@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}

}

@article{Watson2023,

title = {De novo design of protein structure and function with RFdiffusion},

author = {Watson, Joseph L.

and Juergens, David

and Bennett, Nathaniel R.

and Trippe, Brian L.

and Yim, Jason

and Eisenach, Helen E.

and Ahern, Woody

and Borst, Andrew J.

and Ragotte, Robert J.

and Milles, Lukas F.

and Wicky, Basile I. M.

and Hanikel, Nikita

and Pellock, Samuel J.

and Courbet, Alexis

and Sheffler, William

and Wang, Jue

and Venkatesh, Preetham

and Sappington, Isaac

and Torres, Susana Vázquez

and Lauko, Anna

and De Bortoli, Valentin

and Mathieu, Emile

and Ovchinnikov, Sergey

and Barzilay, Regina

and Jaakkola, Tommi S.

and DiMaio, Frank

and Baek, Minkyung

and Baker, David},

url = {https://www.nature.com/articles/s41586-023-06415-8, Nature

https://www.bakerlab.org/wp-content/uploads/2023/07/s41586-023-06415-8_reference.pdf, PDF (29MB)},

doi = {10.1038/s41586-023-06415-8},

year  = {2023},

date = {2023-07-11},

journal = {Nature},

abstract = {There has been considerable recent progress in designing new proteins using deep learning methods1–9. Despite this progress, a general deep learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher order symmetric architectures, has yet to be described. Diffusion models10,11 have had considerable success in image and language generative modeling but limited success when applied to protein modeling, likely due to the complexity of protein backbone geometry and sequence-structure relationships. Here we show that by fine tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding, and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold Diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryo-EM structure of a designed binder in complex with Influenza hemagglutinin which is nearly identical to the design model. In a manner analogous to networks which produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Design of Heme Enzymes with a Tunable Substrate Binding Pocket Adjacent to an Open Metal Coordination Site},

author = {Kalvet, Indrek

and Ortmayer, Mary

and Zhao, Jingming

and Crawshaw, Rebecca

and Ennist, Nathan M.

and Levy, Colin

and Roy, Anindya

and Green, Anthony P.

and Baker, David},

url = {https://pubs.acs.org/doi/full/10.1021/jacs.3c02742, ACS (Open Access)},

doi = {10.1021/jacs.3c02742},

year  = {2023},

date = {2023-07-05},

urldate = {2023-07-05},

journal = {J. Am. Chem. Soc.},

abstract = {The catalytic versatility of pentacoordinated iron is highlighted by the broad range of natural and engineered activities of heme enzymes such as cytochrome P450s, which position a porphyrin cofactor coordinating a central iron atom below an open substrate binding pocket. This catalytic prowess has inspired efforts to design de novo helical bundle scaffolds that bind porphyrin cofactors. However, such designs lack the large open substrate binding pocket of P450s, and hence, the range of chemical transformations accessible is limited. Here, with the goal of combining the advantages of the P450 catalytic site geometry with the almost unlimited customizability of de novo protein design, we design a high-affinity heme-binding protein, dnHEM1, with an axial histidine ligand, a vacant coordination site for generating reactive intermediates, and a tunable distal pocket for substrate binding. A 1.6 Å X-ray crystal structure of dnHEM1 reveals excellent agreement to the design model with key features programmed as intended. The incorporation of distal pocket substitutions converted dnHEM1 into a proficient peroxidase with a stable neutral ferryl intermediate. In parallel, dnHEM1 was redesigned to generate enantiocomplementary carbene transferases for styrene cyclopropanation (up to 93% isolated yield, 5000 turnovers, 97:3 e.r.) by reconfiguring the distal pocket to accommodate calculated transition state models. Our approach now enables the custom design of enzymes containing cofactors adjacent to binding pockets with an almost unlimited variety of shapes and functionalities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Yeh2023,

title = {De novo design of luciferases using deep learning},

author = {Yeh, Andy Hsien-Wei

 Norn, Christoffer

 Kipnis, Yakov

 Tischer, Doug

 Pellock, Samuel J.

 Evans, Declan

 Ma, Pengchen

 Lee, Gyu Rie

 Zhang, Jason Z.

 Anishchenko, Ivan

 Coventry, Brian

 Cao, Longxing

 Dauparas, Justas

 Halabiya, Samer

 DeWitt, Michelle

 Carter, Lauren

 Houk, K. N.

 Baker, David},

url = {https://www.nature.com/articles/s41586-023-05696-3, Nature (Open Access)},

doi = {10.1038/s41586-023-05696-3},

year  = {2023},

date = {2023-02-22},

journal = {Nature},

abstract = {De novo enzyme design has sought to introduce active sites and substrate-binding pockets that are predicted to catalyse a reaction of interest into geometrically compatible native scaffolds1,2, but has been limited by a lack of suitable protein structures and the complexity of native protein sequence–structure relationships. Here we describe a deep-learning-based ‘family-wide hallucination’ approach that generates large numbers of idealized protein structures containing diverse pocket shapes and designed sequences that encode them. We use these scaffolds to design artificial luciferases that selectively catalyse the oxidative chemiluminescence of the synthetic luciferin substrates diphenylterazine3 and 2-deoxycoelenterazine. The designed active sites position an arginine guanidinium group adjacent to an anion that develops during the reaction in a binding pocket with high shape complementarity. For both luciferin substrates, we obtain designed luciferases with high selectivity; the most active of these is a small (13.9 kDa) and thermostable (with a melting temperature higher than 95 °C) enzyme that has a catalytic efficiency on diphenylterazine (kcat/Km = 106 M−1 s−1) comparable to that of native luciferases, but a much higher substrate specificity. The creation of highly active and specific biocatalysts from scratch with broad applications in biomedicine is a key milestone for computational enzyme design, and our approach should enable generation of a wide range of luciferases and other enzymes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Watson0000,

title = {Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6},

author = {Watson, Paris R.

and Gupta, Suchetana

and Hosseinzadeh, Parisa

and Brown, Benjamin P.

and Baker, David

and Christianson, David W.},

url = {https://pubs.acs.org/doi/full/10.1021/acschembio.3c00113, ACS Chem. Biol.

https://www.bakerlab.org/wp-content/uploads/2023/04/acschembio.3c00113.pdf, PDF},

doi = {10.1021/acschembio.3c00113},

year  = {2023},

date = {2023-04-07},

urldate = {2023-04-07},

journal = {ACS Chemical Biology},

abstract = {Histone deacetylases (HDACs) are essential for the regulation of myriad biological processes, and their aberrant function is implicated in cancer, neurodegeneration, and other diseases. The cytosolic isozyme HDAC6 is unique among the greater family of deacetylases in that it contains two catalytic domains, CD1 and CD2. HDAC6 CD2 is responsible for tubulin deacetylase and tau deacetylase activities, inhibition of which is a key goal as new therapeutic approaches are explored. Of particular interest as HDAC inhibitors are naturally occurring cyclic tetrapeptides such as Trapoxin A or HC Toxin, or the cyclic depsipeptides Largazole and Romidepsin. Even more intriguing are larger, computationally designed macrocyclic peptide inhibitors. Here, we report the 2.0 Å resolution crystal structure of HDAC6 CD2 complexed with macrocyclic octapeptide 1. Comparison with the previously reported structure of the complex with macrocyclic octapeptide 2 reveals that a potent thiolate–zinc interaction made by the unnatural amino acid (S)-2-amino-7-sulfanylheptanoic acid contributes to nanomolar inhibitory potency for each inhibitor. Apart from this zinc-binding residue, octapeptides adopt strikingly different overall conformations and make few direct hydrogen bonds with the protein. Intermolecular interactions are dominated by water-mediated hydrogen bonds; in essence, water molecules appear to cushion the enzyme–octapeptide interface. In view of the broad specificity observed for protein substrates of HDAC6 CD2, we suggest that the binding of macrocyclic octapeptides may mimic certain features of the binding of macromolecular protein substrates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kipnis2022,

title = {Design and optimization of enzymatic activity in a de novo β-barrel scaffold},

author = {Kipnis, Yakov

and Chaib, Anissa Ouald

and Vorobieva, Anastassia A.

and Cai, Guangyang

and Reggiano, Gabriella

and Basanta, Benjamin

and Kumar, Eshan

and Mittl, Peer R.E.

and Hilvert, Donald

and Baker, David},

url = {https://onlinelibrary.wiley.com/doi/full/10.1002/pro.4405, Protein Science

https://www.bakerlab.org/wp-content/uploads/2022/10/Protein-Science-2022-Kipnis-Design-and-optimization-of-enzymatic-activity-in-a-de-novo-‐barrel-scaffold.pdf, PDF},

doi = {10.1002/pro.4405},

year  = {2022},

date = {2022-11-01},

urldate = {2022-11-01},

journal = {Protein Science},

abstract = {While native scaffolds offer a large diversity of shapes and topologies for enzyme engineering, their often unpredictable behavior in response to sequence modification makes de novo generated scaffolds an exciting alternative. Here we explore the customization of the backbone and sequence of a de novo designed eight stranded ?-barrel protein to create catalysts for a retro-aldolase model reaction. We show that active and specific catalysts can be designed in this fold and use directed evolution to further optimize activity and stereoselectivity. Our results support previous suggestions that different folds have different inherent amenability to evolution and this property could account, in part, for the distribution of natural enzymes among different folds.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2022,

title = {Scaffolding protein functional sites using deep learning},

author = {Jue Wang and Sidney Lisanza and David Juergens and Doug Tischer and Joseph L. Watson and Karla M. Castro and Robert Ragotte and Amijai Saragovi and Lukas F. Milles and Minkyung Baek and Ivan Anishchenko and Wei Yang and Derrick R. Hicks and Marc Expòsit and Thomas Schlichthaerle and Jung-Ho Chun and Justas Dauparas and Nathaniel Bennett and Basile I. M. Wicky and Andrew Muenks and Frank DiMaio and Bruno Correia and Sergey Ovchinnikov and David Baker },

url = {https://www.science.org/doi/abs/10.1126/science.abn2100, Science

https://www.ipd.uw.edu/wp-content/uploads/2022/07/science.abn2100.pdf, Download PDF},

doi = {10.1126/science.abn2100},

year  = {2022},

date = {2022-07-21},

urldate = {2022-07-21},

journal = {Science},

abstract = {The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without needing to prespecify the fold or secondary structure of the scaffold. The first approach, “constrained hallucination,” optimizes sequences such that their predicted structures contain the desired functional site. The second approach, “inpainting,” starts from the functional site and fills in additional sequence and structure to create a viable protein scaffold in a single forward pass through a specifically trained RoseTTAFold network. We use these two methods to design candidate immunogens, receptor traps, metalloproteins, enzymes, and protein-binding proteins and validate the designs using a combination of in silico and experimental tests. Protein design has had success in finding sequences that fold into a desired conformation, but designing functional proteins remains challenging. Wang et al. describe two deep-learning methods to design proteins that contain prespecified functional sites. In the first, they found sequences predicted to fold into stable structures that contain the functional site. In the second, they retrained a structure prediction network to recover the sequence and full structure of a protein given only the functional site. The authors demonstrate their methods by designing proteins containing a variety of functional motifs. —VV Deep-learning methods enable the scaffolding of desired functional residues within a well-folded designed protein.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhang2022,

title = {Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants},

author = {Zhang, Jason Z.

