@article{Rankovic2025,

title = {Computational design of bifaceted protein nanomaterials},

author = {Sanela Rankovic and Kenneth D. Carr and Justin Decarreau and Rebecca Skotheim and Ryan D. Kibler and Sebastian Ols and Sangmin Lee and Jung-Ho Chun and Marti R. Tooley and Justas Dauparas and Helen E. Eisenach and Matthias Glögl and Connor Weidle and Andrew J. Borst and David Baker and Neil P. King},

url = {https://www.nature.com/articles/s41563-025-02295-7, Nature Materials [Open Access]},

doi = {10.1038/s41563-025-02295-7},

year  = {2025},

date = {2025-07-31},

urldate = {2025-07-31},

journal = {Nature Materials},

publisher = {Springer Science and Business Media LLC},

abstract = {Advances in computational methods have led to considerable progress in the design of protein nanomaterials. However, nearly all nanoparticles designed so far exhibit strict point group symmetry, which limits structural diversity and precludes anisotropic functionalization. Here we describe a computational strategy for designing multicomponent bifaceted protein nanomaterials with two distinctly addressable sides. The method centres on docking pseudosymmetric hetero-oligomeric building blocks in architectures with dihedral symmetry and designing an asymmetric protein–protein interface between them. We obtain an initial 30-subunit assembly with pseudo-D5 symmetry and generate variants in which we alter the size and morphology of the bifaceted nanoparticles by designing extensions to one of the subunits. Functionalization of the two nanoparticle faces with protein minibinders enables the specific colocalization of two populations of polystyrene microparticles coated with the target protein receptors. The ability to accurately design anisotropic protein nanoparticles could be broadly useful in applications requiring the colocalization of distinct target moieties.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Liu2025,

title = {Diffusing protein binders to intrinsically disordered proteins},

author = {Caixuan Liu and Kejia Wu and Hojun Choi and Hannah L. Han and Xueli Zhang and Joseph L. Watson and Green Ahn and Jason Z. Zhang and Sara Shijo and Lydia L. Good and Charlotte M. Fischer and Asim K. Bera and Alex Kang and Evans Brackenbrough and Brian Coventry and Derrick R. Hick and Seema Qamar and Xinting Li and Justin Decarreau and Stacey R. Gerben and Wei Yang and Inna Goreshnik and Dionne Vafeados and Xinru Wang and Mila Lamb and Analisa Murray and Sebastian Kenny and Magnus S. Bauer and Andrew N. Hoofnagle and Ping Zhu and Tuomas P. J. Knowles and David Baker},

url = {https://www.nature.com/articles/s41586-025-09248-9, Nature [Open Access]

https://www.ipd.uw.edu/wp-content/uploads/2025/08/s41586-025-09248-9-compressed.pdf, PDF},

doi = {10.1038/s41586-025-09248-9},

year  = {2025},

date = {2025-07-30},

urldate = {2025-07-30},

journal = {Nature},

publisher = {Springer Science and Business Media LLC},

abstract = {Proteins that bind to intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) with high affinity and specificity could be useful for therapeutic and diagnostic applications. However, a general methodology for targeting IDPs or IDRs has yet to be developed. Here we show that starting only from the target sequence of the input, and freely sampling both target and binding protein conformations, RFdiffusion can generate binders to IDPs and IDRs in a wide range of conformations. We used this approach to generate binders to the IDPs amylin, C-peptide, VP48 and BRCA1_ARATH in diverse conformations with a dissociation constant (Kd) ranging from 3 to 100 nM. For the IDRs G3BP1, common cytokine receptor γ-chain (IL-2RG) and prion protein, we diffused binders to β-strand conformations of the targets, obtaining Kd between 10 and 100 nM. Fluorescence imaging experiments show that the binders bind to their respective targets in cells. The G3BP1 binder disrupts stress granule formation in cells, and the amylin binder inhibits amyloid fibril formation and dissociates existing fibres, enables targeting of both monomeric and fibrillar amylin to lysosomes, and increases the sensitivity of mass spectrometry-based amylin detection. Our approach should be useful for creating binders to flexible IDPs or IDRs spanning a wide range of intrinsic conformational preferences.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Liu2025b,

