Hence, de novo design of TMBs has potential both for understanding the determinants of TMB folding and membrane insertion and for the custom engineering of TMB nanopores.RATIONALEWe used de novo protein design to distill key principles of TMB folding through several design-build-test cycles. We iterated between hypothesis formulation, its implementation into computational design methods, and experimental characterization of the resulting proteins. To focus on the fundamental principles of TMB folding in the absence of complications due to interactions with chaperones and BAM in vivo, we focused on the challenge of de novo design of eight-stranded TMBs, which can fold and assemble into synthetic lipid membranes.RESULTSWe used a combination of purely geometric models and explicit Rosetta protein structure simulations to determine the constraints that β-strand connectivity and membrane embedding place on the TMB architecture. Through a series of design-build-test cycles, we found that, unlike almost all other classes of proteins, locally destabilizing sequences are critical for expression and folding of TMBs, and that the β-turns that translocate through the bilayer during folding have to be destabilized to enable correct assembly in the membrane. Our results suggest that premature formation of β hairpins may result in off-target β-sheet structures that compete with proper membrane insertion and folding, and hence the β hairpins of TMBs must be designed such that they are only transiently formed prior to membrane insertion, when the protein is in an aqueous environment. In the hydrophobic environment of the lipid bilayer, the full TMB can assemble because the membrane-facing nonpolar residues, which would tend to cluster nonspecifically in an aqueous environment, instead make favorable interactions with the lipids. As the TMB assembles, the β hairpins are stabilized by interactions with the neighboring β strands.Using computational methods that incorporate the above insights, we designed TMB sequences that successfully fold and assemble into both detergent micelles and lipid bilayers. Two of the designs were highly stable and could fold into liposomes more rapidly and reversibly than the transmembrane domain of the model outer membrane protein A (tOmpA) of Escherichia coli. A nuclear magnetic resonance solution structure and a high-resolution crystal structure for two different designs closely match the design models, showing that the TMB design method developed here can generate new structures with atomic-level accuracy.CONCLUSIONThis study elucidates key principles for de novo design of transmembrane β barrels, ranging from constraints on β-barrel architecture and β-hairpin design, as well as local and global sequence features. Our designs provide starting points for the bottom-up elucidation of the molecular mechanisms underlying TMB folding and interactions with the cellular outer membrane folding and insertion machinery. More generally, our work demonstrates that TMBs can be designed with atomic-level accuracy and opens the door to custom design of nanopores tailored for applications such as single-molecule sensing and sequencing.De novo{textendash}designed eight-stranded transmembrane β barrels fold spontaneously and reversibly into synthetic lipid membranes.The illustration shows the crystal structure of the protein TMB2.17 designed in this study, which adopts a structure identical to the design model.Credit: Ian Haydon.Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a {textquotedblleft}hypothesis, design, and test{textquotedblright} approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.
Ben-Sasson, Ariel J., Watson, Joseph L., Sheffler, William, Johnson, Matthew Camp, Bittleston, Alice, Somasundaram, Logeshwaran, Decarreau, Justin, Jiao, Fang, Chen, Jiajun, Mela, Ioanna, Drabek, Andrew A., Jarrett, Sanchez M., Blacklow, Stephen C., Kaminski, Clemens F., Hura, Greg L., De Yoreo, James J., Kollman, Justin M., Ruohola-Baker, Hannele, Derivery, Emmanuel, Baker, David
Design of biologically active binary protein 2D materials Journal Article
In: Nature, 2021.
@article{Ben-Sasson2020,
title = {Design of biologically active binary protein 2D materials},
author = {Ben-Sasson, Ariel J. and Watson, Joseph L. and Sheffler, William and Johnson, Matthew Camp and Bittleston, Alice and Somasundaram, Logeshwaran and Decarreau, Justin and Jiao, Fang and Chen, Jiajun and Mela, Ioanna and Drabek, Andrew A. and Jarrett, Sanchez M. and Blacklow, Stephen C. and Kaminski, Clemens F. and Hura, Greg L. and De Yoreo, James J. and Kollman, Justin M. and Ruohola-Baker, Hannele and Derivery, Emmanuel and Baker, David},
url = {https://www.nature.com/articles/s41586-020-03120-8, Nature
https://www.bakerlab.org/wp-content/uploads/2021/02/Ben-Sasson_Nature2021_Binary_2D_arrays.pdf, Download PDF},
doi = {10.1038/s41586-020-03120-8},
year = {2021},
date = {2021-01-06},
urldate = {2021-01-06},
journal = {Nature},
abstract = {Ordered two-dimensional arrays such as S-layers1,2 and designed analogues3–5 have intrigued bioengineers6,7, but with the exception of a single lattice formed with flexible linkers8, they are constituted from just one protein component. Materials composed of two components have considerable potential advantages for modulating assembly dynamics and incorporating more complex functionality9–12. Here we describe a computational method to generate co-assembling binary layers by designing rigid interfaces between pairs of dihedral protein building blocks, and use it to design a p6m lattice. The designed array components are soluble at millimolar concentrations, but when combined at nanomolar concentrations, they rapidly assemble into nearly crystalline micrometre-scale arrays nearly identical to the computational design model in vitro and in cells without the need for a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces, which we demonstrate can drive extensive receptor clustering, downstream protein recruitment and signalling. Using atomic force microscopy on supported bilayers and quantitative microscopy on living cells, we show that arrays assembled on membranes have component stoichiometry and structure similar to arrays formed in vitro, and that our material can therefore impose order onto fundamentally disordered substrates such as cell membranes. In contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, we find that large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work provides a foundation for a synthetic cell biology in which multi-protein macroscale materials are designed to modulate cell responses and reshape synthetic and living systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ordered two-dimensional arrays such as S-layers1,2 and designed analogues3–5 have intrigued bioengineers6,7, but with the exception of a single lattice formed with flexible linkers8, they are constituted from just one protein component. Materials composed of two components have considerable potential advantages for modulating assembly dynamics and incorporating more complex functionality9–12. Here we describe a computational method to generate co-assembling binary layers by designing rigid interfaces between pairs of dihedral protein building blocks, and use it to design a p6m lattice. The designed array components are soluble at millimolar concentrations, but when combined at nanomolar concentrations, they rapidly assemble into nearly crystalline micrometre-scale arrays nearly identical to the computational design model in vitro and in cells without the need for a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces, which we demonstrate can drive extensive receptor clustering, downstream protein recruitment and signalling. Using atomic force microscopy on supported bilayers and quantitative microscopy on living cells, we show that arrays assembled on membranes have component stoichiometry and structure similar to arrays formed in vitro, and that our material can therefore impose order onto fundamentally disordered substrates such as cell membranes. In contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, we find that large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work provides a foundation for a synthetic cell biology in which multi-protein macroscale materials are designed to modulate cell responses and reshape synthetic and living systems.
COLLABORATOR LED
Sorry, no publications matched your criteria.
2020
FROM THE LAB
Chunfu Xu, Peilong Lu, Tamer M. Gamal El-Din, Xue Y. Pei, Matthew C. Johnson, Atsuko Uyeda, Matthew J. Bick, Qi Xu, Daohua Jiang, Hua Bai, Gabriella Reggiano, Yang Hsia, T J Brunette, Jiayi Dou, Dan Ma, Eric M. Lynch, Scott E. Boyken, Po-Ssu Huang, Lance Stewart, Frank DiMaio, Justin M. Kollman, Ben F. Luisi, Tomoaki Matsuura, William A. Catterall, David Baker
Computational design of transmembrane pores Journal Article
In: Nature, vol. 585, pp. 129–134, 2020.