and Yeh, Hsien-Wei

and Walls, Alexandra C.

and Wicky, Basile I. M.

and Sprouse, Kaitlin R.

and VanBlargan, Laura A.

and Treger, Rebecca

and Quijano-Rubio, Alfredo

and Pham, Minh N.

and Kraft, John C.

and Haydon, Ian C.

and Yang, Wei

and DeWitt, Michelle

and Bowen, John E.

and Chow, Cameron M.

and Carter, Lauren

and Ravichandran, Rashmi

and Wener, Mark H.

and Stewart, Lance

and Veesler, David

and Diamond, Michael S.

and Greninger, Alexander L.

and Koelle, David M.

and Baker, David},

url = {https://www.nature.com/articles/s41587-022-01280-8, Nature Biotechnology

https://www.bakerlab.org/wp-content/uploads/2022/04/Zhang_etal_NatureBiotech_Thermodynamically_coupled_biosensors_for_detecting_nAbs_against_SARSCoV2_variants.pdf, Download PDF},

year  = {2022},

date = {2022-04-28},

urldate = {2022-04-28},

journal = {Nature Biotechnology},

abstract = {We designed a protein biosensor that uses thermodynamic coupling for sensitive and rapid detection of neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in serum. The biosensor is a switchable, caged luciferase–receptor-binding domain (RBD) construct that detects serum-antibody interference with the binding of virus RBD to angiotensin-converting enzyme 2 (ACE-2) as a proxy for neutralization. Our coupling approach does not require target modification and can better distinguish sample-to-sample differences in analyte binding affinity and abundance than traditional competition-based assays.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hunt2022,

title = {Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice},

author = {Andrew C. Hunt and James Brett Case and Young-Jun Park and Longxing Cao and Kejia Wu and Alexandra C. Walls and Zhuoming Liu and John E. Bowen and Hsien-Wei Yeh and Shally Saini and Louisa Helms and Yan Ting Zhao and Tien-Ying Hsiang and Tyler N. Starr and Inna Goreshnik and Lisa Kozodoy and Lauren Carter and Rashmi Ravichandran and Lydia B. Green and Wadim L. Matochko and Christy A. Thomson and Bastian Vögeli and Antje Krüger and Laura A. VanBlargan and Rita E. Chen and Baoling Ying and Adam L. Bailey and Natasha M. Kafai and Scott E. Boyken and Ajasja Ljubetič and Natasha Edman and George Ueda and Cameron M. Chow and Max Johnson and Amin Addetia and Mary Jane Navarro and Nuttada Panpradist and Michael Gale and Benjamin S. Freedman and Jesse D. Bloom and Hannele Ruohola-Baker and Sean P. J. Whelan and Lance Stewart and Michael S. Diamond and David Veesler and Michael C. Jewett and David Baker},

url = {https://www.science.org/doi/abs/10.1126/scitranslmed.abn1252, Science Translational Medicine

https://www.bakerlab.org/wp-content/uploads/2022/04/scitranslmed.abn1252.pdf, Download PDF},

doi = {10.1126/scitranslmed.abn1252},

year  = {2022},

date = {2022-04-12},

urldate = {2022-04-12},

journal = {Science Translational Medicine},

abstract = {New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise and prolong the coronavirus disease 2019 (COVID-19) pandemic. Here we used a cell-free expression workflow to rapidly screen and optimize constructs containing multiple computationally designed miniprotein inhibitors of SARS-CoV-2. We found the broadest efficacy with a homo-trimeric version of the 75-residue angiotensin converting enzyme 2 (ACE2) mimic AHB2 (TRI2-2) designed to geometrically match the trimeric spike architecture. In the cryo-electron microscopy structure, TRI2 formed a tripod on top of the spike protein which engaged all three receptor binding domains (RBDs) simultaneously as in the design model. TRI2-2 neutralized Omicron (B.1.1.529), Delta (B.1.617.2), and all other variants tested with greater potency than that of monoclonal antibodies used clinically for the treatment of COVID-19. TRI2-2 also conferred prophylactic and therapeutic protection against SARS-CoV-2 challenge when administered intranasally in mice. Designed miniprotein receptor mimics geometrically arrayed to match pathogen receptor binding sites could be a widely applicable antiviral therapeutic strategy with advantages over antibodies and native receptor traps. By comparison, the designed proteins have resistance to viral escape and antigenic drift by construction, precisely tuned avidity, and greatly reduced chance of autoimmune responses. Computationally designed trivalent minibinders provide therapeutic protection in mice against emerging SARS-CoV-2 variants of concern.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lovelock2022,

title = {The road to fully programmable protein catalysis},

author = {Sarah L. Lovelock and Rebecca Crawshaw and Sophie Basler and Colin Levy and David Baker and Donald Hilvert and Anthony P. Green 

},

url = {https://www.nature.com/articles/s41586-022-04456-z, Nature

https://www.bakerlab.org/wp-content/uploads/2022/06/s41586-022-04456-z.pdf, Download PDF},

doi = {10.1038/s41586-022-04456-z},

year  = {2022},

date = {2022-06-01},

journal = {Nature},

abstract = {The ability to design efficient enzymes from scratch would have a profound effect on chemistry, biotechnology and medicine. Rapid progress in protein engineering over the past decade makes us optimistic that this ambition is within reach. The development of artificial enzymes containing metal cofactors and noncanonical organocatalytic groups shows how protein structure can be optimized to harness the reactivity of nonproteinogenic elements. In parallel, computational methods have been used to design protein catalysts for diverse reactions on the basis of fundamental principles of transition state stabilization. Although the activities of designed catalysts have been quite low, extensive laboratory evolution has been used to generate efficient enzymes. Structural analysis of these systems has revealed the high degree of precision that will be needed to design catalysts with greater activity. To this end, emerging protein design methods, including deep learning, hold particular promise for improving model accuracy. Here we take stock of key developments in the field and highlight new opportunities for innovation that should allow us to transition beyond the current state of the art and enable the robust design of biocatalysts to address societal needs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/cbic.202100435,

title = {Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions},

author = {Toshifumi Fujioka and Nobutaka Numoto and Hiroyuki Akama and Kola Shilpa and Michiko Oka and Prodip K. Roy and Yarkali Krishna and Nobutoshi Ito and David Baker and Masayuki Oda and Fujie Tanaka},

url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cbic.202100435},

doi = {https://doi.org/10.1002/cbic.202100435},

year  = {2022},

date = {2022-01-01},

journal = {ChemBioChem},

volume = {23},

number = {2},

pages = {e202100435},

abstract = {Abstract Natural aldolase enzymes and created retro-aldolase protein catalysts often catalyze both aldol and retro-aldol reactions depending on the concentrations of the reactants and the products. Here, we report that the directionality of protein catalysts can be altered by replacing one amino acid. The protein catalyst derived from a scaffold of a previously reported retro-aldolase catalyst, catalyzed aldol reactions more efficiently than the previously reported retro-aldolase catalyst. The retro-aldolase catalyst efficiently catalyzed the retro-aldol reaction but was less efficient in catalyzing the aldol reaction. The results indicate that protein catalysts with varying levels of directionality in usually reversibly catalyzed aldol and retro-aldol reactions can be generated from the same protein scaffold.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hosseinzadeh2021,

title = {Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites},

author = {Hosseinzadeh, Parisa

and Watson, Paris R.

and Craven, Timothy W.

and Li, Xinting

and Rettie, Stephen

and Pardo-Avila, Fátima

and Bera, Asim K.

and Mulligan, Vikram Khipple

and Lu, Peilong

and Ford, Alexander S.

and Weitzner, Brian D.

and Stewart, Lance J.

and Moyer, Adam P.

and Di Piazza, Maddalena

and Whalen, Joshua G.

and Greisen, Per Jr.

and Christianson, David W.

and Baker, David},

url = {https://www.nature.com/articles/s41467-021-23609-8, Nature Communications

https://www.bakerlab.org/wp-content/uploads/2021/06/Hosseinzadeh_etal_NatureComms2021_AnchorExtention.pdf, Download PDF},

doi = {10.1038/s41467-021-23609-8},

year  = {2021},

date = {2021-06-07},

urldate = {2021-06-07},

journal = {Nature Communications},

abstract = {Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site remains difficult. To address this challenge, we develop a computational “anchor extension” methodology for targeting protein interfaces by extending a peptide chain around a non-canonical amino acid residue anchor. To test our approach using a well characterized model system, we design cyclic peptides that inhibit histone deacetylases 2 and 6 (HDAC2 and HDAC6) with enhanced potency compared to the original anchor (IC50 values of 9.1 and 4.4 nM for the best binders compared to 5.4 and 0.6 µM for the anchor, respectively). The HDAC6 inhibitor is among the most potent reported so far. These results highlight the potential for de novo design of high-affinity protein-peptide interfaces, as well as the challenges that remain.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Divine2021,

title = {Designed proteins assemble antibodies into modular nanocages},

author = {Divine, Robby and Dang, Ha V. and Ueda, George and Fallas, Jorge A. and Vulovic, Ivan and Sheffler, William and Saini, Shally and Zhao, Yan Ting and Raj, Infencia Xavier and Morawski, Peter A. and Jennewein, Madeleine F. and Homad, Leah J. and Wan, Yu-Hsin and Tooley, Marti R. and Seeger, Franziska and Etemadi, Ali and Fahning, Mitchell L. and Lazarovits, James and Roederer, Alex and Walls, Alexandra C. and Stewart, Lance and Mazloomi, Mohammadali and King, Neil P. and Campbell, Daniel J. and McGuire, Andrew T. and Stamatatos, Leonidas and Ruohola-Baker, Hannele and Mathieu, Julie and Veesler, David and Baker, David},