title = {Design of high-specificity binders for peptide–MHC-I complexes},

author = {Bingxu Liu and Nathan F. Greenwood and Julia E. Bonzanini and Amir Motmaen and Jeremy Meyerberg and Tao Dao and Xinyu Xiang and Russell Ault and Jazmin Sharp and Chunyu Wang and Gian Marco Visani and Dionne K. Vafeados and Nicole Roullier and Armita Nourmohammad and David A. Scheinberg and K. Christopher Garcia and David Baker},

url = {https://www.science.org/doi/10.1126/science.adv0185, Science

https://www.bakerlab.org/wp-content/uploads/2025/08/science.adv0185.pdf, PDF},

doi = {10.1126/science.adv0185},

year  = {2025},

date = {2025-07-24},

urldate = {2025-07-24},

journal = {Science},

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

abstract = {Class I major histocompatibility complex (MHC-I) molecules present peptides derived from intracellular antigens on the cell surface for immune surveillance. Proteins that recognize peptide–MHC-I (pMHCI) complexes with specificity for diseased cells could have considerable therapeutic utility. Specificity requires recognition of outward-facing amino acid residues within the disease-associated peptide as well as avoidance of extensive contacts with ubiquitously expressed MHC. We used RFdiffusion to design pMHCI-binding proteins that make extensive contacts with the peptide and identified specific binders for 11 target pMHCs starting from either experimental or predicted pMHCI structures. Upon incorporation into chimeric antigen receptors, designs for eight targets conferred peptide-specific T cell activation. Our approach should have broad utility for both protein- and cell-based pMHCI targeting.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wu2025,

title = {Design of intrinsically disordered region binding proteins},

author = {Kejia Wu and Hanlun Jiang and Derrick R. Hicks and Caixuan Liu and Edin Muratspahić and Theresa A. Ramelot and Yuexuan Liu and Kerrie McNally and Sebastian Kenny and Andrei Mihut and Amit Gaur and Brian Coventry and Wei Chen and Asim K. Bera and Alex Kang and Stacey Gerben and Mila Ya-Lan Lamb and Analisa Murray and Xinting Li and Madison A. Kennedy and Wei Yang and Zihao Song and Gudrun Schober and Stuart M. Brierley and John O’Neill and Michael H. Gelb and Gaetano T. Montelione and Emmanuel Derivery and David Baker},

url = {https://www.science.org/doi/10.1126/science.adr8063, Science

https://www.bakerlab.org/wp-content/uploads/2025/07/science.adr8063.pdf, PDF},

doi = {10.1126/science.adr8063},

year  = {2025},

date = {2025-07-17},

urldate = {2025-07-17},

journal = {Science},

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

abstract = {Intrinsically disordered proteins and peptides play key roles in biology, but a lack of defined structures and high variability in sequence and conformational preferences have made targeting such systems challenging. We describe a general approach for designing proteins that bind intrinsically disordered protein regions in diverse extended conformations with side chains fitting into complementary binding pockets. We used the approach to design binders for 39 highly diverse unstructured targets, including polar targets, and obtained designs with 100-picomolar to 100-nanomolar affinities in 34 cases, testing ~22 designs per target. The designs function in cells and as detection reagents and are specific for their intended targets in all-by-all binding experiments. Our approach is a major step toward a general solution to the intrinsically disordered protein and peptide recognition problem.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40011465,

title = {Design of high-affinity binders to immune modulating receptors for cancer immunotherapy},

author = {Wei Yang and Derrick R Hicks and Agnidipta Ghosh and Tristin A Schwartze and Brian Conventry and Inna Goreshnik and Aza Allen and Samer F Halabiya and Chan Johng Kim and Cynthia S Hinck and David S Lee and Asim K Bera and Zhe Li and Yujia Wang and Thomas Schlichthaerle and Longxing Cao and Buwei Huang and Sarah Garrett and Stacey R Gerben and Stephen Rettie and Piper Heine and Analisa Murray and Natasha Edman and Lauren Carter and Lance Stewart and Steven C Almo and Andrew P Hinck and David Baker},

url = {https://www.nature.com/articles/s41467-025-57192-z, Nature Communications

https://www.bakerlab.org/wp-content/uploads/2025/03/s41467-025-57192-z.pdf, PDF},