@article{Xu2020,
title = {Computational design of transmembrane pores},
author = {Chunfu Xu and Peilong Lu and Tamer M. Gamal El-Din and Xue Y. Pei and Matthew C. Johnson and Atsuko Uyeda and Matthew J. Bick and Qi Xu and Daohua Jiang and Hua Bai and Gabriella Reggiano and Yang Hsia and T J Brunette and Jiayi Dou and Dan Ma and Eric M. Lynch and Scott E. Boyken and Po-Ssu Huang and Lance Stewart and Frank DiMaio and Justin M. Kollman and Ben F. Luisi and Tomoaki Matsuura and William A. Catterall and David Baker },
url = {https://www.bakerlab.org/wp-content/uploads/2020/08/Xuetal_Nature2020_DeNovoPores.pdf
https://www.nature.com/articles/s41586-020-2646-5},
doi = {10.1038/s41586-020-2646-5},
year = {2020},
date = {2020-08-26},
journal = {Nature},
volume = {585},
pages = {129–134},
abstract = {Transmembrane channels and pores have key roles in fundamental biological processes and in biotechnological applications such as DNA nanopore sequencing, resulting in considerable interest in the design of pore-containing proteins. Synthetic amphiphilic peptides have been found to form ion channels, and there have been recent advances in de novo membrane protein design and in redesigning naturally occurring channel-containing proteins. However, the de novo design of stable, well-defined transmembrane protein pores that are capable of conducting ions selectively or are large enough to enable the passage of small-molecule fluorophores remains an outstanding challenge. Here we report the computational design of protein pores formed by two concentric rings of α-helices that are stable and monodisperse in both their water-soluble and their transmembrane forms. Crystal structures of the water-soluble forms of a 12-helical pore and a 16-helical pore closely match the computational design models. Patch-clamp electrophysiology experiments show that, when expressed in insect cells, the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium; ion passage is blocked by specific chemical modification at the pore entrance. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore—but not the 12-helix pore—enables the passage of biotinylated Alexa Fluor 488. A cryo-electron microscopy structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer channels and pores for a wide variety of applications.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Transmembrane channels and pores have key roles in fundamental biological processes and in biotechnological applications such as DNA nanopore sequencing, resulting in considerable interest in the design of pore-containing proteins. Synthetic amphiphilic peptides have been found to form ion channels, and there have been recent advances in de novo membrane protein design and in redesigning naturally occurring channel-containing proteins. However, the de novo design of stable, well-defined transmembrane protein pores that are capable of conducting ions selectively or are large enough to enable the passage of small-molecule fluorophores remains an outstanding challenge. Here we report the computational design of protein pores formed by two concentric rings of α-helices that are stable and monodisperse in both their water-soluble and their transmembrane forms. Crystal structures of the water-soluble forms of a 12-helical pore and a 16-helical pore closely match the computational design models. Patch-clamp electrophysiology experiments show that, when expressed in insect cells, the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium; ion passage is blocked by specific chemical modification at the pore entrance. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore—but not the 12-helix pore—enables the passage of biotinylated Alexa Fluor 488. A cryo-electron microscopy structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer channels and pores for a wide variety of applications.
COLLABORATOR LED
Sorry, no publications matched your criteria.
2019
FROM THE LAB
Boyken, Scott E., Benhaim, Mark A., Busch, Florian, Jia, Mengxuan, Bick, Matthew J., Choi, Heejun, Klima, Jason C., Chen, Zibo, Walkey, Carl, Mileant, Alexander, Sahasrabuddhe, Aniruddha, Wei, Kathy Y., Hodge, Edgar A., Byron, Sarah, Quijano-Rubio, Alfredo, Sankaran, Banumathi, King, Neil P., Lippincott-Schwartz, Jennifer, Wysocki, Vicki H., Lee, Kelly K., Baker, David
De novo design of tunable, pH-driven conformational changes Journal Article
In: Science, vol. 364, no. 6441, pp. 658-664, 2019.
@article{Boyken2019,
title = {De novo design of tunable, pH-driven conformational changes},
author = {Boyken, Scott E. and Benhaim, Mark A. and Busch, Florian and Jia, Mengxuan and Bick, Matthew J. and Choi, Heejun and Klima, Jason C. and Chen, Zibo and Walkey, Carl and Mileant, Alexander and Sahasrabuddhe, Aniruddha and Wei, Kathy Y. and Hodge, Edgar A. and Byron, Sarah and Quijano-Rubio, Alfredo and Sankaran, Banumathi and King, Neil P. and Lippincott-Schwartz, Jennifer and Wysocki, Vicki H. and Lee, Kelly K. and Baker, David
},
url = {https://science.sciencemag.org/content/364/6441/658
https://www.bakerlab.org/wp-content/uploads/2019/06/Boyken_etal2019_pH_conformational_changes.pdf},
doi = {10.1126/science.aav7897},
year = {2019},
date = {2019-05-17},
journal = {Science},
volume = {364},
number = {6441},
pages = {658-664},
abstract = {The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.
COLLABORATOR LED
Sorry, no publications matched your criteria.
2018
FROM THE LAB
Lu, Peilong, Min, Duyoung, DiMaio, Frank, Wei, Kathy Y., Vahey, Michael D., Boyken, Scott E., Chen, Zibo, Fallas, Jorge A., Ueda, George, Sheffler, William, Mulligan, Vikram Khipple, Xu, Wenqing, Bowie, James U., Baker, David
Accurate computational design of multipass transmembrane proteins Journal Article
In: Science, vol. 359, no. 6379, pp. 1042–1046, 2018, ISSN: 0036-8075.
@article{Lu1042,
title = {Accurate computational design of multipass transmembrane proteins},
author = {Lu, Peilong and Min, Duyoung and DiMaio, Frank and Wei, Kathy Y. and Vahey, Michael D. and Boyken, Scott E. and Chen, Zibo and Fallas, Jorge A. and Ueda, George and Sheffler, William and Mulligan, Vikram Khipple and Xu, Wenqing and Bowie, James U. and Baker, David},
url = {http://science.sciencemag.org/content/359/6379/1042
https://www.bakerlab.org/wp-content/uploads/2018/03/Lu_Science_2018.pdf},
doi = {10.1126/science.aaq1739},
issn = {0036-8075},
year = {2018},
date = {2018-03-02},
journal = {Science},
volume = {359},
number = {6379},
pages = {1042--1046},
abstract = {In recent years, soluble protein design has achieved successes such as artificial enzymes and large protein cages. Membrane proteins present a considerable design challenge, but here too there have been advances, including the design of a zinc-transporting tetramer. Lu et al. report the design of stable transmembrane monomers, homodimers, trimers, and tetramers with up to eight membrane-spanning regions in an oligomer. The designed proteins adopted the target oligomerization state and localized to the predicted cellular membranes, and crystal structures of the designed dimer and tetramer reflected the design models.Science, this issue p. 1042The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer{textemdash}a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices{textemdash}are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In recent years, soluble protein design has achieved successes such as artificial enzymes and large protein cages. Membrane proteins present a considerable design challenge, but here too there have been advances, including the design of a zinc-transporting tetramer. Lu et al. report the design of stable transmembrane monomers, homodimers, trimers, and tetramers with up to eight membrane-spanning regions in an oligomer. The designed proteins adopted the target oligomerization state and localized to the predicted cellular membranes, and crystal structures of the designed dimer and tetramer reflected the design models.Science, this issue p. 1042The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer{textemdash}a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices{textemdash}are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions.
COLLABORATOR LED
Sorry, no publications matched your criteria.
2017-1988
ALL PAPERS
2017
Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A. Pavlopoulos, David E. Kim, Hetunandan Kamisetty, Nikos C. Kyrpides, David Baker
Protein structure determination using metagenome sequence data Journal Article
In: Science, vol. 355, no. 6322, pp. 294–298, 2017, ISSN: 0036-8075.
@article{Ovchinnikov294,
title = {Protein structure determination using metagenome sequence data},
author = { Sergey Ovchinnikov and Hahnbeom Park and Neha Varghese and Po-Ssu Huang and Georgios A. Pavlopoulos and David E. Kim and Hetunandan Kamisetty and Nikos C. Kyrpides and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2017/01/ovchinnikov_science_2017.pdf
http://science.sciencemag.org/content/355/6322/294},
doi = {10.1126/science.aah4043},
issn = {0036-8075},
year = {2017},
date = {2017-01-01},
journal = {Science},
volume = {355},
number = {6322},
pages = {294--298},
publisher = {American Association for the Advancement of Science},
abstract = {Fewer than a third of the 14,849 known protein families have at least one member with an experimentally determined structure. This leaves more than 5000 protein families with no structural information. Protein modeling using residue-residue contacts inferred from evolutionary data has been successful in modeling unknown structures, but it requires large numbers of aligned sequences. Ovchinnikov et al. augmented such sequence alignments with metagenome sequence data (see the Perspective by S"oding). They determined the number of sequences required to allow modeling, developed criteria for model quality, and, where possible, improved modeling by matching predicted contacts to known structures. Their method predicted quality structural models for 614 protein families, of which about 140 represent newly discovered protein folds.Science, this issue p. 294; see also p. 248Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fewer than a third of the 14,849 known protein families have at least one member with an experimentally determined structure. This leaves more than 5000 protein families with no structural information. Protein modeling using residue-residue contacts inferred from evolutionary data has been successful in modeling unknown structures, but it requires large numbers of aligned sequences. Ovchinnikov et al. augmented such sequence alignments with metagenome sequence data (see the Perspective by S"oding). They determined the number of sequences required to allow modeling, developed criteria for model quality, and, where possible, improved modeling by matching predicted contacts to known structures. Their method predicted quality structural models for 614 protein families, of which about 140 represent newly discovered protein folds.Science, this issue p. 294; see also p. 248Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost.
2015
Carly A Holstein, Aaron Chevalier, Steven Bennett, Caitlin E Anderson, Karen Keniston, Cathryn Olsen, Bing Li, Brian Bales, David R Moore, Elain Fu, David Baker, Paul Yager
Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers. Journal Article
In: Analytical and bioanalytical chemistry, 2015, ISSN: 1618-2650.