url = {https://science.sciencemag.org/content/372/6537/eabd9994.full.pdf, Science

https://www.bakerlab.org/wp-content/uploads/2021/04/Divine_etal_Science2021_Antibody_nanocages.pdf, Download PDF},

doi = {10.1126/science.abd9994},

year  = {2021},

date = {2021-04-02},

urldate = {2021-04-02},

journal = {Science},

volume = {372},

number = {6537},

abstract = {Antibodies are broadly used in therapies and as research tools because they can be generated against a wide range of targets. Efficacy can often be increased by clustering antibodies in multivalent assemblies. Divine et al. designed antibody nanocages from two components: One is an antibody-binding homo-oligomic protein and the other is the antibody itself. Computationally designed proteins drive the assembly of antibody nanocages in a range of architectures, allowing control of the symmetry and the antibody valency. The multivalent display enhances antibody-dependent signaling, and nanocages displaying antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein effectively neutralize pseudovirus.Science, this issue p. eabd9994INTRODUCTIONAntibodies that bind tightly to targets of interest play central roles in biological research and medicine. Clusters of antibodies, typically generated by fusing antibodies to polymers or genetically linking antibody fragments together, can enhance signaling. Currently lacking are approaches for making antibody assemblies with a range of precisely specified architectures and valencies.RATIONALEWe set out to computationally design proteins that assemble antibodies into precise architectures with different valencies and symmetries. We developed an approach to designing proteins that position antibodies or Fc-fusions on the twofold symmetry axes of regular dihedral and polyhedral architectures. We hypothesized that such designs could robustly drive arbitrary antibodies into homogeneous and structurally well-defined nanocages and that such assemblies could have pronounced effects on cell signaling.RESULTSAntibody cage (AbC){textendash}forming designs were created by rigidly fusing antibody constant domain{textendash}binding modules to cyclic oligomers through helical spacer domains such that the symmetry axes of the dimeric antibody and cyclic oligomer are at orientations that generate different dihedral or polyhedral (e.g., tetrahedral, octahedral, or icosahedral) architectures. The junction regions between the connected building blocks were optimized to fold to the designed structures. Synthetic genes encoding the designs were expressed in bacterial cultures; of 48 structurally characterized designs, eight assemblies matched the design models. Successful designs encompass D2 dihedral (three designs), T32 tetrahedral (two designs), O42 octahedral (one design), and I52 icosahedral (two designs) architectures; these contain 2, 6, 12, or 30 antibodies, respectively.We investigated the effects of AbCs on cell signaling. AbCs formed with a death receptor{textendash}targeting antibody induced apoptosis of tumor cell lines that were unaffected by the soluble antibody or the native ligand. Angiopoietin pathway signaling, CD40 signaling, and T cell proliferation were all enhanced by assembling Fc-fusions or antibodies in AbCs. AbC formation also enhanced in vitro viral neutralization of a severe acute respiratory syndrome coronavirus 2 pseudovirus.CONCLUSIONWe have designed multiple antibody cage{textendash}forming proteins that precisely cluster any protein A{textendash}binding antibody into nanocages with controlled valency and geometry. AbCs can be formed with 2, 6, 12, or 30 antibodies simply by mixing the antibody with the corresponding designed protein, without the need for any covalent modification of the antibody. Incorporating receptor binding or virus-neutralizing antibodies into AbCs enhanced their biological activity across a range of cell systems. We expect that our rapid and robust approach for assembling antibodies into homogeneous and ordered nanocages without the need for covalent modification will have broad utility in research and medicine.Designed proteins assemble antibodies into large symmetric architectures.Designed antibody-clustering proteins (light gray) assemble antibodies (purple) into diverse nanocage architectures (top). Antibody nanocages enhance cell signaling compared with free antibodies (bottom).IMAGE: IAN HAYDON, INSTITUTE FOR PROTEIN DESIGNMultivalent display of receptor-engaging antibodies or ligands can enhance their activity. Instead of achieving multivalency by attachment to preexisting scaffolds, here we unite form and function by the computational design of nanocages in which one structural component is an antibody or Fc-ligand fusion and the second is a designed antibody-binding homo-oligomer that drives nanocage assembly. Structures of eight nanocages determined by electron microscopy spanning dihedral, tetrahedral, octahedral, and icosahedral architectures with 2, 6, 12, and 30 antibodies per nanocage, respectively, closely match the corresponding computational models. Antibody nanocages targeting cell surface receptors enhance signaling compared with free antibodies or Fc-fusions in death receptor 5 (DR5){textendash}mediated apoptosis, angiopoietin-1 receptor (Tie2){textendash}mediated angiogenesis, CD40 activation, and T cell proliferation. Nanocage assembly also increases severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudovirus neutralization by α-SARS-CoV-2 monoclonal antibodies and Fc{textendash}angiotensin-converting enzyme 2 (ACE2) fusion proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mulligan2021,

title = {Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1},

author = {Mulligan, Vikram Khipple and Workman, Sean and Sun, Tianjun and Rettie, Stephen and Li, Xinting and Worrall, Liam J. and Craven, Timothy W. and King, Dustin T. and Hosseinzadeh, Parisa and Watkins, Andrew M. and Renfrew, P. Douglas and Guffy, Sharon and Labonte, Jason W. and Moretti, Rocco and Bonneau, Richard and Strynadka, Natalie C. J. and Baker, David},

url = {https://www.pnas.org/content/118/12/e2012800118.full, PNAS

https://www.bakerlab.org/wp-content/uploads/2021/03/Mulligen_etal_PNAS2021_Macrocycle_inhibitors.pdf, Download PDF},

doi = {10.1073/pnas.2012800118},

year  = {2021},

date = {2021-03-23},

urldate = {2021-03-23},

journal = {Proceedings of the National Academy of Sciences},

volume = {118},

number = {12},

abstract = {The rise of antibiotic resistance calls for new therapeutics targeting resistance factors such as the New Delhi metallo-β-lactamase 1 (NDM-1), a bacterial enzyme that degrades β-lactam antibiotics. We present structure-guided computational methods for designing peptide macrocycles built from mixtures of L- and D-amino acids that are able to bind to and inhibit targets of therapeutic interest. Our methods explicitly consider the propensity of a peptide to favor a binding-competent conformation, which we found to predict rank order of experimentally observed IC50 values across seven designed NDM-1- inhibiting peptides. We were able to determine X-ray crystal structures of three of the designed inhibitors in complex with NDM-1, and in all three the conformation of the peptide is very close to the computationally designed model. In two of the three structures, the binding mode with NDM-1 is also very similar to the design model, while in the third, we observed an alternative binding mode likely arising from internal symmetry in the shape of the design combined with flexibility of the target. Although challenges remain in robustly predicting target backbone changes, binding mode, and the effects of mutations on binding affinity, our methods for designing ordered, binding-competent macrocycles should have broad applicability to a wide range of therapeutic targets.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Crawshaw2021,

title = {Engineering an efficient and enantioselective enzyme for the Morita-Baylis-Hillman reaction},

author = {Crawshaw, Rebecca

and Crossley, Amy E.

and Johannissen, Linus

and Burke, Ashleigh J.

and Hay, Sam

and Levy, Colin

and Baker, David

and Lovelock, Sarah L.

and Green, Anthony P.},

url = {https://www.nature.com/articles/s41557-021-00833-9

https://www.bakerlab.org/wp-content/uploads/2022/01/Crawshaw_etal_NatChem_Engineering_enantioselective_enzyme_Morita-Baylis-Hillman_reaction.pdf},

doi = {10.1038/s41557-021-00833-9},

year  = {2021},

date = {2021-12-16},

journal = {Nature Chemistry},

abstract = {The combination of computational design and directed evolution could offer a general strategy to create enzymes with new functions. So far, this approach has delivered enzymes for a handful of model reactions. Here we show that new catalytic mechanisms can be engineered into proteins to accelerate more challenging chemical transformations. Evolutionary optimization of a primitive design afforded an efficient and enantioselective enzyme (BH32.14) for the Morita–Baylis–Hillman (MBH) reaction. BH32.14 is suitable for preparative-scale transformations, accepts a broad range of aldehyde and enone coupling partners and is able to promote selective monofunctionalizations of dialdehydes. Crystallographic, biochemical and computational studies reveal that BH32.14 operates via a sophisticated catalytic mechanism comprising a His23 nucleophile paired with a judiciously positioned Arg124. This catalytic arginine shuttles between conformational states to stabilize multiple oxyanion intermediates and serves as a genetically encoded surrogate of privileged bidentate hydrogen-bonding catalysts (for example, thioureas). This study demonstrates that elaborate catalytic devices can be built from scratch to promote demanding multi-step processes not observed in nature.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Friedlander2021,

title = {Treatment of experimental anthrax with pegylated circularly permuted capsule depolymerase},

author = {Patricia M. Legler

and Stephen F. Little

and Jeffrey Senft

and Rowena Schokman

and John H. Carra

and Jaimee R. Compton

and Donald Chabot

and Steven Tobery

and David P. Fetterer

and Justin B. Siegel

and David Baker

and Arthur M. Friedlander},

url = {https://www.science.org/doi/10.1126/scitranslmed.abh1682

https://www.bakerlab.org/wp-content/uploads/2022/01/Legler_etal_ScienceTransMed2021_Treatment_of_anthrax_by_capsule_depolymerase.pdf},

doi = {10.1126/scitranslmed.abh1682},

year  = {2021},

date = {2021-12-08},

journal = {Science Translational Medicine},

abstract = {Anthrax is considered one of the most dangerous bioweapon agents, and concern about multidrug-resistant strains has led to the development of alternative therapeutic approaches that target the antiphagocytic capsule, an essential virulence determinant of Bacillus anthracis, the causative agent. Capsule depolymerase is a γ-glutamyltransferase that anchors the capsule to the cell wall of B. anthracis. Encapsulated strains of B. anthracis can be treated with recombinant capsule depolymerase to enzymatically remove the capsule and promote phagocytosis and killing by human neutrophils. Here, we show that pegylation improved the pharmacokinetic and therapeutic properties of a previously described variant of capsule depolymerase, CapD-CP, when delivered 24 hours after exposure every 8 hours for 2 days for the treatment of mice infected with B. anthracis. Mice infected with 382 LD50 of B. anthracis spores from a nontoxigenic encapsulated strain were completely protected (10 of 10) after treatment with the pegylated PEG-CapD-CPS334C, whereas 10% of control mice (1 of 10) survived with control treatment using bovine serum albumin (P < 0.0001, log-rank analysis). Treatment of mice infected with five LD50 of a fully virulent toxigenic, encapsulated B. anthracis strain with PEG-CapD-CPS334C protected 80% (8 of 10) of the animals, whereas 20% of controls (2 of 10) survived (P = 0.0125, log-rank analysis). This strategy renders B. anthracis susceptible to innate immune responses and does not rely on antibiotics. These findings suggest that enzyme-catalyzed removal of the capsule may be a potential therapeutic strategy for the treatment of multidrug- or vaccine-resistant anthrax and other bacterial infections.