doi = {10.1038/s41467-025-57192-z},

year  = {2025},

date = {2025-02-26},

urldate = {2025-02-01},

journal = {Nature Communications},

abstract = {Immune receptors have emerged as critical therapeutic targets for cancer immunotherapy. Designed protein binders can have high affinity, modularity, and stability and hence could be attractive components of protein therapeutics directed against these receptors, but traditional Rosetta based protein binder methods using small globular scaffolds have difficulty achieving high affinity on convex targets. Here we describe the development of helical concave scaffolds tailored to the convex target sites typically involved in immune receptor interactions. We employed these scaffolds to design proteins that bind to TGFβRII, CTLA-4, and PD-L1, achieving low nanomolar to picomolar affinities and potent biological activity following experimental optimization. Co-crystal structures of the TGFβRII and CTLA-4 binders in complex with their respective receptors closely match the design models. These designs should have considerable utility for downstream therapeutic applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Glögl2024,

title = {Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists},

author = {Matthias Glögl and Aditya Krishnakumar and Robert J. Ragotte and Inna Goreshnik and Brian Coventry and Asim K. Bera and Alex Kang and Emily Joyce and Green Ahn and Buwei Huang and Wei Yang and Wei Chen and Mariana Garcia Sanchez and Brian Koepnick and David Baker},

url = {https://www.science.org/doi/abs/10.1126/science.adp1779, Science

https://www.bakerlab.org/wp-content/uploads/2024/12/Glogl-et-al-Science-Diffusion-of-TNF-binders.pdf, PDF},

doi = {10.1126/science.adp1779},

year  = {2024},

date = {2024-12-06},

urldate = {2024-12-06},

journal = {Science},

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

abstract = {Despite progress in designing protein-binding proteins, the shape matching of designs to targets is lower than in many native protein complexes, and design efforts have failed for the tumor necrosis factor receptor 1 (TNFR1) and other protein targets with relatively flat and polar surfaces. We hypothesized that free diffusion from random noise could generate shape-matched binders for challenging targets and tested this approach on TNFR1. We obtain designs with low picomolar affinity whose specificity can be completely switched to other family members using partial diffusion. Designs function as antagonists or as superagonists when presented at higher valency for OX40 and 4-1BB. The ability to design high-affinity and high-specificity antagonists and agonists for pharmacologically important targets in silico presages a coming era in protein design in which binders are made by computation rather than immunization or random screening approaches.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Huang2024b,

title = {Designed endocytosis-inducing proteins degrade targets and amplify signals},

author = {Buwei Huang and Mohamad Abedi and Green Ahn and Brian Coventry and Isaac Sappington and Cong Tang and Rong Wang and Thomas Schlichthaerle and Jason Z. Zhang and Yujia Wang and Inna Goreshnik and Ching Wen Chiu and Adam Chazin-Gray and Sidney Chan and Stacey Gerben and Analisa Murray and Shunzhi Wang and Jason O’Neill and Li Yi and Ronald Yeh and Ayesha Misquith and Anitra Wolf and Luke M. Tomasovic and Dan I. Piraner and Maria J. Duran Gonzalez and Nathaniel R. Bennett and Preetham Venkatesh and Maggie Ahlrichs and Craig Dobbins and Wei Yang and Xinru Wang and Danny D. Sahtoe and Dionne Vafeados and Rubul Mout and Shirin Shivaei and Longxing Cao and Lauren Carter and Lance Stewart and Jamie B. Spangler and Kole T. Roybal and Per Jr Greisen and Xiaochun Li and Gonçalo J. L. Bernardes and Carolyn R. Bertozzi and David Baker},

url = {https://www.nature.com/articles/s41586-024-07948-2, Nature [Open Access] 

https://www.bakerlab.org/wp-content/uploads/2025/03/Huang-et-al-EndoTags-Nature-25Sep2024.pdf, PDF},

doi = {10.1038/s41586-024-07948-2},

year  = {2024},

date = {2024-09-25},

urldate = {2024-09-25},

journal = {Nature},

publisher = {Springer Science and Business Media LLC},

abstract = {Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by endogenous ligands. Therapeutic approaches such as lysosome-targeting chimaeras1,2 (LYTACs) and cytokine receptor-targeting chimeras3 (KineTACs) have used this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. Although powerful, these approaches can be limited by competition with native ligands and requirements for chemical modification that limit genetic encodability and can complicate manufacturing, and, more generally, there may be no native ligands that stimulate endocytosis through a given receptor. Here we describe computational design approaches for endocytosis-triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for insulin-like growth factor 2 receptor (IGF2R) and asialoglycoprotein receptor (ASGPR), sortilin and transferrin receptors, and show that fusing these tags to soluble or transmembrane target protein binders leads to lysosomal trafficking and target degradation. As these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. EndoTag fusion to a PD-L1 antibody considerably increases efficacy in a mouse tumour model compared to antibody alone. The modularity and genetic encodability of EndoTags enables AND gate control for higher-specificity targeted degradation, and the localized secretion of degraders from engineered cells. By promoting endocytosis, EndoTag fusion increases signalling through an engineered ligand–receptor system by nearly 100-fold. EndoTags have considerable therapeutic potential as targeted degradation inducers, signalling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody–drug and antibody–RNA conjugates.