@article{626,
title = {Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers.},
author = { Carly A Holstein and Aaron Chevalier and Steven Bennett and Caitlin E Anderson and Karen Keniston and Cathryn Olsen and Bing Li and Brian Bales and David R Moore and Elain Fu and David Baker and Paul Yager},
url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Holstien_Anal_Bioanal_Chem_2015.pdf},
doi = {10.1007/s00216-015-9052-0},
issn = {1618-2650},
year = {2015},
date = {2015-10-01},
journal = {Analytical and bioanalytical chemistry},
abstract = {To enable enhanced paper-based diagnostics with improved detection capabilities, new methods are needed to immobilize affinity reagents to porous substrates, especially for capture molecules other than IgG. To this end, we have developed and characterized three novel methods for immobilizing protein-based affinity reagents to nitrocellulose membranes. We have demonstrated these methods using recombinant affinity proteins for the influenza surface protein hemagglutinin, leveraging the customizability of these recombinant "flu binders" for the design of features for immobilization. The three approaches shown are: (1) covalent attachment of thiolated affinity protein to an epoxide-functionalized nitrocellulose membrane, (2) attachment of biotinylated affinity protein through a nitrocellulose-binding streptavidin anchor protein, and (3) fusion of affinity protein to a novel nitrocellulose-binding anchor protein for direct coupling and immobilization. We also characterized the use of direct adsorption for the flu binders, as a point of comparison and motivation for these novel methods. Finally, we demonstrated that these novel methods can provide improved performance to an influenza hemagglutinin assay, compared to a traditional antibody-based capture system. Taken together, this work advances the toolkit available for the development of next-generation paper-based diagnostics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
To enable enhanced paper-based diagnostics with improved detection capabilities, new methods are needed to immobilize affinity reagents to porous substrates, especially for capture molecules other than IgG. To this end, we have developed and characterized three novel methods for immobilizing protein-based affinity reagents to nitrocellulose membranes. We have demonstrated these methods using recombinant affinity proteins for the influenza surface protein hemagglutinin, leveraging the customizability of these recombinant "flu binders" for the design of features for immobilization. The three approaches shown are: (1) covalent attachment of thiolated affinity protein to an epoxide-functionalized nitrocellulose membrane, (2) attachment of biotinylated affinity protein through a nitrocellulose-binding streptavidin anchor protein, and (3) fusion of affinity protein to a novel nitrocellulose-binding anchor protein for direct coupling and immobilization. We also characterized the use of direct adsorption for the flu binders, as a point of comparison and motivation for these novel methods. Finally, we demonstrated that these novel methods can provide improved performance to an influenza hemagglutinin assay, compared to a traditional antibody-based capture system. Taken together, this work advances the toolkit available for the development of next-generation paper-based diagnostics.
Julien R C Bergeron, Liam J Worrall, Soumya De, Nikolaos G Sgourakis, Adrienne H Cheung, Emilie Lameignere, Mark Okon, Gregory A Wasney, David Baker, Lawrence P McIntosh, Natalie C J Strynadka
The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body Journal Article
In: Structure (London, England : 1993), vol. 23, pp. 161-72, 2015, ISSN: 1878-4186.
@article{608,
title = {The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body},
author = { Julien R C Bergeron and Liam J Worrall and Soumya De and Nikolaos G Sgourakis and Adrienne H Cheung and Emilie Lameignere and Mark Okon and Gregory A Wasney and David Baker and Lawrence P McIntosh and Natalie C J Strynadka},
url = {http://www.bakerlab.org/wp-content/uploads/2015/12/themodularstructure_Baker2015.pdf},
doi = {10.1016/j.str.2014.10.021},
issn = {1878-4186},
year = {2015},
date = {2015-01-01},
journal = {Structure (London, England : 1993)},
volume = {23},
pages = {161-72},
abstract = {The type III secretion system (T3SS) is a large macromolecular assembly found at the surface of many pathogenic Gram-negative bacteria. Its role is to inject toxic "effector" proteins into the cells of infected organisms. The molecular details of the assembly of this large, multimembrane-spanning complex remain poorly understood. Here, we report structural, biochemical, and functional analyses of PrgK, an inner-membrane component of the prototypical Salmonella typhimurium T3SS. We have obtained the atomic structures of the two ring building globular domains and show that the C-terminal transmembrane helix is not essential for assembly and secretion. We also demonstrate that structural rearrangement of the two PrgK globular domains, driven by an interconnecting linker region, may promote oligomerization into ring structures. Finally, we used electron microscopy-guided symmetry modeling to propose a structural model for the intimately associated PrgH-PrgK ring interaction within the assembled basal body.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The type III secretion system (T3SS) is a large macromolecular assembly found at the surface of many pathogenic Gram-negative bacteria. Its role is to inject toxic "effector" proteins into the cells of infected organisms. The molecular details of the assembly of this large, multimembrane-spanning complex remain poorly understood. Here, we report structural, biochemical, and functional analyses of PrgK, an inner-membrane component of the prototypical Salmonella typhimurium T3SS. We have obtained the atomic structures of the two ring building globular domains and show that the C-terminal transmembrane helix is not essential for assembly and secretion. We also demonstrate that structural rearrangement of the two PrgK globular domains, driven by an interconnecting linker region, may promote oligomerization into ring structures. Finally, we used electron microscopy-guided symmetry modeling to propose a structural model for the intimately associated PrgH-PrgK ring interaction within the assembled basal body.
2014
Kuang-Yui M Chen, Jiaming Sun, Jason S Salvo, David Baker, Patrick Barth
High-resolution modeling of transmembrane helical protein structures from distant homologues. Journal Article
In: PLoS computational biology, vol. 10, pp. e1003636, 2014, ISSN: 1553-7358.
@article{622,
title = {High-resolution modeling of transmembrane helical protein structures from distant homologues.},
author = { Kuang-Yui M Chen and Jiaming Sun and Jason S Salvo and David Baker and Patrick Barth},
url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Chen_PLOS_2014.pdf},
doi = {10.1371/journal.pcbi.1003636},
issn = {1553-7358},
year = {2014},
date = {2014-05-01},
journal = {PLoS computational biology},
volume = {10},
pages = {e1003636},
abstract = {Eukaryotic transmembrane helical (TMH) proteins perform a wide diversity of critical cellular functions, but remain structurally largely uncharacterized and their high-resolution structure prediction is currently hindered by the lack of close structural homologues. To address this problem, we present a novel and generic method for accurately modeling large TMH protein structures from distant homologues exhibiting distinct loop and TMH conformations. Models of the adenosine A2AR and chemokine CXCR4 receptors were first ranked in GPCR-DOCK blind prediction contests in the receptor structure accuracy category. In a benchmark of 50 TMH protein homolog pairs of diverse topology (from 5 to 12 TMHs), size (from 183 to 420 residues) and sequence identity (from 15% to 70%), the method improves most starting templates, and achieves near-atomic accuracy prediction of membrane-embedded regions. Unlike starting templates, the models are of suitable quality for computer-based protein engineering: redesigned models and redesigned X-ray structures exhibit very similar native interactions. The method should prove useful for the atom-level modeling and design of a large fraction of structurally uncharacterized TMH proteins from a wide range of structural homologues.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Eukaryotic transmembrane helical (TMH) proteins perform a wide diversity of critical cellular functions, but remain structurally largely uncharacterized and their high-resolution structure prediction is currently hindered by the lack of close structural homologues. To address this problem, we present a novel and generic method for accurately modeling large TMH protein structures from distant homologues exhibiting distinct loop and TMH conformations. Models of the adenosine A2AR and chemokine CXCR4 receptors were first ranked in GPCR-DOCK blind prediction contests in the receptor structure accuracy category. In a benchmark of 50 TMH protein homolog pairs of diverse topology (from 5 to 12 TMHs), size (from 183 to 420 residues) and sequence identity (from 15% to 70%), the method improves most starting templates, and achieves near-atomic accuracy prediction of membrane-embedded regions. Unlike starting templates, the models are of suitable quality for computer-based protein engineering: redesigned models and redesigned X-ray structures exhibit very similar native interactions. The method should prove useful for the atom-level modeling and design of a large fraction of structurally uncharacterized TMH proteins from a wide range of structural homologues.
2013
Sebastian Geibel, Erik Procko, Scott J Hultgren, David Baker, Gabriel Waksman
Structural and energetic basis of folded-protein transport by the FimD usher Journal Article
In: Nature, vol. 496, pp. 243-6, 2013, ISSN: 1476-4687.