},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Basanta2020,

title = {An enumerative algorithm for de novo design of proteins with diverse pocket structures},

author = {Basanta, Benjamin and Bick, Matthew J. and Bera, Asim K. and Norn, Christoffer and Chow, Cameron M. and Carter, Lauren P. and Goreshnik, Inna and Dimaio, Frank and Baker, David},

url = {https://www.pnas.org/content/117/36/22135

https://www.bakerlab.org/wp-content/uploads/2020/12/Basanta_etal_2020_PNAS_enumerative-algorithm-for-de-novo-design-of-proteins-with-diverse-pocket-structures.pdf},

doi = {10.1073/pnas.2005412117},

isbn = {0027-8424},

year  = {2020},

date = {2020-08-11},

journal = {Proceedings of the National Academy of Sciences},

volume = {117},

number = {36},

pages = {22135–22145},

abstract = {Reengineering naturally occurring proteins to have new functions has had considerable impact on industrial and biomedical applications, but is limited by the finite number of known proteins. A promise of de novo protein design is to generate a larger and more diverse set of protein structures than is currently available. This vision has not yet been realized for small-molecule binder or enzyme design due to the complexity of pocket-containing structures. Here we present an algorithm that systematically generates NTF2-like protein structures with diverse pocket geometries. The scaffold sets, the insights gained from detailed structural characterization, and the computational method for generating unlimited numbers of structures should contribute to a new generation of de novo small-molecule binding proteins and catalysts.To create new enzymes and biosensors from scratch, precise control over the structure of small-molecule binding sites is of paramount importance, but systematically designing arbitrary protein pocket shapes and sizes remains an outstanding challenge. Using the NTF2-like structural superfamily as a model system, we developed an enumerative algorithm for creating a virtually unlimited number of de novo proteins supporting diverse pocket structures. The enumerative algorithm was tested and refined through feedback from two rounds of large-scale experimental testing, involving in total the assembly of synthetic genes encoding 7,896 designs and assessment of their stability on yeast cell surface, detailed biophysical characterization of 64 designs, and crystal structures of 5 designs. The refined algorithm generates proteins that remain folded at high temperatures and exhibit more pocket diversity than naturally occurring NTF2-like proteins. We expect this approach to transform the design of small-molecule sensors and enzymes by enabling the creation of binding and active site geometries much more optimal for specific design challenges than is accessible by repurposing the limited number of naturally occurring NTF2-like proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chen2020,

title = {De novo design of protein logic gates},

author = {Chen, Zibo and Kibler, Ryan D. and Hunt, Andrew and Busch, Florian and Pearl, Jocelynn and Jia, Mengxuan and VanAernum, Zachary L. and Wicky, Basile I. M. and Dods, Galen and Liao, Hanna and Wilken, Matthew S. and Ciarlo, Christie and Green, Shon and El-Samad, Hana and Stamatoyannopoulos, John and Wysocki, Vicki H. and Jewett, Michael C. and Boyken, Scott E. and Baker, David},

url = {https://science.sciencemag.org/content/368/6486/78

https://www.bakerlab.org/wp-content/uploads/2020/04/Chen2020_DeNovoProteinLogicGates.pdf},

doi = {10.1126/science.aay2790},

year  = {2020},

date = {2020-03-04},

journal = {Science},

volume = {368},

number = {6486},

pages = {78-84},

abstract = {The design of modular protein logic for regulating protein function at the posttranscriptional level is a challenge for synthetic biology. Here, we describe the design of two-input AND, OR, NAND, NOR, XNOR, and NOT gates built from de novo–designed proteins. These gates regulate the association of arbitrary protein units ranging from split enzymes to transcriptional machinery in vitro, in yeast and in primary human T cells, where they control the expression of the TIM3 gene related to T cell exhaustion. Designed binding interaction cooperativity, confirmed by native mass spectrometry, makes the gates largely insensitive to stoichiometric imbalances in the inputs, and the modularity of the approach enables ready extension to three-input OR, AND, and disjunctive normal form gates. The modularity and cooperativity of the control elements, coupled with the ability to de novo design an essentially unlimited number of protein components, should enable the design of sophisticated posttranslational control logic over a wide range of biological functions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Weitzner2019,

title = {A computational method for design of connected catalytic networks in proteins},

author = {Brian D. Weitzner, Yakov Kipnis, A. Gerard Daniel, Donald Hilvert, David Baker},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.3757

https://www.bakerlab.org/wp-content/uploads/2020/02/Weitzner_et_al-2019-Protein_Science-1.pdf},

doi = {DOI10.1002/pro .3757},

year  = {2019},

date = {2019-10-23},

journal = {Protein Science},

abstract = {Computational design of new active sites has generally proceeded by geometrically defining interactions between the reaction transition state(s) and surrounding side-chain functional groups which maximize transition-state stabilization, and then searching for sites in protein scaffolds where the specified side-chain–transition-state interactions can be realized. A limitation of this approach is that the interactions between the side chains themselves are not constrained. An extensive connected hydrogen bond network involving the catalytic residues was observed in a designed retroaldolase following directed evolution. Such connected networks could increase catalytic activity by preorganizing active site residues in catalytically competent orientations, and enabling concerted interactions between side chains during catalysis, for example proton shuffling. We developed a method for designing active sites in which the catalytic side chains, in addition to making interactions with the transition state, are also involved in extensive hydrogen bond networks. Because of the added constraint of hydrogen-bond connectivity between the catalytic side chains, to find solutions, a wider range of interactions between these side chains and the transition state must be considered. Our new method starts from a ChemDraw-like 2D representation of the transition state with hydrogen-bond donors, acceptors, and covalent interaction sites indicated, and all placements of side-chain functional groups that make the indicated interactions with the transition state, and are fully connected in a single hydrogen-bond network are systematically enumerated. The RosettaMatch method can then be used to identify realizations of these fully-connected active sites in protein scaffolds. The method generates many fully-connected active site solutions for a set of model reactions that are promising starting points for the design of fully-preorganized enzyme catalysts.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{Romero2018,

title = {Simple yet functional phosphate-loop proteins},

author = {Romero Romero, Maria Luisa and Yang, Fan and Lin, Yu-Ru and Toth-Petroczy, Agnes and Berezovsky, Igor N. and Goncearenco, Alexander and Yang, Wen and Wellner, Alon and Kumar-Deshmukh, Fanindra and Sharon, Michal and Baker, David and Varani, Gabriele and Tawfik, Dan S.},

url = {https://www.bakerlab.org/wp-content/uploads/2019/02/Romero2018.pdfhttps://www.pnas.org/content/115/51/E11943

},

doi = {10.1073/pnas.1812400115},

issn = {0027-8424},

year  = {2018},

date = {2018-11-18},

journal = {PNAS},

volume = {115},

number = {51},

pages = {E11943--E11950},

abstract = {The complexity of modern proteins makes the understanding of how proteins evolved from simple beginnings a daunting challenge. The Walker-A motif is a phosphate-binding loop (P-loop) found in possibly the most ancient and abundant protein class, so-called P-loop NTPases. By combining phylogenetic analysis and computational protein design, we have generated simple proteins, of only 55 residues, that contain the P-loop and thereby confer binding of a range of phosphate-containing ligands{textemdash}and even more avidly, RNA and single-strand DNA. Our results show that biochemical function can be implemented in small and simple proteins; they intriguingly suggest that the P-loop emerged as a polynucleotide binder and catalysis of phosphoryl transfer evolved later upon acquisition of higher sequence and structural complexity.Abundant and essential motifs, such as phosphate-binding loops (P-loops), are presumed to be the seeds of modern enzymes. The Walker-A P-loop is absolutely essential in modern NTPase enzymes, in mediating binding, and transfer of the terminal phosphate groups of NTPs. However, NTPase function depends on many additional active-site residues placed throughout the protein{textquoteright}s scaffold. Can motifs such as P-loops confer function in a simpler context? We applied a phylogenetic analysis that yielded a sequence logo of the putative ancestral Walker-A P-loop element: a β-strand connected to an α-helix via the P-loop. Computational design incorporated this element into de novo designed β-α repeat proteins with relatively few sequence modifications. We obtained soluble, stable proteins that unlike modern P-loop NTPases bound ATP in a magnesium-independent manner. Foremost, these simple P-loop proteins avidly bound polynucleotides, RNA, and single-strand DNA, and mutations in the P-loop{textquoteright}s key residues abolished binding. Binding appears to be facilitated by the structural plasticity of these proteins, including quaternary structure polymorphism that promotes a combined action of multiple P-loops. Accordingly, oligomerization enabled a 55-aa protein carrying a single P-loop to confer avid polynucleotide binding. Overall, our results show that the P-loop Walker-A motif can be implemented in small and simple β-α repeat proteins, primarily as a polynucleotide binding motif.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lau2018,

title = {Discovery and engineering of enhanced SUMO protease enzymes},

author = {Yue-Ting K. Lau, and Vladimir Baytshtok, and Tessa A. Howard, and Brooke M. Fiala, and JayLee M. Johnson, and Lauren P. Carter, and David Baker, and Christopher D. Lima, and Christopher D. Bahl},