},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Huang2024,

title = {De novo design of miniprotein antagonists of cytokine storm inducers},

author = {Buwei Huang and Brian Coventry and Marta T. Borowska and Dimitrios C. Arhontoulis and Marc Exposit and Mohamad Abedi and Kevin M. Jude and Samer F. Halabiya and Aza Allen and Cami Cordray and Inna Goreshnik and Maggie Ahlrichs and Sidney Chan and Hillary Tunggal and Michelle DeWitt and Nathaniel Hyams and Lauren Carter and Lance Stewart and Deborah H. Fuller and Ying Mei and K. Christopher Garcia and David Baker},

url = {https://www.nature.com/articles/s41467-024-50919-4, Nature Communications [Open Access]},

doi = {10.1038/s41467-024-50919-4},

year  = {2024},

date = {2024-08-16},

urldate = {2024-08-16},

journal = {Nature Communications},

publisher = {Springer Science and Business Media LLC},

abstract = {Cytokine release syndrome (CRS), commonly known as cytokine storm, is an acute systemic inflammatory response that is a significant global health threat. Interleukin-6 (IL-6) and interleukin-1 (IL-1) are key pro-inflammatory cytokines involved in CRS and are hence critical therapeutic targets. Current antagonists, such as tocilizumab and anakinra, target IL-6R/IL-1R but have limitations due to their long half-life and systemic anti-inflammatory effects, making them less suitable for acute or localized treatments. Here we present the de novo design of small protein antagonists that prevent IL-1 and IL-6 from interacting with their receptors to activate signaling. The designed proteins bind to the IL-6R, GP130 (an IL-6 co-receptor), and IL-1R1 receptor subunits with binding affinities in the picomolar to low-nanomolar range. X-ray crystallography studies reveal that the structures of these antagonists closely match their computational design models. In a human cardiac organoid disease model, the IL-1R antagonists demonstrated protective effects against inflammation and cardiac damage induced by IL-1β. These minibinders show promise for administration via subcutaneous injection or intranasal/inhaled routes to mitigate acute cytokine storm effects.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sun2024,

title = {Accurate de novo design of heterochiral protein–protein interactions},

author = {Ke Sun and Sicong Li and Bowen Zheng and Yanlei Zhu and Tongyue Wang and Mingfu Liang and Yue Yao and Kairan Zhang and Jizhong Zhang and Hongyong Li and Dongyang Han and Jishen Zheng and Brian Coventry and Longxing Cao and David Baker and Lei Liu and Peilong Lu},

url = {https://www.nature.com/articles/s41422-024-01014-2, Cell Research [Open Access]},

doi = {10.1038/s41422-024-01014-2},

year  = {2024},

date = {2024-08-14},

urldate = {2024-08-14},

journal = {Cell Research},

publisher = {Springer Science and Business Media LLC},

abstract = {Abiotic d-proteins that selectively bind to natural l-proteins have gained significant biotechnological interest. However, the underlying structural principles governing such heterochiral protein–protein interactions remain largely unknown. In this study, we present the de novo design of d-proteins consisting of 50–65 residues, aiming to target specific surface regions of l-proteins or l-peptides. Our designer d-protein binders exhibit nanomolar affinity toward an artificial l-peptide, as well as two naturally occurring proteins of therapeutic significance: the D5 domain of human tropomyosin receptor kinase A (TrkA) and human interleukin-6 (IL-6). Notably, these d-protein binders demonstrate high enantiomeric specificity and target specificity. In cell-based experiments, designer d-protein binders effectively inhibited the downstream signaling of TrkA and IL-6 with high potency. Moreover, these binders exhibited remarkable thermal stability and resistance to protease degradation. Crystal structure of the designed heterochiral d-protein–l-peptide complex, obtained at a resolution of 2.0 Å, closely resembled the design model, indicating that the computational method employed is highly accurate. Furthermore, the crystal structure provides valuable information regarding the interactions between helical l-peptides and d-proteins, particularly elucidating a novel mode of heterochiral helix–helix interactions. Leveraging the design of d-proteins specifically targeting l-peptides or l-proteins opens up avenues for systematic exploration of the mirror-image protein universe, paving the way for a diverse range of applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{An2024,