@article{469,
title = {Structural and energetic basis of folded-protein transport by the FimD usher},
author = { Sebastian Geibel and Erik Procko and Scott J Hultgren and David Baker and Gabriel Waksman},
url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Geibel_nature12007_13S.pdf},
doi = {10.1038/nature12007},
issn = {1476-4687},
year = {2013},
date = {2013-04-01},
journal = {Nature},
volume = {496},
pages = {243-6},
abstract = {Type 1 pili, produced by uropathogenic Escherichia coli, are multisubunit fibres crucial in recognition of and adhesion to host tissues. During pilus biogenesis, subunits are recruited to an outer membrane assembly platform, the FimD usher, which catalyses their polymerization and mediates pilus secretion. The recent determination of the crystal structure of an initiation complex provided insight into the initiation step of pilus biogenesis resulting in pore activation, but very little is known about the elongation steps that follow. Here, to address this question, we determine the structure of an elongation complex in which the tip complex assembly composed of FimC, FimF, FimG and FimH passes through FimD. This structure demonstrates the conformational changes required to prevent backsliding of the nascent pilus through the FimD pore and also reveals unexpected properties of the usher pore. We show that the circular binding interface between the pore lumen and the folded substrate participates in transport by defining a low-energy pathway along which the nascent pilus polymer is guided during secretion.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Type 1 pili, produced by uropathogenic Escherichia coli, are multisubunit fibres crucial in recognition of and adhesion to host tissues. During pilus biogenesis, subunits are recruited to an outer membrane assembly platform, the FimD usher, which catalyses their polymerization and mediates pilus secretion. The recent determination of the crystal structure of an initiation complex provided insight into the initiation step of pilus biogenesis resulting in pore activation, but very little is known about the elongation steps that follow. Here, to address this question, we determine the structure of an elongation complex in which the tip complex assembly composed of FimC, FimF, FimG and FimH passes through FimD. This structure demonstrates the conformational changes required to prevent backsliding of the nascent pilus through the FimD pore and also reveals unexpected properties of the usher pore. We show that the circular binding interface between the pore lumen and the folded substrate participates in transport by defining a low-energy pathway along which the nascent pilus polymer is guided during secretion.
Julien R C Bergeron, Liam J Worrall, Nikolaos G Sgourakis, Frank DiMaio, Richard A Pfuetzner, Heather B Felise, Marija Vuckovic, Angel C Yu, Samuel I Miller, David Baker, Natalie C J Strynadka
A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly Journal Article
In: PLoS pathogens, vol. 9, pp. e1003307, 2013, ISSN: 1553-7374.
@article{468,
title = {A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly},
author = { Julien R C Bergeron and Liam J Worrall and Nikolaos G Sgourakis and Frank DiMaio and Richard A Pfuetzner and Heather B Felise and Marija Vuckovic and Angel C Yu and Samuel I Miller and David Baker and Natalie C J Strynadka},
url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Bergeron_ppat1003307_13T.pdf},
doi = {10.1371/journal.ppat.1003307},
issn = {1553-7374},
year = {2013},
date = {2013-04-01},
journal = {PLoS pathogens},
volume = {9},
pages = {e1003307},
abstract = {The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed of a "basal body", a lock-nut structure spanning both bacterial membranes, and a "needle" that protrudes away from the bacterial surface. A hollow channel spans throughout the apparatus, permitting the translocation of effector proteins from the bacterial cytosol to the host plasma membrane. The basal body is composed largely of three membrane-embedded proteins that form oligomerized concentric rings. Here, we report the crystal structures of three domains of the prototypical Salmonella SPI-1 basal body, and use a new approach incorporating symmetric flexible backbone docking and EM data to produce a model for their oligomeric assembly. The obtained models, validated by biochemical and in vivo assays, reveal the molecular details of the interactions driving basal body assembly, and notably demonstrate a conserved oligomerization mechanism.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed of a "basal body", a lock-nut structure spanning both bacterial membranes, and a "needle" that protrudes away from the bacterial surface. A hollow channel spans throughout the apparatus, permitting the translocation of effector proteins from the bacterial cytosol to the host plasma membrane. The basal body is composed largely of three membrane-embedded proteins that form oligomerized concentric rings. Here, we report the crystal structures of three domains of the prototypical Salmonella SPI-1 basal body, and use a new approach incorporating symmetric flexible backbone docking and EM data to produce a model for their oligomeric assembly. The obtained models, validated by biochemical and in vivo assays, reveal the molecular details of the interactions driving basal body assembly, and notably demonstrate a conserved oligomerization mechanism.
Jean-Philippe Demers, Nikolaos G Sgourakis, Rashmi Gupta, Antoine Loquet, Karin Giller, Dietmar Riedel, Britta Laube, Michael Kolbe, David Baker, Stefan Becker, Adam Lange
The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles Journal Article
In: PLoS pathogens, vol. 9, pp. e1003245, 2013, ISSN: 1553-7374.
@article{471,
title = {The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles},
author = { Jean-Philippe Demers and Nikolaos G Sgourakis and Rashmi Gupta and Antoine Loquet and Karin Giller and Dietmar Riedel and Britta Laube and Michael Kolbe and David Baker and Stefan Becker and Adam Lange},
url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Demers_PLosPathogen_13P.pdf},
doi = {10.1371/journal.ppat.1003245},
issn = {1553-7374},
year = {2013},
date = {2013-03-01},
journal = {PLoS pathogens},
volume = {9},
pages = {e1003245},
abstract = {The Type Three Secretion System (T3SS), or injectisome, is a macromolecular infection machinery present in many pathogenic Gram-negative bacteria. It consists of a basal body, anchored in both bacterial membranes, and a hollow needle through which effector proteins are delivered into the target host cell. Two different architectures of the T3SS needle have been previously proposed. First, an atomic model of the Salmonella typhimurium needle was generated from solid-state NMR data. The needle subunit protein, PrgI, comprises a rigid-extended N-terminal segment and a helix-loop-helix motif with the N-terminus located on the outside face of the needle. Second, a model of the Shigella flexneri needle was generated from a high-resolution 7.7-r A cryo-electron microscopy density map. The subunit protein, MxiH, contains an N-terminal α-helix, a loop, another α-helix, a 14-residue-long β-hairpin (Q51-Q64) and a C-terminal α-helix, with the N-terminus facing inward to the lumen of the needle. In the current study, we carried out solid-state NMR measurements of wild-type Shigella flexneri needles polymerized in vitro and identified the following secondary structure elements for MxiH: a rigid-extended N-terminal segment (S2-T11), an α-helix (L12-A38), a loop (E39-P44) and a C-terminal α-helix (Q45-R83). Using immunogold labeling in vitro and in vivo on functional needles, we located the N-terminus of MxiH subunits on the exterior of the assembly, consistent with evolutionary sequence conservation patterns and mutagenesis data. We generated a homology model of Shigella flexneri needles compatible with both experimental data: the MxiH solid-state NMR chemical shifts and the state-of-the-art cryoEM density map. These results corroborate the solid-state NMR structure previously solved for Salmonella typhimurium PrgI needles and establish that Shigella flexneri and Salmonella typhimurium subunit proteins adopt a conserved structure and orientation in their assembled state. Our study reveals a common structural architecture of T3SS needles, essential to understand T3SS-mediated infection and develop treatments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The Type Three Secretion System (T3SS), or injectisome, is a macromolecular infection machinery present in many pathogenic Gram-negative bacteria. It consists of a basal body, anchored in both bacterial membranes, and a hollow needle through which effector proteins are delivered into the target host cell. Two different architectures of the T3SS needle have been previously proposed. First, an atomic model of the Salmonella typhimurium needle was generated from solid-state NMR data. The needle subunit protein, PrgI, comprises a rigid-extended N-terminal segment and a helix-loop-helix motif with the N-terminus located on the outside face of the needle. Second, a model of the Shigella flexneri needle was generated from a high-resolution 7.7-r A cryo-electron microscopy density map. The subunit protein, MxiH, contains an N-terminal α-helix, a loop, another α-helix, a 14-residue-long β-hairpin (Q51-Q64) and a C-terminal α-helix, with the N-terminus facing inward to the lumen of the needle. In the current study, we carried out solid-state NMR measurements of wild-type Shigella flexneri needles polymerized in vitro and identified the following secondary structure elements for MxiH: a rigid-extended N-terminal segment (S2-T11), an α-helix (L12-A38), a loop (E39-P44) and a C-terminal α-helix (Q45-R83). Using immunogold labeling in vitro and in vivo on functional needles, we located the N-terminus of MxiH subunits on the exterior of the assembly, consistent with evolutionary sequence conservation patterns and mutagenesis data. We generated a homology model of Shigella flexneri needles compatible with both experimental data: the MxiH solid-state NMR chemical shifts and the state-of-the-art cryoEM density map. These results corroborate the solid-state NMR structure previously solved for Salmonella typhimurium PrgI needles and establish that Shigella flexneri and Salmonella typhimurium subunit proteins adopt a conserved structure and orientation in their assembled state. Our study reveals a common structural architecture of T3SS needles, essential to understand T3SS-mediated infection and develop treatments.
2012
Vladimir Yarov-Yarovoy, Paul G DeCaen, Ruth E Westenbroek, Chien-Yuan Pan, Todd Scheuer, David Baker, William A Catterall
Structural basis for gating charge movement in the voltage sensor of a sodium channel Journal Article
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 109, pp. E93-102, 2012, ISSN: 1091-6490.