url = {http://www.jbc.org/content/293/34/13224.short

https://www.bakerlab.org/wp-content/uploads/2019/02/Lau2018.pdf},

doi = {10.1074/jbc.RA118.004146},

year  = {2018},

date = {2018-07-05},

journal = {The Journal of Biological Chemistry},

volume = {293},

pages = {13224-13233},

abstract = {Small ubiquitin-like modifier (SUMO) is commonly used as a protein fusion domain to facilitate expression and purification of recombinant proteins, and a SUMO-specific protease is then used to remove SUMO from these proteins. Although this protease is highly specific, its limited solubility and stability hamper its utility as an in vitro reagent. Here, we report improved SUMO protease enzymes obtained via two approaches. First, we developed a computational method and used it to re-engineer WT Ulp1 from Saccharomyces cerevisiae to improve protein solubility. Second, we discovered an improved SUMO protease via genomic mining of the thermophilic fungus Chaetomium thermophilum, as proteins from thermophilic organisms are commonly employed as reagent enzymes. Following expression in Escherichia coli, we found that these re-engineered enzymes can be more thermostable and up to 12 times more soluble, all while retaining WT-or-better levels of SUMO protease activity. The computational method we developed to design solubility-enhancing substitutions is based on the RosettaScripts application for the macromolecular modeling suite Rosetta, and it is broadly applicable for the improvement of solution properties of other proteins. Moreover, we determined the X-ray crystal structure of a SUMO protease from C. thermophilum to 1.44 Å resolution. This structure revealed that this enzyme exhibits structural and functional conservation with the S. cerevisiae SUMO protease, despite exhibiting only 28% sequence identity. In summary, by re-engineering the Ulp1 protease and discovering a SUMO protease from C. thermophilum, we have obtained proteases that are more soluble, more thermostable, and more efficient than the current commercially available Ulp1 enzyme.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Marcos2017,

title = {Principles for designing proteins with cavities formed by curved β sheets},

author = {Marcos, Enrique* and Basanta, Benjamin* and Chidyausiku, Tamuka M. and Tang, Yuefeng and Oberdorfer, Gustav and Liu, Gaohua and Swapna, G. V. T. and Guan, Rongjin and Silva, Daniel-Adriano and Dou, Jiayi and Pereira, Jose Henrique and Xiao, Rong and Sankaran, Banumathi and Zwart, Peter H. and Montelione, Gaetano T. and Baker, David},

url = {https://www.bakerlab.org/wp-content/uploads/2017/01/Marcos_Science_2017.pdf

http://science.sciencemag.org/content/355/6321/201},

doi = {10.1126/science.aah7389},

issn = {0036-8075},

year  = {2017},

date = {2017-01-01},

journal = {Science},

volume = {355},

number = {6321},

pages = {201--206},

publisher = {American Association for the Advancement of Science},

abstract = {In de novo protein design, creating custom-tailored binding sites is a particular challenge because these sites often involve nonideal backbone structures. For example, curved b sheets are a common ligand binding motif. Marcos et al. investigated the principles that drive β-sheet curvature by studying the geometry of β sheets in natural proteins and folding simulations. In a step toward custom design of enzyme catalysts, they used these principles to control β-sheet geometry and design proteins with differently shaped cavities.Science, this issue p. 201Active sites and ligand-binding cavities in native proteins are often formed by curved β sheets, and the ability to control β-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we investigated the mechanisms controlling β-sheet curvature by studying the geometry of β sheets in naturally occurring protein structures and folding simulations. The principles emerging from this analysis were used to design, de novo, a series of proteins with curved β sheets topped with α helices. Nuclear magnetic resonance and crystal structures of the designs closely match the computational models, showing that β-sheet curvature can be controlled with atomic-level accuracy. Our approach enables the design of proteins with cavities and provides a route to custom design ligand-binding and catalytic sites.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bale2016,

title = {Accurate design of megadalton-scale two-component icosahedral protein complexes},

author = {Jacob B. Bale and Shane Gonen and Yuxi Liu and William Sheffler and Daniel Ellis and Chantz Thomas and Duilio Cascio and Todd O. Yeates and Tamir Gonen and Neil P. King and David Baker},

url = {https://www.bakerlab.org/wp-content/uploads/2016/07/Bale_Science_2016.pdf},

doi = {10.1126/science.aaf8818},

year  = {2016},

date = {2016-07-22},

journal = {Science},

volume = {353},

number = {6297},

pages = {389-394},

abstract = {Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{L2015,

title = {Rational design of α-helical tandem repeat proteins with closed architectures},

author = {L Doyle and J Hallinan and J Bolduc and F Parmeggiani and D Baker and BL Stoddard and P Bradley},

url = {https://www.bakerlab.org/wp-content/uploads/2015/12/Doyle_Nature_2015.pdf},

doi = {10.1038/nature16191},

year  = {2015},

date = {2015-12-24},

journal = {Nature},

volume = {528(7583)},

pages = {585-8},

abstract = {Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures--which is dictated by the internal geometry and local packing of the repeat building blocks--is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed α-solenoid repeat structures (α-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed α-solenoid repeats with a left-handed helical architecture that--to our knowledge--is not yet present in the protein structure database.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{M2015,

title = {Catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro},

author = {M Goldsmith and S Eckstein and Y Ashani and P Jr Greisen and H Leader and JL Sussman and N Aggarwal and S Ovchinnikov and DS Tawfik and D Baker and H Thiermann and F Worek},

url = {https://www.bakerlab.org/wp-content/uploads/2015/12/Goldsmith_ArchToxicol_2015.pdf},

doi = {10.1007/s00204-015-1626-2},

year  = {2015},

date = {2015-11-26},

journal = {Archives of Toxicology},

abstract = {The nearly 200,000 fatalities following exposure to organophosphorus (OP) pesticides each year and the omnipresent danger of a terroristic attack with OP nerve agents emphasize the demand for the development of effective OP antidotes. Standard treatments for intoxicated patients with a combination of atropine and an oxime are limited in their efficacy. Thus, research focuses on developing catalytic bioscavengers as an alternative approach using OP-hydrolyzing enzymes such as Brevundimonas diminuta phosphotriesterase (PTE). Recently, a PTE mutant dubbed C23 was engineered, exhibiting reversed stereoselectivity and high catalytic efficiency (k cat/K M) for the hydrolysis of the toxic enantiomers of VX, CVX, and VR. Additionally, C23's ability to prevent systemic toxicity of VX using a low protein dose has been shown in vivo. In this study, the catalytic efficiencies of V-agent hydrolysis by two newly selected PTE variants were determined. Moreover, in order to establish trends in sequence-activity relationships along the pathway of PTE's laboratory evolution, we examined k cat/K M values of several variants with a number of V-type and G-type nerve agents as well as with different OP pesticides. Although none of the new PTE variants exhibited k cat/K M values >107 M-1 min-1 with V-type nerve agents, which is required for effective prophylaxis, they were improved with VR relative to previously evolved variants. The new variants detoxify a broad spectrum of OPs and provide insight into OP hydrolysis and sequence-activity relationships.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{PS2015,

title = {De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy},

author = {PS Huang and K Feldmeier and F Parmeggiani and DA Fernandez Velasco and B Höcker and D Baker},

url = {https://www.bakerlab.org/wp-content/uploads/2015/12/Huang_NatChemBio_2015.pdf},

doi = {10.1038/nchembio.1966},

year  = {2015},

date = {2015-11-23},

journal = {Nature Chemical Biology},

volume = {12(1)},

pages = {29-34},

abstract = {Despite efforts for over 25 years, de novo protein design has not succeeded in achieving the TIM-barrel fold. Here we describe the computational design of four-fold symmetrical (β/α)8 barrels guided by geometrical and chemical principles. Experimental characterization of 33 designs revealed the importance of side chain-backbone hydrogen bonds for defining the strand register between repeat units. The X-ray crystal structure of a designed thermostable 184-residue protein is nearly identical to that of the designed TIM-barrel model. PSI-BLAST searches do not identify sequence similarities to known TIM-barrel proteins, and sensitive profile-profile searches indicate that the design sequence is distant from other naturally occurring TIM-barrel superfamilies, suggesting that Nature has sampled only a subset of the sequence space available to the TIM-barrel fold. The ability to design TIM barrels de novo opens new possibilities for custom-made enzymes. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{617,

title = {Engineering of Kuma030: a gliadin peptidase that rapidly degrades immunogenic gliadin peptides in gastric conditions.},

author = { Clancey Wolf and Justin B Siegel and Christine Tinberg and Alessandra Camarca and Carmen Gianfrani and Shirley Paski and Rongjin Guan and Gaetano T Montelione and David Baker and Ingrid S Pultz},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Wolf_JACS_2015.pdf},

doi = {10.1021/jacs.5b08325},

issn = {1520-5126},

year  = {2015},

date = {2015-09-01},

journal = {Journal of the American Chemical Society},

abstract = {Celiac disease is characterized by intestinal inflammation triggered by gliadin, a component of dietary gluten. Oral administration of proteases that can rapidly degrade gliadin in the gastric compartment has been proposed as a treatment for celiac disease; however, no protease has been shown to specifically reduce the immunogenic gliadin content, in gastric conditions, to below the threshold shown to be toxic for celiac patients. Here, we used the Rosetta Molecular Modeling Suite to redesign the active site of the acid-active gliadin endopeptidase KumaMax. The resulting protease, Kuma030, specifically recognizes tripeptide sequences that are found throughout the immunogenic regions of gliadin, as well as in homologous proteins in barley and rye. Indeed, treatment of gliadin with Kuma030 eliminates the ability of gliadin to stimulate a T cell response. Kuma030 is capable of degrading >99% of the immunogenic gliadin fraction in laboratory-simulated gastric digestions with minutes, to a level below the toxic threshold for celiac patients, suggesting great potential for this enzyme as an oral therapeutic for celiac disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{565,

title = {Computational protein design enables a novel one-carbon assimilation pathway},

author = { Justin B Siegel and Amanda Lee Smith and Sean Poust and Adam J Wargacki and Arren Bar-Even and Catherine Louw and Betty W Shen and Christopher B Eiben and Huu M Tran and Elad Noor and Jasmine L Gallaher and Jacob Bale and Yasuo Yoshikuni and Michael H Gelb and Jay D Keasling and Barry L Stoddard and Mary E Lidstrom and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/siegel15A.pdf},

doi = {10.1073/pnas.1500545112},

issn = {1091-6490},

year  = {2015},

date = {2015-03-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

abstract = {We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence of FLS enables the design of a new carbon fixation pathway, the formolase pathway, consisting of a small number of thermodynamically favorable chemical transformations that convert formate into a three-carbon sugar in central metabolism. The formolase pathway is predicted to use carbon more efficiently and with less backward flux than any naturally occurring one-carbon assimilation pathway. When supplemented with enzymes carrying out the other steps in the pathway, FLS converts formate into dihydroxyacetone phosphate and other central metabolites in vitro. These results demonstrate how modern protein engineering and design tools can facilitate the construction of a completely new biosynthetic pathway.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{610,