title = {Binding and sensing diverse small molecules using shape-complementary pseudocycles},

author = {Linna An and Meerit Said and Long Tran and Sagardip Majumder and Inna Goreshnik and Gyu Rie Lee and David Juergens and Justas Dauparas and Ivan Anishchenko and Brian Coventry and Asim K. Bera and Alex Kang and Paul M. Levine and Valentina Alvarez and Arvind Pillai and Christoffer Norn and David Feldman and Dmitri Zorine and Derrick R. Hicks and Xinting Li and Mariana Garcia Sanchez and Dionne K. Vafeados and Patrick J. Salveson and Anastassia A. Vorobieva and David Baker},

url = {https://www.science.org/doi/10.1126/science.adn3780, Science},

doi = {10.1126/science.adn3780},

year  = {2024},

date = {2024-07-19},

urldate = {2024-07-19},

journal = {Science},

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

abstract = {We describe an approach for designing high-affinity small molecule–binding proteins poised for downstream sensing. We use deep learning–generated pseudocycles with repeating structural units surrounding central binding pockets with widely varying shapes that depend on the geometry and number of the repeat units. We dock small molecules of interest into the most shape complementary of these pseudocycles, design the interaction surfaces for high binding affinity, and experimentally screen to identify designs with the highest affinity. We obtain binders to four diverse molecules, including the polar and flexible methotrexate and thyroxine. Taking advantage of the modular repeat structure and central binding pockets, we construct chemically induced dimerization systems and low-noise nanopore sensors by splitting designs into domains that reassemble upon ligand addition.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Berger2024,

title = {Preclinical proof of principle for orally delivered Th17 antagonist miniproteins},

author = {Stephanie Berger and Franziska Seeger and Ta-Yi Yu and Merve Aydin and Huilin Yang and Daniel Rosenblum and Laure Guenin-Macé and Caleb Glassman and Lauren Arguinchona and Catherine Sniezek and Alyssa Blackstone and Lauren Carter and Rashmi Ravichandran and Maggie Ahlrichs and Michael Murphy and Ingrid Swanson Pultz and Alex Kang and Asim K. Bera and Lance Stewart and K. Christopher Garcia and Shruti Naik and Jamie B. Spangler and Florian Beigel and Matthias Siebeck and Roswitha Gropp and David Baker},

url = {https://www.cell.com/cell/fulltext/S0092-8674(24)00631-7, Cell [Open Access]},

doi = {10.1016/j.cell.2024.05.052},

year  = {2024},

date = {2024-06-26},

urldate = {2024-06-00},

journal = {Cell},

publisher = {Elsevier BV},

abstract = {Interleukin (IL)-23 and IL-17 are well-validated therapeutic targets in autoinflammatory diseases. Antibodies targeting IL-23 and IL-17 have shown clinical efficacy but are limited by high costs, safety risks, lack of sustained efficacy, and poor patient convenience as they require parenteral administration. Here, we present designed miniproteins inhibiting IL-23R and IL-17 with antibody-like, low picomolar affinities at a fraction of the molecular size. The minibinders potently block cell signaling in vitro and are extremely stable, enabling oral administration and low-cost manufacturing. The orally administered IL-23R minibinder shows efficacy better than a clinical anti-IL-23 antibody in mouse colitis and has a favorable pharmacokinetics (PK) and biodistribution profile in rats. This work demonstrates that orally administered de novo-designed minibinders can reach a therapeutic target past the gut epithelial barrier. With high potency, gut stability, and straightforward manufacturability, de novo-designed minibinders are a promising modality for oral biologics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jiang2024,

title = {De novo design of buttressed loops for sculpting protein functions},

author = {Jiang, Hanlun

and Jude, Kevin M.

and Wu, Kejia

and Fallas, Jorge

and Ueda, George

and Brunette, T. J.

and Hicks, Derrick R.