@article{433,
title = {Structural basis for gating charge movement in the voltage sensor of a sodium channel},
author = { Vladimir Yarov-Yarovoy and Paul G DeCaen and Ruth E Westenbroek and Chien-Yuan Pan and Todd Scheuer and David Baker and William A Catterall},
url = {https://www.bakerlab.org/wp-content/uploads/2018/06/1.full_.pdf
http://www.pnas.org/content/109/2/E93/1},
doi = {10.1073/pnas.1118434109},
issn = {1091-6490},
year = {2012},
date = {2012-01-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {109},
pages = {E93-102},
abstract = {Voltage-dependent gating of ion channels is essential for electrical signaling in excitable cells, but the structural basis for voltage sensor function is unknown. We constructed high-resolution structural models of resting, intermediate, and activated states of the voltage-sensing domain of the bacterial sodium channel NaChBac using the Rosetta modeling method, crystal structures of related channels, and experimental data showing state-dependent interactions between the gating charge-carrying arginines in the S4 segment and negatively charged residues in neighboring transmembrane segments. The resulting structural models illustrate a network of ionic and hydrogen-bonding interactions that are made sequentially by the gating charges as they move out under the influence of the electric field. The S4 segment slides 6-8 r A outward through a narrow groove formed by the S1, S2, and S3 segments, rotates ~30textdegree, and tilts sideways at a pivot point formed by a highly conserved hydrophobic region near the middle of the voltage sensor. The S4 segment has a 3(10)-helical conformation in the narrow inner gating pore, which allows linear movement of the gating charges across the inner one-half of the membrane. Conformational changes of the intracellular one-half of S4 during activation are rigidly coupled to lateral movement of the S4-S5 linker, which could induce movement of the S5 and S6 segments and open the intracellular gate of the pore. We confirmed the validity of these structural models by comparing with a high-resolution structure of a NaChBac homolog and showing predicted molecular interactions of hydrophobic residues in the S4 segment in disulfide-locking studies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Voltage-dependent gating of ion channels is essential for electrical signaling in excitable cells, but the structural basis for voltage sensor function is unknown. We constructed high-resolution structural models of resting, intermediate, and activated states of the voltage-sensing domain of the bacterial sodium channel NaChBac using the Rosetta modeling method, crystal structures of related channels, and experimental data showing state-dependent interactions between the gating charge-carrying arginines in the S4 segment and negatively charged residues in neighboring transmembrane segments. The resulting structural models illustrate a network of ionic and hydrogen-bonding interactions that are made sequentially by the gating charges as they move out under the influence of the electric field. The S4 segment slides 6-8 r A outward through a narrow groove formed by the S1, S2, and S3 segments, rotates ~30textdegree, and tilts sideways at a pivot point formed by a highly conserved hydrophobic region near the middle of the voltage sensor. The S4 segment has a 3(10)-helical conformation in the narrow inner gating pore, which allows linear movement of the gating charges across the inner one-half of the membrane. Conformational changes of the intracellular one-half of S4 during activation are rigidly coupled to lateral movement of the S4-S5 linker, which could induce movement of the S5 and S6 segments and open the intracellular gate of the pore. We confirmed the validity of these structural models by comparing with a high-resolution structure of a NaChBac homolog and showing predicted molecular interactions of hydrophobic residues in the S4 segment in disulfide-locking studies.
2011
Piyali Saha, Bipasha Barua, Sanchari Bhattacharyya, M M Balamurali, William R Schief, David Baker, Raghavan Varadarajan
Design and characterization of stabilized derivatives of human CD4D12 and CD4D1 Journal Article
In: Biochemistry, vol. 50, pp. 7891-900, 2011, ISSN: 1520-4995.
@article{594,
title = {Design and characterization of stabilized derivatives of human CD4D12 and CD4D1},
author = { Piyali Saha and Bipasha Barua and Sanchari Bhattacharyya and M M Balamurali and William R Schief and David Baker and Raghavan Varadarajan},
url = {https://www.bakerlab.org/wp-content/uploads/2018/06/bi200870r.pdf
https://pubs.acs.org/doi/abs/10.1021/bi200870r},
doi = {10.1021/bi200870r},
issn = {1520-4995},
year = {2011},
date = {2011-09-01},
journal = {Biochemistry},
volume = {50},
pages = {7891-900},
abstract = {CD4 is present on the surface of T-lymphocytes and is the primary cellular receptor for HIV-1. CD4 consists of a cytoplasmic tail, one transmembrane region, and four extracellular domains, D1-D4. A construct consisting of the first two domains of CD4 (CD4D12) is folded and binds gp120 with similar affinity as soluble 4-domain CD4 (sCD4). However, the first domain alone (CD4D1) was previously shown to be largely unfolded and had 3-fold weaker affinity for gp120 when compared to sCD4 [Sharma, D.; et al. (2005) Biochemistry 44, 16192-16202]. We now report the design and characterization of three single-site mutants of CD4D12 (G6A, L51I, and V86L) and one multisite mutant of CD4D1 (G6A/L51I/L5K/F98T). G6A, L51I, and V86L are cavity-filling mutations while L5K and F98T are surface mutations which were introduced to minimize the aggregation of CD4D1 upon removal of the second domain. Two mutations, G6A and V86L in CD4D12 increased the stability and yield of the protein relative to the wild-type protein. The mutant CD4D1 (CD4D1a) with the 4 mutations was folded and more stable compared to the original CD4D1, but both bound gp120 with comparable affinity. In in vitro neutralization assays, both CD4D1a and G6A-CD4D12 were able to neutralize diverse HIV-1 viruses with similar IC(50)s as 4-domain CD4. These stabilized derivatives of human CD4 can be useful starting points for the design of other more complex viral entry inhibitors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
CD4 is present on the surface of T-lymphocytes and is the primary cellular receptor for HIV-1. CD4 consists of a cytoplasmic tail, one transmembrane region, and four extracellular domains, D1-D4. A construct consisting of the first two domains of CD4 (CD4D12) is folded and binds gp120 with similar affinity as soluble 4-domain CD4 (sCD4). However, the first domain alone (CD4D1) was previously shown to be largely unfolded and had 3-fold weaker affinity for gp120 when compared to sCD4 [Sharma, D.; et al. (2005) Biochemistry 44, 16192-16202]. We now report the design and characterization of three single-site mutants of CD4D12 (G6A, L51I, and V86L) and one multisite mutant of CD4D1 (G6A/L51I/L5K/F98T). G6A, L51I, and V86L are cavity-filling mutations while L5K and F98T are surface mutations which were introduced to minimize the aggregation of CD4D1 upon removal of the second domain. Two mutations, G6A and V86L in CD4D12 increased the stability and yield of the protein relative to the wild-type protein. The mutant CD4D1 (CD4D1a) with the 4 mutations was folded and more stable compared to the original CD4D1, but both bound gp120 with comparable affinity. In in vitro neutralization assays, both CD4D1a and G6A-CD4D12 were able to neutralize diverse HIV-1 viruses with similar IC(50)s as 4-domain CD4. These stabilized derivatives of human CD4 can be useful starting points for the design of other more complex viral entry inhibitors.
2010
Sarah Sanowar, Pragya Singh, Richard A Pfuetzner, Ingemar Andr’e, Hongjin Zheng, Thomas Spreter, Natalie C J Strynadka, Tamir Gonen, David Baker, David R Goodlett, Samuel I Miller
Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System Journal Article
In: mBio, vol. 1, 2010, ISSN: 2150-7511.
@article{261,
title = {Interactions of the Transmembrane Polymeric Rings of the Salmonella enterica Serovar Typhimurium Type III Secretion System},
author = { Sarah Sanowar and Pragya Singh and Richard A Pfuetzner and Ingemar Andr'e and Hongjin Zheng and Thomas Spreter and Natalie C J Strynadka and Tamir Gonen and David Baker and David R Goodlett and Samuel I Miller},
issn = {2150-7511},
year = {2010},
date = {2010-00-01},
journal = {mBio},
volume = {1},
abstract = {The type III secretion system (T3SS) is an interspecies protein transport machine that plays a major role in interactions of Gram-negative bacteria with animals and plants by delivering bacterial effector proteins into host cells. T3SSs span both membranes of Gram-negative bacteria by forming a structure of connected oligomeric rings termed the needle complex (NC). Here, the localization of subunits in the Salmonella enterica serovar Typhimurium T3SS NC were probed via mass spectrometry-assisted identification of chemical cross-links in intact NC preparations. Cross-links between amino acids near the amino terminus of the outer membrane ring component InvG and the carboxyl terminus of the inner membrane ring component PrgH and between the two inner membrane components PrgH and PrgK allowed for spatial localization of the three ring components within the electron density map structures of NCs. Mutational and biochemical analysis demonstrated that the amino terminus of InvG and the carboxyl terminus of PrgH play a critical role in the assembly and function of the T3SS apparatus. Analysis of an InvG mutant indicates that the structure of the InvG oligomer can affect the switching of the T3SS substrate to translocon and effector components. This study provides insights into how structural organization of needle complex base components promotes T3SS assembly and function.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The type III secretion system (T3SS) is an interspecies protein transport machine that plays a major role in interactions of Gram-negative bacteria with animals and plants by delivering bacterial effector proteins into host cells. T3SSs span both membranes of Gram-negative bacteria by forming a structure of connected oligomeric rings termed the needle complex (NC). Here, the localization of subunits in the Salmonella enterica serovar Typhimurium T3SS NC were probed via mass spectrometry-assisted identification of chemical cross-links in intact NC preparations. Cross-links between amino acids near the amino terminus of the outer membrane ring component InvG and the carboxyl terminus of the inner membrane ring component PrgH and between the two inner membrane components PrgH and PrgK allowed for spatial localization of the three ring components within the electron density map structures of NCs. Mutational and biochemical analysis demonstrated that the amino terminus of InvG and the carboxyl terminus of PrgH play a critical role in the assembly and function of the T3SS apparatus. Analysis of an InvG mutant indicates that the structure of the InvG oligomer can affect the switching of the T3SS substrate to translocon and effector components. This study provides insights into how structural organization of needle complex base components promotes T3SS assembly and function.