title = {Intrinsic disorder drives N-terminal ubiquitination by Ube2w},

author = { Vinayak Vittal and Lei Shi and Dawn M Wenzel and K Matthew Scaglione and Emily D Duncan and Venkatesha Basrur and Kojo S J Elenitoba-Johnson and David Baker and Henry L Paulson and Peter S Brzovic and Rachel E Klevit},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/intrinsicdisorderdrives_Baker2015.pdf},

doi = {10.1038/nchembio.1700},

issn = {1552-4469},

year  = {2015},

date = {2015-01-01},

journal = {Nature Chemical Biology},

volume = {11},

pages = {83-9},

abstract = {Ubiquitination of the αN-terminus of protein substrates has been reported sporadically since the early 1980s. However, the identity of an enzyme responsible for this unique ubiquitin (Ub) modification has only recently been elucidated. We show the Ub-conjugating enzyme (E2) Ube2w uses a unique mechanism to facilitate the specific ubiquitination of the α-amino group of its substrates that involves recognition of backbone atoms of intrinsically disordered N termini. We present the NMR-based solution ensemble of full-length Ube2w that reveals a structural architecture unlike that of any other E2 in which its C terminus is partly disordered and flexible to accommodate variable substrate N termini. Flexibility of the substrate is critical for recognition by Ube2w, and either point mutations in or the removal of the flexible C terminus of Ube2w inhibits substrate binding and modification. Mechanistic insights reported here provide guiding principles for future efforts to define the N-terminal ubiquitome in cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{619,

title = {Computational design of a red fluorophore ligase for site-specific protein labeling in living cells.},

author = { Daniel S Liu and Lucas G Niv'on and Florian Richter and Peter J Goldman and Thomas J Deerinck and Jennifer Z Yao and Douglas Richardson and William S Phipps and Anne Z Ye and Mark H Ellisman and Catherine L Drennan and David Baker and Alice Y Ting},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Liu_computational_PNAS_2014.pdf},

doi = {10.1073/pnas.1404736111},

issn = {1091-6490},

year  = {2014},

date = {2014-10-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {111},

pages = {E4551-9},

abstract = {Chemical fluorophores offer tremendous size and photophysical advantages over fluorescent proteins but are much more challenging to target to specific cellular proteins. Here, we used Rosetta-based computation to design a fluorophore ligase that accepts the red dye resorufin, starting from Escherichia coli lipoic acid ligase. X-ray crystallography showed that the design closely matched the experimental structure. Resorufin ligase catalyzed the site-specific and covalent attachment of resorufin to various cellular proteins genetically fused to a 13-aa recognition peptide in multiple mammalian cell lines and in primary cultured neurons. We used resorufin ligase to perform superresolution imaging of the intermediate filament protein vimentin by stimulated emission depletion and electron microscopies. This work illustrates the power of Rosetta for major redesign of enzyme specificity and introduces a tool for minimally invasive, highly specific imaging of cellular proteins by both conventional and superresolution microscopies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{621,

title = {De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters.},

author = { Yu Liu and Xin Zhang and Yun Lei Tan and Gira Bhabha and Damian C Ekiert and Yakov Kipnis and Sinisa Bjelic and David Baker and Jeffery W Kelly},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Liu_JACS_2014.pdf},

doi = {10.1021/ja5056356},

issn = {1520-5126},

year  = {2014},

date = {2014-09-01},

journal = {Journal of the American Chemical Society},

volume = {136},

pages = {13102-5},

abstract = {Enzyme-based tags attached to a protein-of-interest (POI) that react with a small molecule, rendering the conjugate fluorescent, are very useful for studying the POI in living cells. These tags are typically based on endogenous enzymes, so protein engineering is required to ensure that the small-molecule probe does not react with the endogenous enzyme in the cell of interest. Here we demonstrate that de novo-designed enzymes can be used as tags to attach to POIs. The inherent bioorthogonality of the de novo-designed enzyme-small-molecule probe reaction circumvents the need for protein engineering, since these enzyme activities are not present in living organisms. Herein, we transform a family of de novo-designed retroaldolases into variable-molecular-weight tags exhibiting fluorescence imaging, reporter, and electrophoresis applications that are regulated by tailored, reactive small-molecule fluorophores.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{623,

title = {Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase.},

author = { Nathalie Preiswerk and Tobias Beck and Jessica D Schulz and Peter Milovn'ik and Clemens Mayer and Justin B Siegel and David Baker and Donald Hilvert},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Preiswerk_PNAS_2014.pdf},

doi = {10.1073/pnas.1401073111},

issn = {1091-6490},

year  = {2014},

date = {2014-06-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {111},

pages = {8013-8},

abstract = {By combining targeted mutagenesis, computational refinement, and directed evolution, a modestly active, computationally designed Diels-Alderase was converted into the most proficient biocatalyst for [4+2] cycloadditions known. The high stereoselectivity and minimal product inhibition of the evolved enzyme enabled preparative scale synthesis of a single product diastereomer. X-ray crystallography of the enzyme-product complex shows that the molecular changes introduced over the course of optimization, including addition of a lid structure, gradually reshaped the pocket for more effective substrate preorganization and transition state stabilization. The good overall agreement between the experimental structure and the original design model with respect to the orientations of both the bound product and the catalytic side chains contrasts with other computationally designed enzymes. Because design accuracy appears to correlate with scaffold rigidity, improved control over backbone conformation will likely be the key to future efforts to design more efficient enzymes for diverse chemical reactions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{540,

title = {Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.},

author = { Sergey Ovchinnikov and Hetunandan Kamisetty and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Ovchinnikov_2014A.pdf},

doi = {10.7554/eLife.02030},

issn = {2050-084X},

year  = {2014},

date = {2014-05-01},

journal = {eLife},

volume = {3},

pages = {e02030},

abstract = {Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. We find that residue pairs identified using a pseudo-likelihood-based method to covary across protein-protein interfaces in the 50S ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex, provided that the number of aligned sequences is greater than the average length of the two proteins. We use this method to make subunit contact predictions for an additional 36 protein complexes with unknown structures, and present models based on these predictions for the tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite efflux system, the pyruvate formate lyase-activating enzyme complex, and the methionine ABC transporter.DOI: http://dx.doi.org/10.7554/eLife.02030.001.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{528,

title = {Design of activated serine-containing catalytic triads with atomic-level accuracy},

author = { Sridharan Rajagopalan and Chu Wang and Kai Yu and Alexandre P Kuzin and Florian Richter and Scott Lew and Aleksandr E Miklos and Megan L Matthews and Jayaraman Seetharaman and Min Su and John F Hunt and Benjamin F Cravatt and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Rajagopalan_nchembio_2014A.pdf},

doi = {10.1038/nchembio.1498},

issn = {1552-4469},

year  = {2014},

date = {2014-04-01},

journal = {Nature chemical biology},

volume = {10},

pages = {386-391},

abstract = {A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{527,

title = {Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus.},

author = { Yupeng Wang and Iram F Khan and Sandrine Boissel and Jordan Jarjour and Joseph Pangallo and Summer Thyme and David Baker and Andrew M Scharenberg and David J Rawlings},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Boissel_NucleicAcids_2014.pdf},

issn = {1362-4962},

year  = {2014},

date = {2014-03-01},

journal = {Nucleic acids research},

abstract = {LAGLIDADG homing endonucleases (LHEs) are compact endonucleases with 20-22 bp recognition sites, and thus are ideal scaffolds for engineering site-specific DNA cleavage enzymes for genome editing applications. Here, we describe a general approach to LHE engineering that combines rational design with directed evolution, using a yeast surface display high-throughput cleavage selection. This approach was employed to alter the binding and cleavage specificity of the I-Anil LHE to recognize a mutation in the mouse Bruton tyrosine kinase (Btk) gene causative for mouse X-linked immunodeficiency (XID)-a model of human X-linked agammaglobulinemia (XLA). The required re-targeting of I-AniI involved progressive resculpting of the DNA contact interface to accommodate nine base differences from the native cleavage sequence. The enzyme emerging from the progressive engineering process was specific for the XID mutant allele versus the wild-type (WT) allele, and exhibited activity equivalent to WT I-AniI in vitro and in cellulo reporter assays. Fusion of the enzyme to a site-specific DNA binding domain of transcription activator-like effector (TALE) resulted in a further enhancement of gene editing efficiency. These results illustrate the potential of LHE enzymes as specific and efficient tools for therapeutic genome engineering.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{526,

title = {Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts.},

author = { Yu Liu and Yun Lei Tan and Xin Zhang and Gira Bhabha and Damian C Ekiert and Joseph C Genereux and Younhee Cho and Yakov Kipnis and Sinisa Bjelic and David Baker and Jeffery W Kelly},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Liu_PNAS_2014.pdf},

issn = {1091-6490},

year  = {2014},

date = {2014-03-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

abstract = {Although much is known about protein folding in buffers, it remains unclear how the cellular protein homeostasis network functions as a system to partition client proteins between folded and functional, soluble and misfolded, and aggregated conformations. Herein, we develop small molecule folding probes that specifically react with the folded and functional fraction of the protein of interest, enabling fluorescence-based quantification of this fraction in cell lysate at a time point of interest. Importantly, these probes minimally perturb a proteintextquoterights folding equilibria within cells during and after cell lysis, because sufficient cellular chaperone/chaperonin holdase activity is created by rapid ATP depletion during cell lysis. The folding probe strategy and the faithful quantification of a particular proteintextquoterights functional fraction are exemplified with retroaldolase, a de novo designed enzyme, and transthyretin, a nonenzyme protein. Our findings challenge the often invoked assumption that the soluble fraction of a client protein is fully folded in the cell. Moreover, our results reveal that the partitioning of destabilized retroaldolase and transthyretin mutants between the aforementioned conformational states is strongly influenced by cytosolic proteostasis network perturbations. Overall, our results suggest that applying a chemical folding probe strategy to other client proteins offers opportunities to reveal how the proteostasis network functions as a system to regulate the folding and function of individual client proteins in vivo.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{520,

title = {Computationally designed libraries for rapid enzyme stabilization.},

author = { Hein J Wijma and Robert J Floor and Peter A Jekel and David Baker and Siewert J Marrink and Dick B Janssen},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Wijma_PEDS_2014.pdf},