and Pyles, Harley

and Yang, Aerin

and Carter, Lauren

and Lamb, Mila

and Li, Xinting

and Levine, Paul M.

and Stewart, Lance

and Garcia, K. Christopher

and Baker, David},

url = {https://www.nature.com/articles/s41589-024-01632-2, Nature Chemical Biology [Open Access]

https://www.bakerlab.org/wp-content/uploads/2024/05/s41589-024-01632-2.pdf, PDF},

doi = {10.1038/s41589-024-01632-2},

year  = {2024},

date = {2024-05-30},

urldate = {2024-05-30},

journal = {Nature Chemical Biology},

abstract = {In natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9–14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sahtoe2024,

title = {Design of amyloidogenic peptide traps},

author = {Danny D. Sahtoe and Ewa A. Andrzejewska and Hannah L. Han and Enrico Rennella and Matthias M. Schneider and Georg Meisl and Maggie Ahlrichs and Justin Decarreau and Hannah Nguyen and Alex Kang and Paul Levine and Mila Lamb and Xinting Li and Asim K. Bera and Lewis E. Kay and Tuomas P. J. Knowles and David Baker},

url = {https://www.nature.com/articles/s41589-024-01578-5, Nature Chemical Biology [Open Access]},

doi = {10.1038/s41589-024-01578-5},

year  = {2024},

date = {2024-03-19},

urldate = {2024-03-19},

journal = {Nature Chemical Biology},

publisher = {Springer Science and Business Media LLC},

abstract = {Segments of proteins with high β-strand propensity can self-associate to form amyloid fibrils implicated in many diseases. We describe a general approach to bind such segments in β-strand and β-hairpin conformations using de novo designed scaffolds that contain deep peptide-binding clefts. The designs bind their cognate peptides in vitro with nanomolar affinities. The crystal structure of a designed protein−peptide complex is close to the design model, and NMR characterization reveals how the peptide-binding cleft is protected in the apo state. We use the approach to design binders to the amyloid-forming proteins transthyretin, tau, serum amyloid A1 and amyloid β1−42 (Aβ42). The Aβ binders block the assembly of Aβ fibrils as effectively as the most potent of the clinically tested antibodies to date and protect cells from toxic Aβ42 species.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mateos2024,

title = {Computational design of binders targeting the VSDIV from NaV1.7 sodium channel},

author = {Diego Lopez Mateos and Adam M. Murray and Hai M. Nguyen and Preetham Venkatesh and Brian Koepnick and David Baker and Heike Wulff and Vladimir Yarov-Yarovoy},

url = {https://www.cell.com/biophysj/abstract/S0006-3495(23)01470-4, Biophysical Journal},

doi = {10.1016/j.bpj.2023.11.770},

year  = {2024},

date = {2024-02-08},

urldate = {2024-02-00},

journal = {Biophysical Journal},

publisher = {Elsevier BV},

abstract = {Chronic pain affects about 20% of the US population, but safe treatments are limited. There is an urgent need for effective and non-addictive therapies for chronic pan conditions. Voltage-gated sodium (NaV) channel, NaV1.7, is a key player in pain signaling pathway, making it a promising target for novel pain therapeutics. Achieving high subtype selectivity when targeting NaV channels is of primary importance to avoid impairing vital physiological functions mediated by off-target channels. Efforts to selectively target NaV1.7 have been hindered by the difficulties in targeting NaV1.7 over other NaV channel subtypes. Peptidic gating modifier toxins (GMTs), such as Protoxin-II (ProTx2), are promising scaffolds for novel peptide design targeting ion channels with high potency and subtype selectivity. ProTx2 binds to the second and fourth voltage-sensing domains (VSDII and VSDIV) from NaV1.7 with moderate subtype selectivity and can modulate channel activation and inactivation. In this project, we modeled ProTx2 bound to human NaV1.7 VSDIV in an activated state. We used RoseTTAFold Diffusion and Protein MPNN protein design methods to generate protein binders inspired by ProTx2 binding motif with increased predicted binding affinity for human NaV1.7 VSDIV in an activated state. Additionally, we applied these protein design methods to create de novo binders targeting human NaV1.7 VSDIV in an activated state. We anticipate that trapping the VSDIV in an activated conformation will stabilize an inactivated state of the channel, as activation of VSDIV is coupled with channel fast inactivation. Initial electrophysiological screening of our top in silico binders identified promising candidates that inhibited NaV1.7 in the micromolar range. These binders will undergo further testing and optimization against NaV1.7 to create novel molecular tools to study NaV channel activity and effective and safe therapies for chronic pain.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38109936,