2009
Thomas Spreter, Calvin K Yip, Sarah Sanowar, Ingemar Andr’e, Tyler G Kimbrough, Marija Vuckovic, Richard A Pfuetzner, Wanyin Deng, Angel C Yu, B Brett Finlay, David Baker, Samuel I Miller, Natalie C J Strynadka
A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system Journal Article
In: Nature structural & molecular biology, vol. 16, pp. 468-76, 2009, ISSN: 1545-9985.
@article{274,
title = {A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system},
author = { Thomas Spreter and Calvin K Yip and Sarah Sanowar and Ingemar Andr'e and Tyler G Kimbrough and Marija Vuckovic and Richard A Pfuetzner and Wanyin Deng and Angel C Yu and B Brett Finlay and David Baker and Samuel I Miller and Natalie C J Strynadka},
issn = {1545-9985},
year = {2009},
date = {2009-05-01},
journal = {Nature structural & molecular biology},
volume = {16},
pages = {468-76},
abstract = {The type III secretion system (T3SS) is a macromolecular textquoterightinjectisometextquoteright that allows bacterial pathogens to transport virulence proteins into the eukaryotic host cell. This macromolecular complex is composed of connected ring-like structures that span both bacterial membranes. The crystal structures of the periplasmic domain of the outer membrane secretin EscC and the inner membrane protein PrgH reveal the conservation of a modular fold among the three proteins that form the outer membrane and inner membrane rings of the T3SS. This leads to the hypothesis that this conserved fold provides a common ring-building motif that allows for the assembly of the variably sized outer membrane and inner membrane rings characteristic of the T3SS. Using an integrated structural and experimental approach, we generated ring models for the periplasmic domain of EscC and placed them in the context of the assembled T3SS, providing evidence for direct interaction between the outer membrane and inner membrane ring components and an unprecedented span of the outer membrane secretin.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The type III secretion system (T3SS) is a macromolecular textquoterightinjectisometextquoteright that allows bacterial pathogens to transport virulence proteins into the eukaryotic host cell. This macromolecular complex is composed of connected ring-like structures that span both bacterial membranes. The crystal structures of the periplasmic domain of the outer membrane secretin EscC and the inner membrane protein PrgH reveal the conservation of a modular fold among the three proteins that form the outer membrane and inner membrane rings of the T3SS. This leads to the hypothesis that this conserved fold provides a common ring-building motif that allows for the assembly of the variably sized outer membrane and inner membrane rings characteristic of the T3SS. Using an integrated structural and experimental approach, we generated ring models for the periplasmic domain of EscC and placed them in the context of the assembled T3SS, providing evidence for direct interaction between the outer membrane and inner membrane ring components and an unprecedented span of the outer membrane secretin.
Jieqing Zhu, Bing-Hao Luo, Patrick Barth, Jack Schonbrun, David Baker, Timothy A Springer
The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3 Journal Article
In: Molecular cell, vol. 34, pp. 234-49, 2009, ISSN: 1097-4164.
@article{139,
title = {The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3},
author = { Jieqing Zhu and Bing-Hao Luo and Patrick Barth and Jack Schonbrun and David Baker and Timothy A Springer},
issn = {1097-4164},
year = {2009},
date = {2009-04-01},
journal = {Molecular cell},
volume = {34},
pages = {234-49},
abstract = {Structures of intact receptors with single-pass transmembrane domains are essential to understand how extracellular and cytoplasmic domains regulate association and signaling through transmembrane domains. A chemical and computational method to determine structures of the membrane regions of such receptors on the cell surface is developed here and validated with glycophorin A. An integrin heterodimer structure reveals association over most of the lengths of the alpha and beta transmembrane domains and shows that the principles governing association of hetero and homo transmembrane dimers differ. A turn at the Gly of the juxtamembrane GFFKR motif caps the alpha TM helix and brings the two Phe of GFFKR into the alpha/beta interface. A juxtamembrane Lys residue in beta also has an important role in the interface. The structure shows how transmembrane association/dissociation regulates integrin signaling. A joint ectodomain and membrane structure shows that substantial flexibility between the extracellular and TM domains is compatible with TM signaling.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Structures of intact receptors with single-pass transmembrane domains are essential to understand how extracellular and cytoplasmic domains regulate association and signaling through transmembrane domains. A chemical and computational method to determine structures of the membrane regions of such receptors on the cell surface is developed here and validated with glycophorin A. An integrin heterodimer structure reveals association over most of the lengths of the alpha and beta transmembrane domains and shows that the principles governing association of hetero and homo transmembrane dimers differ. A turn at the Gly of the juxtamembrane GFFKR motif caps the alpha TM helix and brings the two Phe of GFFKR into the alpha/beta interface. A juxtamembrane Lys residue in beta also has an important role in the interface. The structure shows how transmembrane association/dissociation regulates integrin signaling. A joint ectodomain and membrane structure shows that substantial flexibility between the extracellular and TM domains is compatible with TM signaling.
Bing-Hao Luo, John Karanicolas, Laura D Harmacek, David Baker, Timothy A Springer
Rationally designed integrin beta3 mutants stabilized in the high affinity conformation Journal Article
In: The Journal of biological chemistry, vol. 284, pp. 3917-24, 2009, ISSN: 0021-9258.
@article{132,
title = {Rationally designed integrin beta3 mutants stabilized in the high affinity conformation},
author = { Bing-Hao Luo and John Karanicolas and Laura D Harmacek and David Baker and Timothy A Springer},
issn = {0021-9258},
year = {2009},
date = {2009-02-01},
journal = {The Journal of biological chemistry},
volume = {284},
pages = {3917-24},
abstract = {Integrins are important cell surface receptors that transmit bidirectional signals across the membrane. It has been shown that a conformational change of the integrin beta-subunit headpiece (i.e. the beta I domain and the hybrid domain) plays a critical role in regulating integrin ligand binding affinity and function. Previous studies have used coarse methods (a glycan wedge, mutations in transmembrane contacts) to force the beta-subunit into either the open or closed conformation. Here, we demonstrate a detailed understanding of this conformational change by applying computational design techniques to select five amino acid side chains that play an important role in the energetic balance between the open and closed conformations of alphaIIbbeta3. Eight single-point mutants were designed at these sites, of which five bound ligands much better than wild type. Further, these mutants were found to be in a more extended conformation than wild type, suggesting that the conformational change at the ligand binding headpiece was propagated to the legs of the integrin. This detailed understanding of the conformational change will assist in the development of allosteric drugs that either stabilize or destabilize specific integrin conformations without occluding the ligand-binding site.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Integrins are important cell surface receptors that transmit bidirectional signals across the membrane. It has been shown that a conformational change of the integrin beta-subunit headpiece (i.e. the beta I domain and the hybrid domain) plays a critical role in regulating integrin ligand binding affinity and function. Previous studies have used coarse methods (a glycan wedge, mutations in transmembrane contacts) to force the beta-subunit into either the open or closed conformation. Here, we demonstrate a detailed understanding of this conformational change by applying computational design techniques to select five amino acid side chains that play an important role in the energetic balance between the open and closed conformations of alphaIIbbeta3. Eight single-point mutants were designed at these sites, of which five bound ligands much better than wild type. Further, these mutants were found to be in a more extended conformation than wild type, suggesting that the conformational change at the ligand binding headpiece was propagated to the legs of the integrin. This detailed understanding of the conformational change will assist in the development of allosteric drugs that either stabilize or destabilize specific integrin conformations without occluding the ligand-binding site.
P Barth, B Wallner, David Baker
Prediction of membrane protein structures with complex topologies using limited constraints Journal Article
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 106, pp. 1409-14, 2009, ISSN: 1091-6490.