doi = {10.1093/protein/gzt061},

issn = {1741-0134},

year  = {2014},

date = {2014-02-01},

journal = {Protein engineering, design & selection : PEDS},

volume = {27},

pages = {49-58},

abstract = {The ability to engineer enzymes and other proteins to any desired stability would have wide-ranging applications. Here, we demonstrate that computational design of a library with chemically diverse stabilizing mutations allows the engineering of drastically stabilized and fully functional variants of the mesostable enzyme limonene epoxide hydrolase. First, point mutations were selected if they significantly improved the predicted free energy of protein folding. Disulfide bonds were designed using sampling of backbone conformational space, which tripled the number of experimentally stabilizing disulfide bridges. Next, orthogonal in silico screening steps were used to remove chemically unreasonable mutations and mutations that are predicted to increase protein flexibility. The resulting library of 64 variants was experimentally screened, which revealed 21 (pairs of) stabilizing mutations located both in relatively rigid and in flexible areas of the enzyme. Finally, combining 10-12 of these confirmed mutations resulted in multi-site mutants with an increase in apparent melting temperature from 50 to 85textdegreeC, enhanced catalytic activity, preserved regioselectivity and a >250-fold longer half-life. The developed Framework for Rapid Enzyme Stabilization by Computational libraries (FRESCO) requires far less screening than conventional directed evolution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{510,

title = {Amyloid β peptide cleavage by kallikrein 7 attenuates fibril growth and rescues neurons from Aβ-mediated toxicity in vitro.},

author = { Tyler D Shropshire and Jack Reifert and Sridharan Rajagopalan and David Baker and Stuart C Feinstein and Patrick S Daugherty},

doi = {10.1515/hsz-2013-0230},

issn = {1437-4315},

year  = {2014},

date = {2014-01-01},

journal = {Biological chemistry},

volume = {395},

pages = {109-18},

abstract = {Abstract The gradual accumulation and assembly of β-amyloid (Aβ) peptide into neuritic plaques is a major pathological hallmark of Alzheimer disease (AD). Proteolytic degradation of Aβ is an important clearance mechanism under normal circumstances, and it has been found to be compromised in those with AD. Here, the extended substrate specificity and Aβ-degrading capacity of kallikrein 7 (KLK7), a serine protease with a unique chymotrypsin-like specificity, was characterized. Preferred peptide substrates of KLK7 identified using a bacterial display substrate library were found to exhibit a consensus motif of RXΦ(Y/F)textdownarrow(Y/F)textdownarrow(S/A/G/T) or RXΦ(Y/F)textdownarrow(S/T/A) (Φ=hydrophobic), which is remarkably similar to the hydrophobic core motif of Aβ (K16L17V18F19F20 A21) that is largely responsible for aggregation propensity. KLK7 was found to cleave after both Phe residues within the core of Aβ42 in vitro, thereby inhibiting Aβ fibril formation and promoting the degradation of preformed fibrils. Finally, the treatment of Aβ oligomer preparations with KLK7, but not inactive pro-KLK7, significantly reduced Aβ42-mediated toxicity to rat hippocampal neurons to the same extent as the known Aβ-degrading protease insulin-degrading enzyme (IDE). Taken together, these results indicate that KLK7 possesses an Aβ-degrading capacity that can ameliorate the toxic effects of the aggregated peptide in vitro.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{525,

title = {Redesigning the Specificity of Protein-DNA Interactions with Rosetta.},

author = { Summer Thyme and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Thyme_2014.pdf},

doi = {10.1007/978-1-62703-968-0_17},

issn = {1940-6029},

year  = {2014},

date = {2014-01-01},

journal = {Methods in molecular biology (Clifton, N.J.)},

volume = {1123},

pages = {265-82},

abstract = {Building protein tools that can selectively bind or cleave specific DNA sequences requires efficient technologies for modifying protein-DNA interactions. Computational design is one method for accomplishing this goal. In this chapter, we present the current state of protein-DNA interface design with the Rosetta macromolecular modeling program. The LAGLIDADG endonuclease family of DNA-cleaving enzymes, under study as potential gene therapy reagents, has been the main testing ground for these in silico protocols. At this time, the computational methods are most useful for designing endonuclease variants that can accommodate small numbers of target site substitutions. Attempts to engineer for more extensive interface changes will likely benefit from an approach that uses the computational design results in conjunction with a high-throughput directed evolution or screening procedure. The family of enzymes presents an engineering challenge because their interfaces are highly integrated and there is significant coordination between the binding and catalysis events. Future developments in the computational algorithms depend on experimental feedback to improve understanding and modeling of these complex enzymatic features. This chapter presents both the basic method of design that has been successfully used to modulate specificity and more advanced procedures that incorporate DNA flexibility and other properties that are likely necessary for reliable modeling of more extensive target site changes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{497,

title = {Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries},

author = { Izhack Cherny and Per Greisen and Yacov Ashani and Sagar D Khare and Gustav Oberdorfer and Haim Leader and David Baker and Dan S Tawfik},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Cherny_cb4004892_13W.pdf},

doi = {10.1021/cb4004892},

issn = {1554-8937},

year  = {2013},

date = {2013-11-01},

journal = {ACS chemical biology},

volume = {8},

pages = {2394-403},

abstract = {VX and its Russian (RVX) and Chinese (CVX) analogues rapidly inactivate acetylcholinesterase and are the most toxic stockpile nerve agents. These organophosphates have a thiol leaving group with a choline-like moiety and are hydrolyzed very slowly by natural enzymes. We used an integrated computational and experimental approach to increase Brevundimonas diminuta phosphotriesterasetextquoterights (PTE) detoxification rate of V-agents by 5000-fold. Computational models were built of the complex between PTE and V-agents. On the basis of these models, the active site was redesigned to be complementary in shape to VX and RVX and to include favorable electrostatic interactions with their choline-like leaving group. Small libraries based on designed sequences were constructed. The libraries were screened by a direct assay for V-agent detoxification, as our initial studies showed that colorimetric surrogates fail to report the detoxification rates of the actual agents. The experimental results were fed back to improve the computational models. Overall, five rounds of iterating between experiment and model refinement led to variants that hydrolyze the toxic SP isomers of all three V-agents with kcat/KM values of up to 5 texttimes 10(6) M(-1) min(-1) and also efficiently detoxify G-agents. These new catalysts provide the basis for broad spectrum nerve agent detoxification.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{495,

title = {Automating human intuition for protein design},

author = { Lucas G Niv'on and Sinisa Bjelic and Chris King and David Baker},

url = {https://www.bakerlab.org/wp-content/uploads/2015/12/Nivón_prot24463_13M.pdf},

doi = {10.1002/prot.24463},

issn = {1097-0134},

year  = {2013},

date = {2013-10-01},

journal = {Proteins},

abstract = {In the design of new enzymes and binding proteins, human intuition is often used to modify computationally designed amino acid sequences prior to experimental characterization. The manual sequence changes involve both reversions of amino acid mutations back to the identity present in the parent scaffold and the introduction of residues making additional interactions with the binding partner or backing up first shell interactions. Automation of this manual sequence refinement process would allow more systematic evaluation and considerably reduce the amount of human designer effort involved. Here we introduce a benchmark for evaluating the ability of automated methods to recapitulate the sequence changes made to computer-generated models by human designers, and use it to assess alternative computational methods. We find the best performance for a greedy one-position-at-a-time optimization protocol that utilizes metrics (such as shape complementarity) and local refinement methods too computationally expensive for global Monte Carlo (MC) sequence optimization. This protocol should be broadly useful for improving the stability and function of designed binding proteins. Proteins 2013. textcopyright 2013 Wiley Periodicals, Inc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{511,

title = {Computational design of a protein-based enzyme inhibitor.},

author = { Erik Procko and Rickard Hedman and Keith Hamilton and Jayaraman Seetharaman and Sarel J Fleishman and Min Su and James Aramini and Gregory Kornhaber and John F Hunt and Liang Tong and Gaetano T Montelione and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Procko13.pdf},

doi = {10.1016/j.jmb.2013.06.035},

issn = {1089-8638},

year  = {2013},

date = {2013-09-01},

journal = {Journal of molecular biology},

volume = {425},

pages = {3563-75},

abstract = {While there has been considerable progress in designing protein-protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{509,

title = {Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy.},

author = { Jeremy H Mills and Sagar D Khare and Jill M Bolduc and Farhad Forouhar and Vikram Khipple Mulligan and Scott Lew and Jayaraman Seetharaman and Liang Tong and Barry L Stoddard and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Mills13.pdf},

doi = {10.1021/ja403503m},

issn = {1520-5126},

year  = {2013},

date = {2013-09-01},

journal = {Journal of the American Chemical Society},

volume = {135},

pages = {13393-9},

abstract = {Genetically encoded unnatural amino acids could facilitate the design of proteins and enzymes of novel function, but correctly specifying sites of incorporation and the identities and orientations of surrounding residues represents a formidable challenge. Computational design methods have been used to identify optimal locations for functional sites in proteins and design the surrounding residues but have not incorporated unnatural amino acids in this process. We extended the Rosetta design methodology to design metalloproteins in which the amino acid (2,2textquoteright-bipyridin-5yl)alanine (Bpy-Ala) is a primary ligand of a bound metal ion. Following initial results that indicated the importance of buttressing the Bpy-Ala amino acid, we designed a buried metal binding site with octahedral coordination geometry consisting of Bpy-Ala, two protein-based metal ligands, and two metal-bound water molecules. Experimental characterization revealed a Bpy-Ala-mediated metalloprotein with the ability to bind divalent cations including Co(2+), Zn(2+), Fe(2+), and Ni(2+), with a Kd for Zn(2+) of ~40 pM. X-ray crystal structures of the designed protein bound to Co(2+) and Ni(2+) have RMSDs to the design model of 0.9 and 1.0 r A respectively over all atoms in the binding site.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{504,

title = {Evolution of a designed retro-aldolase leads to complete active site remodeling.},

author = { Lars Giger and Sami Caner and Richard Obexer and Peter Kast and David Baker and Nenad Ban and Donald Hilvert},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Giger_nchembio_2013.pdf},

doi = {10.1038/nchembio.1276},

issn = {1552-4469},

year  = {2013},

date = {2013-08-01},

journal = {Nature chemical biology},

volume = {9},

pages = {494-8},

abstract = {Evolutionary advances are often fueled by unanticipated innovation. Directed evolution of a computationally designed enzyme suggests that pronounced molecular changes can also drive the optimization of primitive protein active sites. The specific activity of an artificial retro-aldolase was boosted >4,400-fold by random mutagenesis and screening, affording catalytic efficiencies approaching those of natural enzymes. However, structural and mechanistic studies reveal that the engineered catalytic apparatus, consisting of a reactive lysine and an ordered water molecule, was unexpectedly abandoned in favor of a new lysine residue in a substrate-binding pocket created during the optimization process. Structures of the initial in silico design, a mechanistically promiscuous intermediate and one of the most evolved variants highlight the importance of loop mobility and supporting functional groups in the emergence of the new catalytic center. Such internal competition between alternative reactive sites may have characterized the early evolution of many natural enzymes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{472,