title = {De novo design of high-affinity binders of bioactive helical peptides},

author = {Susana Vázquez Torres and Philip J Y Leung and Preetham Venkatesh and Isaac D Lutz and Fabian Hink and Huu-Hien Huynh and Jessica Becker and Andy Hsien-Wei Yeh and David Juergens and Nathaniel R Bennett and Andrew N Hoofnagle and Eric Huang and Michael J MacCoss and Marc Expòsit and Gyu Rie Lee and Asim K Bera and Alex Kang and Joshmyn De La Cruz and Paul M Levine and Xinting Li and Mila Lamb and Stacey R Gerben and Analisa Murray and Piper Heine and Elif Nihal Korkmaz and Jeff Nivala and Lance Stewart and Joseph L Watson and Joseph M Rogers and David Baker},

url = {https://www.nature.com/articles/s41586-023-06953-1, Nature [Open Access]},

doi = {10.1038/s41586-023-06953-1},

issn = {1476-4687},

year  = {2023},

date = {2023-12-01},

urldate = {2023-12-01},

journal = {Nature},

abstract = {Many peptide hormones form an alpha-helix upon binding their receptors, and sensitive detection methods for them could contribute to better clinical management of disease. De novo protein design can now generate binders with high affinity and specificity to structured proteins. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here, we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar affinity binders can be generated to helical peptide targets both by refining designs generated with other methods, or completely de novo starting from random noise distributions. To our knowledge these are the highest affinity designed binding proteins against any protein or small molecule target generated directly by computation without any experimental optimisation. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimise by partial diffusion both natural and designed proteins, should be broadly useful.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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{Kim2023,

title = {De novo design of small beta barrel proteins},

author = {Kim, David E.

and Jensen, Davin R.

and Feldman, David

and Tischer, Doug

and Saleem, Ayesha

and Chow, Cameron M.

and Li, Xinting

and Carter, Lauren

and Milles, Lukas

and Nguyen, Hannah

and Kang, Alex

and Bera, Asim K.

and Peterson, Francis C.

and Volkman, Brian F.

and Ovchinnikov, Sergey

and Baker, David},

url = {https://www.pnas.org/doi/10.1073/pnas.2207974120, PNAS (Open Access)},

doi = {10.1073/pnas.2207974120},

year  = {2023},

date = {2023-03-10},

urldate = {2023-03-10},

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

abstract = {Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy–based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Agarwal2022,

title = {Rapid and Sensitive Detection of Antigen from SARS-CoV-2 Variants of Concern by a Multivalent Minibinder-Functionalized Nanomechanical Sensor},

author = {Agarwal, Dilip Kumar

and Hunt, Andrew C.

and Shekhawat, Gajendra S.

and Carter, Lauren

and Chan, Sidney

and Wu, Kejia

and Cao, Longxing

and Baker, David

and Lorenzo-Redondo, Ramon

and Ozer, Egon A.

and Simons, Lacy M.

and Hultquist, Judd F.

and Jewett, Michael C.

and Dravid, Vinayak P.},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9211039/, Analytical Chemistry},

year  = {2022},

date = {2022-06-06},

urldate = {2022-06-06},

journal = {Analytical Chemistry},

abstract = {New platforms for the rapid and sensitive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern are urgently needed. Here we report the development of a nanomechanical sensor based on the deflection of a microcantilever capable of detecting the SARS-CoV-2 spike (S) glycoprotein antigen using computationally designed multivalent minibinders immobilized on a microcantilever surface. The sensor exhibits rapid (<5 min) detection of the target antigens down to concentrations of 0.05 ng/mL (362 fM) and is more than an order of magnitude more sensitive than an antibody-based cantilever sensor. Validation of the sensor with clinical samples from 33 patients, including 9 patients infected with the Omicron (BA.1) variant observed detection of antigen from nasopharyngeal swabs with cycle threshold (Ct) values as high as 39, suggesting a limit of detection similar to that of the quantitative reverse transcription polymerase chain reaction (RT-qPCR). Our findings demonstrate the use of minibinders and nanomechanical sensors for the rapid and sensitive detection of SARS-CoV-2 and potentially other disease markers.},

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}

}