@article{123,
title = {Prediction of membrane protein structures with complex topologies using limited constraints},
author = { P Barth and B Wallner and David Baker},
issn = {1091-6490},
year = {2009},
date = {2009-02-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
pages = {1409-14},
abstract = {Reliable structure-prediction methods for membrane proteins are important because the experimental determination of high-resolution membrane protein structures remains very difficult, especially for eukaryotic proteins. However, membrane proteins are typically longer than 200 aa and represent a formidable challenge for structure prediction. We have developed a method for predicting the structures of large membrane proteins by constraining helix-helix packing arrangements at particular positions predicted from sequence or identified by experiments. We tested the method on 12 membrane proteins of diverse topologies and functions with lengths ranging between 190 and 300 residues. Enforcing a single constraint during the folding simulations enriched the population of near-native models for 9 proteins. In 4 of the cases in which the constraint was predicted from the sequence, 1 of the 5 lowest energy models was superimposable within 4 A on the native structure. Near-native structures could also be selected for heme-binding and pore-forming domains from simulations in which pairs of conserved histidine-chelating hemes and one experimentally determined salt bridge were constrained, respectively. These results suggest that models within 4 A of the native structure can be achieved for complex membrane proteins if even limited information on residue-residue interactions can be obtained from protein structure databases or experiments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Reliable structure-prediction methods for membrane proteins are important because the experimental determination of high-resolution membrane protein structures remains very difficult, especially for eukaryotic proteins. However, membrane proteins are typically longer than 200 aa and represent a formidable challenge for structure prediction. We have developed a method for predicting the structures of large membrane proteins by constraining helix-helix packing arrangements at particular positions predicted from sequence or identified by experiments. We tested the method on 12 membrane proteins of diverse topologies and functions with lengths ranging between 190 and 300 residues. Enforcing a single constraint during the folding simulations enriched the population of near-native models for 9 proteins. In 4 of the cases in which the constraint was predicted from the sequence, 1 of the 5 lowest energy models was superimposable within 4 A on the native structure. Near-native structures could also be selected for heme-binding and pore-forming domains from simulations in which pairs of conserved histidine-chelating hemes and one experimentally determined salt bridge were constrained, respectively. These results suggest that models within 4 A of the native structure can be achieved for complex membrane proteins if even limited information on residue-residue interactions can be obtained from protein structure databases or experiments.
2007
P Barth, J Schonbrun, David Baker
Toward high-resolution prediction and design of transmembrane helical protein structures Journal Article
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 104, pp. 15682-7, 2007, ISSN: 0027-8424.
@article{120,
title = {Toward high-resolution prediction and design of transmembrane helical protein structures},
author = { P Barth and J Schonbrun and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/08/barth07A.pdf},
issn = {0027-8424},
year = {2007},
date = {2007-10-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {104},
pages = {15682-7},
abstract = {The prediction and design at the atomic level of membrane protein structures and interactions is a critical but unsolved challenge. To address this problem, we have developed an all-atom physical model that describes intraprotein and protein-solvent interactions in the membrane environment. We evaluated the ability of the model to recapitulate the energetics and structural specificities of polytopic membrane proteins by using a battery of in silico prediction and design tests. First, in side-chain packing and design tests, the model successfully predicts the side-chain conformations at 73% of nonexposed positions and the native amino acid identities at 34% of positions in naturally occurring membrane proteins. Second, the model predicts significant energy gaps between native and nonnative structures of transmembrane helical interfaces and polytopic membrane proteins. Third, distortions in transmembrane helices are successfully recapitulated in docking experiments by using fragments of ideal helices judiciously defined around helical kinks. Finally, de novo structure prediction reaches near-atomic accuracy (<2.5 A) for several small membrane protein domains (<150 residues). The success of the model highlights the critical role of van der Waals and hydrogen-bonding interactions in the stability and structural specificity of membrane protein structures and sets the stage for the high-resolution prediction and design of complex membrane protein architectures.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The prediction and design at the atomic level of membrane protein structures and interactions is a critical but unsolved challenge. To address this problem, we have developed an all-atom physical model that describes intraprotein and protein-solvent interactions in the membrane environment. We evaluated the ability of the model to recapitulate the energetics and structural specificities of polytopic membrane proteins by using a battery of in silico prediction and design tests. First, in side-chain packing and design tests, the model successfully predicts the side-chain conformations at 73% of nonexposed positions and the native amino acid identities at 34% of positions in naturally occurring membrane proteins. Second, the model predicts significant energy gaps between native and nonnative structures of transmembrane helical interfaces and polytopic membrane proteins. Third, distortions in transmembrane helices are successfully recapitulated in docking experiments by using fragments of ideal helices judiciously defined around helical kinks. Finally, de novo structure prediction reaches near-atomic accuracy (<2.5 A) for several small membrane protein domains (<150 residues). The success of the model highlights the critical role of van der Waals and hydrogen-bonding interactions in the stability and structural specificity of membrane protein structures and sets the stage for the high-resolution prediction and design of complex membrane protein architectures.
2006
Vladimir Yarov-Yarovoy, David Baker, William A Catterall
Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels Journal Article
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 103, pp. 7292-7, 2006, ISSN: 0027-8424.
@article{164,
title = {Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels},
author = { Vladimir Yarov-Yarovoy and David Baker and William A Catterall},
url = {https://www.bakerlab.org/wp-content/uploads/2016/08/yarov-yarovoy06A.pdf},
issn = {0027-8424},
year = {2006},
date = {2006-05-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
pages = {7292-7},
abstract = {Voltage-gated ion channels control generation and propagation of action potentials in excitable cells. Significant progress has been made in understanding structure and function of the voltage-gated ion channels, highlighted by the high-resolution open-state structure of the voltage-gated potassium channel, K(v)1.2. However, because the structure of the closed state is unknown, the gating mechanism remains controversial. We adapted the rosetta membrane method to model the structures of the K(v)1.2 and KvAP channels using homology, de novo, and domain assembly methods and selected the most plausible models using a limited number of experimental constraints. Our model of K(v)1.2 in the open state is very similar in overall topology to the x-ray structure of this channel. Modeling of KvAP in the open state suggests that orientation of the voltage-sensing domain relative to the pore-forming domain is considerably different from the orientation in the K(v)1.2 open state and that the magnitude of the vertical movement of S4 is significantly greater. Structural modeling of closed state of K(v)1.2 suggests gating movement that can be viewed as a sum of two previously suggested mechanisms: translation (2-4 A) plus rotation ( approximately 180 degrees ) of the S4 segment as proposed in the original "sliding helix" or "helical screw" models coupled with a rolling motion of the S1-S3 segments around S4, similar to recent "transporter" models of gating. We propose a unified mechanism of voltage-dependent gating for K(v)1.2 and KvAP in which this major conformational change moves the gating charge across the electric field in an analogous way for both channels.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Voltage-gated ion channels control generation and propagation of action potentials in excitable cells. Significant progress has been made in understanding structure and function of the voltage-gated ion channels, highlighted by the high-resolution open-state structure of the voltage-gated potassium channel, K(v)1.2. However, because the structure of the closed state is unknown, the gating mechanism remains controversial. We adapted the rosetta membrane method to model the structures of the K(v)1.2 and KvAP channels using homology, de novo, and domain assembly methods and selected the most plausible models using a limited number of experimental constraints. Our model of K(v)1.2 in the open state is very similar in overall topology to the x-ray structure of this channel. Modeling of KvAP in the open state suggests that orientation of the voltage-sensing domain relative to the pore-forming domain is considerably different from the orientation in the K(v)1.2 open state and that the magnitude of the vertical movement of S4 is significantly greater. Structural modeling of closed state of K(v)1.2 suggests gating movement that can be viewed as a sum of two previously suggested mechanisms: translation (2-4 A) plus rotation ( approximately 180 degrees ) of the S4 segment as proposed in the original "sliding helix" or "helical screw" models coupled with a rolling motion of the S1-S3 segments around S4, similar to recent "transporter" models of gating. We propose a unified mechanism of voltage-dependent gating for K(v)1.2 and KvAP in which this major conformational change moves the gating charge across the electric field in an analogous way for both channels.
Amy E Palmer, Marta Giacomello, Tanja Kortemme, S Andrew Hires, Varda Lev-Ram, David Baker, Roger Y Tsien
Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs Journal Article
In: Chemistry & biology, vol. 13, pp. 521-30, 2006, ISSN: 1074-5521.