title = {Computational enzyme design},

author = { Gert Kiss and Nihan Celebi-"Olc c"um and Rocco Moretti and David Baker and K N Houk},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Kiss_AngewChemIntEd_2013.pdf},

doi = {10.1002/anie.201204077},

issn = {1521-3773},

year  = {2013},

date = {2013-05-01},

journal = {Angewandte Chemie (International ed. in English)},

volume = {52},

pages = {5700-25},

abstract = {Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{503,

title = {Expanding the product profile of a microbial alkane biosynthetic pathway.},

author = { Matthew Harger and Lei Zheng and Austin Moon and Casey Ager and Ju Hye An and Chris Choe and Yi-Ling Lai and Benjamin Mo and David Zong and Matthew D Smith and Robert G Egbert and Jeremy H Mills and David Baker and Ingrid Swanson Pultz and Justin B Siegel},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Harger_ACSSynthBiol_2013.pdf},

doi = {10.1021/sb300061x},

issn = {2161-5063},

year  = {2013},

date = {2013-01-01},

journal = {ACS synthetic biology},

volume = {2},

pages = {59-62},

abstract = {Microbially produced alkanes are a new class of biofuels that closely match the chemical composition of petroleum-based fuels. Alkanes can be generated from the fatty acid biosynthetic pathway by the reduction of acyl-ACPs followed by decarbonylation of the resulting aldehydes. A current limitation of this pathway is the restricted product profile, which consists of n-alkanes of 13, 15, and 17 carbons in length. To expand the product profile, we incorporated a new part, FabH2 from Bacillus subtilis , an enzyme known to have a broader specificity profile for fatty acid initiation than the native FabH of Escherichia coli . When provided with the appropriate substrate, the addition of FabH2 resulted in an altered alkane product profile in which significant levels of n-alkanes of 14 and 16 carbons in length are produced. The production of even chain length alkanes represents initial steps toward the expansion of this recently discovered microbial alkane production pathway to synthesize complex fuels. This work was conceived and performed as part of the 2011 University of Washington international Genetically Engineered Machines (iGEM) project.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{470,

title = {A Pareto-optimal refinement method for protein design scaffolds},

author = { Lucas Gregorio Niv'on and Rocco Moretti and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Nivon_pone0059004_13U.pdf},

doi = {10.1371/journal.pone.0059004},

issn = {1932-6203},

year  = {2013},

date = {2013-00-01},

journal = {PloS one},

volume = {8},

pages = {e59004},

abstract = {Computational design of protein function involves a search for amino acids with the lowest energy subject to a set of constraints specifying function. In many cases a set of natural protein backbone structures, or "scaffolds", are searched to find regions where functional sites (an enzyme active site, ligand binding pocket, protein-protein interaction region, etc.) can be placed, and the identities of the surrounding amino acids are optimized to satisfy functional constraints. Input native protein structures almost invariably have regions that score very poorly with the design force field, and any design based on these unmodified structures may result in mutations away from the native sequence solely as a result of the energetic strain. Because the input structure is already a stable protein, it is desirable to keep the total number of mutations to a minimum and to avoid mutations resulting from poorly-scoring input structures. Here we describe a protocol using cycles of minimization with combined backbone/sidechain restraints that is Pareto-optimal with respect to RMSD to the native structure and energetic strain reduction. The protocol should be broadly useful in the preparation of scaffold libraries for functional site design.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{479,

title = {Computational Design of an α-gliadin Peptidase},

author = { Sydney R Gordon and Elizabeth J Stanley and Sarah Wolf and Angus Toland and Sean J Wu and Daniel Hadidi and Jeremy H Mills and David Baker and Ingrid Swanson Pultz and Justin B Siegel},

url = {https://www.bakerlab.org/wp-content/uploads/2015/12/Gordon12E.pdf

http://www.ncbi.nlm.nih.gov/pubmed/23153249},

doi = {10.1021/ja3094795},

issn = {1520-5126},

year  = {2012},

date = {2012-12-01},

journal = {Journal of the American Chemical Society},

volume = {134},

pages = {20513-20},

abstract = {The ability to rationally modify enzymes to perform novel chemical transformations is essential for the rapid production of next-generation protein therapeutics. Here we describe the use of chemical principles to identify a naturally occurring acid-active peptidase, and the subsequent use of computational protein design tools to reengineer its specificity toward immunogenic elements found in gluten that are the proposed cause of celiac disease. The engineered enzyme exhibits a k(cat)/K(M) of 568 M(-1) s(-1), representing a 116-fold greater proteolytic activity for a model gluten tetrapeptide than the native template enzyme, as well as an over 800-fold switch in substrate specificity toward immunogenic portions of gluten peptides. The computationally engineered enzyme is resistant to proteolysis by digestive proteases and degrades over 95% of an immunogenic peptide implicated in celiac disease in under an hour. Thus, through identification of a natural enzyme with the pre-existing qualities relevant to an ultimate goal and redefinition of its substrate specificity using computational modeling, we were able to generate an enzyme with potential as a therapeutic for celiac disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{452,

title = {Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.},

author = { Florian Richter and Rebecca Blomberg and Sagar D Khare and Gert Kiss and Alexandre P Kuzin and Adam J T Smith and Jasmine Gallaher and Zbigniew Pianowski and Roger C Helgeson and Alexej Grjasnow and Rong Xiao and Jayaraman Seetharaman and Min Su and Sergey Vorobiev and Scott Lew and Farhad Forouhar and Gregory J Kornhaber and John F Hunt and Gaetano T Montelione and Liang Tong and K N Houk and Donald Hilvert and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Richter_JACS_2012.pdf},

doi = {10.1021/ja3037367},

issn = {1520-5126},

year  = {2012},

date = {2012-10-01},

journal = {Journal of the American Chemical Society},

volume = {134},

pages = {16197-206},

abstract = {Nucleophilic catalysis is a general strategy for accelerating ester and amide hydrolysis. In natural active sites, nucleophilic elements such as catalytic dyads and triads are usually paired with oxyanion holes for substrate activation, but it is difficult to parse out the independent contributions of these elements or to understand how they emerged in the course of evolution. Here we explore the minimal requirements for esterase activity by computationally designing artificial catalysts using catalytic dyads and oxyanion holes. We found much higher success rates using designed oxyanion holes formed by backbone NH groups rather than by side chains or bridging water molecules and obtained four active designs in different scaffolds by combining this motif with a Cys-His dyad. Following active site optimization, the most active of the variants exhibited a catalytic efficiency (k(cat)/K(M)) of 400 M(-1) s(-1) for the cleavage of a p-nitrophenyl ester. Kinetic experiments indicate that the active site cysteines are rapidly acylated as programmed by design, but the subsequent slow hydrolysis of the acyl-enzyme intermediate limits overall catalytic efficiency. Moreover, the Cys-His dyads are not properly formed in crystal structures of the designed enzymes. These results highlight the challenges that computational design must overcome to achieve high levels of activity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{455,

title = {Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases.},

author = { Sarah Baxter and Abigail R Lambert and Ryan Kuhar and Jordan Jarjour and Nadia Kulshina and Fabio Parmeggiani and Patrick Danaher and Jacob Gano and David Baker and Barry L Stoddard and Andrew M Scharenberg},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/Baxter_NuclAcRes_2012.pdf},

issn = {1362-4962},

year  = {2012},

date = {2012-09-01},

journal = {Nucleic acids research},

volume = {40},

pages = {7985-8000},

abstract = {Although engineered LAGLIDADG homing endonucleases (LHEs) are finding increasing applications in biotechnology, their generation remains a challenging, industrial-scale process. As new single-chain LAGLIDADG nuclease scaffolds are identified, however, an alternative paradigm is emerging: identification of an LHE scaffold whose native cleavage site is a close match to a desired target sequence, followed by small-scale engineering to modestly refine recognition specificity. The application of this paradigm could be accelerated if methods were available for fusing N- and C-terminal domains from newly identified LHEs into chimeric enzymes with hybrid cleavage sites. Here we have analyzed the structural requirements for fusion of domains extracted from six single-chain I-OnuI family LHEs, spanning 40-70% amino acid identity. Our analyses demonstrate that both the LAGLIDADG helical interface residues and the linker peptide composition have important effects on the stability and activity of chimeric enzymes. Using a simple domain fusion method in which linker peptide residues predicted to contact their respective domains are retained, and in which limited variation is introduced into the LAGLIDADG helix and nearby interface residues, catalytically active enzymes were recoverable for ~70% of domain chimeras. This method will be useful for creating large numbers of chimeric LHEs for genome engineering applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{603,

title = {Comparison of designed and randomly generated catalysts for simple chemical reactions},

author = { Yakov Kipnis and David Baker},

url = {http://www.bakerlab.org/wp-content/uploads/2015/12/comparisonofdesigned_Baker2012.pdf},

doi = {10.1002/pro.2125},

issn = {1469-896X},

year  = {2012},

date = {2012-09-01},

journal = {Protein Science : A Publication of the Protein Society},

volume = {21},

pages = {1388-95},

abstract = {There has been recent success in designing enzymes for simple chemical reactions using a two-step protocol. In the first step, a geometric matching algorithm is used to identify naturally occurring protein scaffolds at which predefined idealized active sites can be realized. In the second step, the residues surrounding the transition state model are optimized to increase transition state binding affinity and to bolster the primary catalytic side chains. To improve the design methodology, we investigated how the set of solutions identified by the design calculations relate to the overall set of solutions for two different chemical reactions. Using a TIM barrel scaffold in which catalytically active Kemp eliminase and retroaldolase designs were obtained previously, we carried out activity screens of random libraries made to be compositionally similar to active designs. A small number of active catalysts were found in screens of 10textthreesuperior variants for each of the two reactions, which differ from the computational designs in that they reuse charged residues already present in the native scaffold. The results suggest that computational design considerably increases the frequency of catalyst generation for active sites involving newly introduced catalytic residues, highlighting the importance of interaction cooperativity in enzyme active sites.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}