Robust de novo design of protein binding proteins from target structural information alone
Robust de novo design of protein binding proteins from target structural information alone
Abstract The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains an outstanding challenge. We describe a general solution to this problem which starts with a broad exploration of the very large space of possible binding modes and interactions, and then intensifies the search in the most promising regions. We demonstrate its very broad applicability by de novo design of binding proteins to 12 diverse protein targets with very different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of four of the binder-target complexes, and all four are very close to the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvement of both. Our approach now enables targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
Cao Longxing、Goreshnik Inna、Huang Buwei、Verstraete Kenneth、Walsh Scott Thomas Russell、Kozodoy Lisa、Picton Lora、Yang Wei、Benard Steffen、Schlessinger Joseph、Lee Sangwon、Savvides Savvas N.、Garcia K. Christopher、Wilson Ian A.、Jude Kevin M.、Yang Aerin、Kadam Rameshwar U.、Park Joon Sung、Halabiya Samer、Verschueren Koen H.G.、Stewart Lance、Markovi? Iva、Baker David、Strauch Eva-Maria、Bennett Nathaniel、Miller Lauren、Coventry Brian、Ruohola-Baker Hannele、Hammerson Bradley、Phal Ashish、DeWitt Michelle
Department of Biochemistry, University of Washington||Institute for Protein Design, University of WashingtonDepartment of Biochemistry, University of Washington||Institute for Protein Design, University of WashingtonDepartment of Biochemistry, University of Washington||Institute for Protein Design, University of Washington||Department of Bioengineering, University of WashingtonVIB-UGent Center for Inflammation Research||Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent UniversityNational Cancer Institute, National Institutes of Health, Chemical Biology Laboratory||J.A.M.E.S. FarmDepartment of Biochemistry, University of Washington||Institute for Protein Design, University of WashingtonHoward Hughes Medical Institute, Stanford University School of Medicine||Department of Structural Biology, Stanford University School of Medicine||Department of Molecular and Cellular Physiology, Stanford University School of MedicineDepartment of Biochemistry, University of Washington||Institute for Protein Design, University of WashingtonDepartment of Integrative Structural and Computational Biology, The Scripps Research InstituteDepartment of Pharmacology, Yale University School of MedicineDepartment of Pharmacology, Yale University School of MedicineVIB-UGent Center for Inflammation Research||Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent UniversityHoward Hughes Medical Institute, Stanford University School of Medicine||Department of Structural Biology, Stanford University School of Medicine||Department of Molecular and Cellular Physiology, Stanford University School of MedicineDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute||The Skaggs Institute for Chemical Biology, The Scripps Research InstituteHoward Hughes Medical Institute, Stanford University School of Medicine||Department of Structural Biology, Stanford University School of Medicine||Department of Molecular and Cellular Physiology, Stanford University School of MedicineHoward Hughes Medical Institute, Stanford University School of Medicine||Department of Structural Biology, Stanford University School of Medicine||Department of Molecular and Cellular Physiology, Stanford University School of MedicineDepartment of Integrative Structural and Computational Biology, The Scripps Research InstituteDepartment of Pharmacology, Yale University School of MedicineDepartment of Electrical and Computer Engineering, University of WashingtonVIB-UGent Center for Inflammation Research||Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent UniversityDepartment of Biochemistry, University of Washington||Institute for Protein Design, University of WashingtonVIB-UGent Center for Inflammation Research||Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent UniversityDepartment of Biochemistry, University of Washington||Institute for Protein Design, University of Washington||Howard Hughes Medical Institute, University of WashingtonDept. of Pharmaceutical and Biomedical Sciences, University of GeorgiaDepartment of Biochemistry, University of Washington||Institute for Protein Design, University of Washington||Molecular Engineering Graduate Program, University of WashingtonDepartment of Biochemistry, University of Washington||Institute for Protein Design, University of WashingtonDepartment of Biochemistry, University of Washington||Institute for Protein Design, University of Washington||Molecular Engineering Graduate Program, University of WashingtonDepartment of Biochemistry, University of Washington||Institute for Stem Cell and Regenerative Medicine, University of WashingtonSeattle Structural Genomics Center for Infectious DiseaseDepartment of Biochemistry, University of Washington||Department of Bioengineering, University of Washington||Institute for Stem Cell and Regenerative Medicine, University of WashingtonDepartment of Biochemistry, University of Washington||Institute for Protein Design, University of Washington
生物科学研究方法、生物科学研究技术生物工程学分子生物学
Cao Longxing,Goreshnik Inna,Huang Buwei,Verstraete Kenneth,Walsh Scott Thomas Russell,Kozodoy Lisa,Picton Lora,Yang Wei,Benard Steffen,Schlessinger Joseph,Lee Sangwon,Savvides Savvas N.,Garcia K. Christopher,Wilson Ian A.,Jude Kevin M.,Yang Aerin,Kadam Rameshwar U.,Park Joon Sung,Halabiya Samer,Verschueren Koen H.G.,Stewart Lance,Markovi? Iva,Baker David,Strauch Eva-Maria,Bennett Nathaniel,Miller Lauren,Coventry Brian,Ruohola-Baker Hannele,Hammerson Bradley,Phal Ashish,DeWitt Michelle.Robust de novo design of protein binding proteins from target structural information alone[EB/OL].(2025-03-28)[2025-08-02].https://www.biorxiv.org/content/10.1101/2021.09.04.459002.点此复制
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