@article{293,
title = {Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs},
author = { Amy E Palmer and Marta Giacomello and Tanja Kortemme and S Andrew Hires and Varda Lev-Ram and David Baker and Roger Y Tsien},
url = {https://www.bakerlab.org/wp-content/uploads/2016/08/palmer06A.pdf},
issn = {1074-5521},
year = {2006},
date = {2006-05-01},
journal = {Chemistry & biology},
volume = {13},
pages = {521-30},
abstract = {The binding interface of calmodulin and a calmodulin binding peptide were reengineered by computationally designing complementary bumps and holes. This redesign led to the development of sensitive and specific pairs of mutant proteins used to sense Ca(2+) in a second generation of genetically encoded Ca(2+) indicators (cameleons). These cameleons are no longer perturbed by large excesses of native calmodulin, and they display Ca(2+) sensitivities tuned over a 100-fold range (0.6-160 microM). Incorporation of circularly permuted Venus in place of Citrine results in a 3- to 5-fold increase in the dynamic range. These redesigned cameleons show significant improvements over previous versions in the ability to monitor Ca(2+) in the cytoplasm as well as distinct subcellular localizations, such as the plasma membrane of neurons and the mitochondria.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The binding interface of calmodulin and a calmodulin binding peptide were reengineered by computationally designing complementary bumps and holes. This redesign led to the development of sensitive and specific pairs of mutant proteins used to sense Ca(2+) in a second generation of genetically encoded Ca(2+) indicators (cameleons). These cameleons are no longer perturbed by large excesses of native calmodulin, and they display Ca(2+) sensitivities tuned over a 100-fold range (0.6-160 microM). Incorporation of circularly permuted Venus in place of Citrine results in a 3- to 5-fold increase in the dynamic range. These redesigned cameleons show significant improvements over previous versions in the ability to monitor Ca(2+) in the cytoplasm as well as distinct subcellular localizations, such as the plasma membrane of neurons and the mitochondria.
Vladimir Yarov-Yarovoy, Jack Schonbrun, David Baker
Multipass membrane protein structure prediction using Rosetta Journal Article
In: Proteins, vol. 62, pp. 1010-25, 2006, ISSN: 1097-0134.
@article{165,
title = {Multipass membrane protein structure prediction using Rosetta},
author = { Vladimir Yarov-Yarovoy and Jack Schonbrun and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/08/yarov-yarovoy06B.pdf},
issn = {1097-0134},
year = {2006},
date = {2006-03-01},
journal = {Proteins},
volume = {62},
pages = {1010-25},
abstract = {We describe the adaptation of the Rosetta de novo structure prediction method for prediction of helical transmembrane protein structures. The membrane environment is modeled by embedding the protein chain into a model membrane represented by parallel planes defining hydrophobic, interface, and polar membrane layers for each energy evaluation. The optimal embedding is determined by maximizing the exposure of surface hydrophobic residues within the membrane and minimizing hydrophobic exposure outside of the membrane. Protein conformations are built up using the Rosetta fragment assembly method and evaluated using a new membrane-specific version of the Rosetta low-resolution energy function in which residue-residue and residue-environment interactions are functions of the membrane layer in addition to amino acid identity, distance, and density. We find that lower energy and more native-like structures are achieved by sequential addition of helices to a growing chain, which may mimic some aspects of helical protein biogenesis after translocation, rather than folding the whole chain simultaneously as in the Rosetta soluble protein prediction method. In tests on 12 membrane proteins for which the structure is known, between 51 and 145 residues were predicted with root-mean-square deviation <4 A from the native structure.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We describe the adaptation of the Rosetta de novo structure prediction method for prediction of helical transmembrane protein structures. The membrane environment is modeled by embedding the protein chain into a model membrane represented by parallel planes defining hydrophobic, interface, and polar membrane layers for each energy evaluation. The optimal embedding is determined by maximizing the exposure of surface hydrophobic residues within the membrane and minimizing hydrophobic exposure outside of the membrane. Protein conformations are built up using the Rosetta fragment assembly method and evaluated using a new membrane-specific version of the Rosetta low-resolution energy function in which residue-residue and residue-environment interactions are functions of the membrane layer in addition to amino acid identity, distance, and density. We find that lower energy and more native-like structures are achieved by sequential addition of helices to a growing chain, which may mimic some aspects of helical protein biogenesis after translocation, rather than folding the whole chain simultaneously as in the Rosetta soluble protein prediction method. In tests on 12 membrane proteins for which the structure is known, between 51 and 145 residues were predicted with root-mean-square deviation <4 A from the native structure.
1991
H Ruohola, K A Bremer, D Baker, J R Swedlow, L Y Jan, Y N Jan
Role of neurogenic genes in establishment of follicle cell fate and oocyte polarity during oogenesis in Drosophila. Journal Article
In: Cell, vol. 66, pp. 433-49, 1991, ISSN: 0092-8674.
@article{330,
title = {Role of neurogenic genes in establishment of follicle cell fate and oocyte polarity during oogenesis in Drosophila.},
author = { H Ruohola and K A Bremer and D Baker and J R Swedlow and L Y Jan and Y N Jan},
issn = {0092-8674},
year = {1991},
date = {1991-08-01},
journal = {Cell},
volume = {66},
pages = {433-49},
abstract = {Oogenesis in Drosophila involves specification of both germ cells and the surrounding somatic follicle cells, as well as the determination of oocyte polarity. We found that two neurogenic genes, Notch and Delta, are required in oogenesis. These genes encode membrane proteins with epidermal growth factor repeats and are essential in the decision of an embryonic ectodermal cell to take on the fate of neuroblast or epidermoblast. In oogenesis, mutation in either gene leads to an excess of posterior follicle cells, a cell fate change reminiscent of the hyperplasia of neuroblasts seen in neurogenic mutant embryos. Furthermore, the Notch mutation in somatic cells causes mislocalization of bicoid in the oocyte. These results suggest that the neurogenic genes Notch and Delta are involved in both follicle cell development and the establishment of anterior-posterior polarity in the oocyte.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Oogenesis in Drosophila involves specification of both germ cells and the surrounding somatic follicle cells, as well as the determination of oocyte polarity. We found that two neurogenic genes, Notch and Delta, are required in oogenesis. These genes encode membrane proteins with epidermal growth factor repeats and are essential in the decision of an embryonic ectodermal cell to take on the fate of neuroblast or epidermoblast. In oogenesis, mutation in either gene leads to an excess of posterior follicle cells, a cell fate change reminiscent of the hyperplasia of neuroblasts seen in neurogenic mutant embryos. Furthermore, the Notch mutation in somatic cells causes mislocalization of bicoid in the oocyte. These results suggest that the neurogenic genes Notch and Delta are involved in both follicle cell development and the establishment of anterior-posterior polarity in the oocyte.
1988
D Baker, L Hicke, M Rexach, M Schleyer, R Schekman
Reconstitution of SEC gene product-dependent intercompartmental protein transport Journal Article
In: Cell, vol. 54, pp. 335-44, 1988, ISSN: 0092-8674.
@article{332,
title = {Reconstitution of SEC gene product-dependent intercompartmental protein transport},
author = { D Baker and L Hicke and M Rexach and M Schleyer and R Schekman},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/baker88.pdf},
issn = {0092-8674},
year = {1988},
date = {1988-07-01},
journal = {Cell},
volume = {54},
pages = {335-44},
abstract = {Transport of alpha-factor precursor from the endoplasmic reticulum to the Golgi apparatus has been reconstituted in gently lysed yeast spheroplasts. Transport is measured through the coupled addition of outer-chain carbohydrate to [35S]methionine-labeled alpha-factor precursor translocated into the endoplasmic reticulum of broken spheroplasts. The reaction is absolutely dependent on ATP, stimulated 6-fold by cytosol, and occurs between physically separable sealed compartments. Transport is inhibited by the guanine nucleotide analog GTP gamma S. sec23 mutant cells have a temperature-sensitive defect in endoplasmic reticulum-to-Golgi transport in vivo. This defect has been reproduced in vitro using sec23 membranes and cytosol. Transport at 30 degrees C with sec23 membranes requires addition of cytosol containing the SEC23 (wild-type) gene product. This demonstrates that an in vitro inter-organelle transport reaction depends on a factor required for transport in vivo. Complementation of sec mutations in vitro provides a functional assay for the purification of individual intercompartmental transport factors.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Transport of alpha-factor precursor from the endoplasmic reticulum to the Golgi apparatus has been reconstituted in gently lysed yeast spheroplasts. Transport is measured through the coupled addition of outer-chain carbohydrate to [35S]methionine-labeled alpha-factor precursor translocated into the endoplasmic reticulum of broken spheroplasts. The reaction is absolutely dependent on ATP, stimulated 6-fold by cytosol, and occurs between physically separable sealed compartments. Transport is inhibited by the guanine nucleotide analog GTP gamma S. sec23 mutant cells have a temperature-sensitive defect in endoplasmic reticulum-to-Golgi transport in vivo. This defect has been reproduced in vitro using sec23 membranes and cytosol. Transport at 30 degrees C with sec23 membranes requires addition of cytosol containing the SEC23 (wild-type) gene product. This demonstrates that an in vitro inter-organelle transport reaction depends on a factor required for transport in vivo. Complementation of sec mutations in vitro provides a functional assay for the purification of individual intercompartmental transport factors.