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Berger S, Seeger F, Yu TY, Aydin M, Yang H, Rosenblum D, Guenin-Macé L, Glassman C, Arguinchona L, Sniezek C, Blackstone A, Carter L, Ravichandran R, Ahlrichs M, Murphy M, Pultz IS, Kang A, Bera AK, Stewart L, Garcia KC, Naik S, Spangler JB, Beigel F, Siebeck M, Gropp R, Baker D. Preclinical proof of principle for orally delivered Th17 antagonist miniproteins. Cell 2024; 187:4305-4317.e18. [PMID: 38936360 PMCID: PMC11316638 DOI: 10.1016/j.cell.2024.05.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/09/2024] [Accepted: 05/29/2024] [Indexed: 06/29/2024]
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.
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Affiliation(s)
- Stephanie Berger
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
| | - Franziska Seeger
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ta-Yi Yu
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Merve Aydin
- Department of General, Visceral and Transplantation Surgery, LMU University Hospital, LMU Munich, 81377 Munich, Germany
| | - Huilin Yang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Daniel Rosenblum
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Laure Guenin-Macé
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA; Immunobiology and Therapy Unit, INSERM U1224, Institut Pasteur, Paris 75015, France
| | - Caleb Glassman
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Lauren Arguinchona
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Catherine Sniezek
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Blackstone
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94304, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94304, USA; Howard Hughes Medical Institute, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Shruti Naik
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA; Department of Medicine, Ronald O. Perelman Department of Dermatology, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Jamie B Spangler
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD 21231, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Florian Beigel
- Department of Medicine II, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Matthias Siebeck
- Department of General, Visceral and Transplantation Surgery, LMU University Hospital, LMU Munich, 81377 Munich, Germany
| | - Roswitha Gropp
- Department of General, Visceral and Transplantation Surgery, LMU University Hospital, LMU Munich, 81377 Munich, Germany
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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2
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Narayanan KK, Weigle AT, Xu L, Mi X, Zhang C, Chen LQ, Procko E, Shukla D. Deep mutational scanning reveals sequence to function constraints for SWEET family transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601307. [PMID: 39005363 PMCID: PMC11244857 DOI: 10.1101/2024.06.28.601307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Protein science is entering a transformative phase enabled by deep mutational scans that provide an unbiased view of the residue level interactions that mediate function. However, it has yet to be extensively used to characterize the mutational and evolutionary landscapes of plant proteins. Here, we apply the method to explore sequence-function relationships within the sugar transporter AtSWEET13. DMS results describe how mutational interrogation throughout different regions of the protein affects AtSWEET13 abundance and transport function. Our results identify novel transport-enhancing mutations that are validated using the FRET sensor assays. Extending DMS results to phylogenetic analyses reveal the role of transmembrane helix 4 (TM4) which makes the SWEET family transporters distinct from prokaryotic SemiSWEETs. We show that transmembrane helix 4 is intolerant to motif swapping with other clade-specific SWEET TM4 compositions, despite accommodating single point-mutations towards aromatic and charged polar amino acids. We further show that the transfer learning approaches based on physics and ML based In silico variant prediction tools have limited utility for engineering plant proteins as they were unable to reproduce our experimental results. We conclude that DMS can produce datasets which, when combined with the right predictive computational frameworks, can direct plant engineering efforts through derivative phenotype selection and evolutionary insights.
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Affiliation(s)
- Krishna K. Narayanan
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Austin T. Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lingyun Xu
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Xuenan Mi
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chen Zhang
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Li-Qing Chen
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Erik Procko
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cyrus Biotechnology, Inc., Seattle, Washington 98121, United States
| | - Diwakar Shukla
- Department of Chemical & Biomolecular Engineering; Department of Plant Biology; Department of Bioengineering; Department of Chemistry, Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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3
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Narayanan KK, Amaya M, Tsang N, Yin R, Jays A, Broder CC, Shukla D, Procko E. Sequence basis for selectivity of ephrin-B2 ligand for Eph receptors and pathogenic henipavirus G glycoproteins. J Virol 2023; 97:e0062123. [PMID: 37931130 PMCID: PMC10688352 DOI: 10.1128/jvi.00621-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/13/2023] [Indexed: 11/08/2023] Open
Abstract
IMPORTANCE Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and regulates multiple cell developmental and signaling processes. It also functions as the cell entry receptor for Nipah virus and Hendra virus, zoonotic viruses that can cause respiratory and/or neurological symptoms in humans with high mortality. Here, we investigate the sequence basis of EFNB2 specificity for binding the Nipah virus attachment G glycoprotein over Eph receptors. We then use this information to engineer EFNB2 as a soluble decoy receptor that specifically binds the attachment glycoproteins of the Nipah virus and other related henipaviruses to neutralize infection. These findings further mechanistic understanding of protein selectivity and may facilitate the development of diagnostics or therapeutics against henipavirus infection.
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Affiliation(s)
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Natalie Tsang
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
| | - Randy Yin
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Alka Jays
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois, USA
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois, USA
- Cyrus Biotechnology, Seattle, Washington, USA
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4
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Tomazini A, Shifman JM. Targeting Ras with protein engineering. Oncotarget 2023; 14:672-687. [PMID: 37395750 DOI: 10.18632/oncotarget.28469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Ras proteins are small GTPases that regulate cell growth and division. Mutations in Ras genes are associated with many types of cancer, making them attractive targets for cancer therapy. Despite extensive efforts, targeting Ras proteins with small molecules has been extremely challenging due to Ras's mostly flat surface and lack of small molecule-binding cavities. These challenges were recently overcome by the development of the first covalent small-molecule anti-Ras drug, sotorasib, highlighting the efficacy of Ras inhibition as a therapeutic strategy. However, this drug exclusively inhibits the Ras G12C mutant, which is not a prevalent mutation in most cancer types. Unlike the G12C variant, other Ras oncogenic mutants lack reactive cysteines, rendering them unsuitable for targeting via the same strategy. Protein engineering has emerged as a promising method to target Ras, as engineered proteins have the ability to recognize various surfaces with high affinity and specificity. Over the past few years, scientists have engineered antibodies, natural Ras effectors, and novel binding domains to bind to Ras and counteract its carcinogenic activities via a variety of strategies. These include inhibiting Ras-effector interactions, disrupting Ras dimerization, interrupting Ras nucleotide exchange, stimulating Ras interaction with tumor suppressor genes, and promoting Ras degradation. In parallel, significant advancements have been made in intracellular protein delivery, enabling the delivery of the engineered anti-Ras agents into the cellular cytoplasm. These advances offer a promising path for targeting Ras proteins and other challenging drug targets, opening up new opportunities for drug discovery and development.
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Affiliation(s)
- Atilio Tomazini
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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5
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Gainza P, Wehrle S, Van Hall-Beauvais A, Marchand A, Scheck A, Harteveld Z, Buckley S, Ni D, Tan S, Sverrisson F, Goverde C, Turelli P, Raclot C, Teslenko A, Pacesa M, Rosset S, Georgeon S, Marsden J, Petruzzella A, Liu K, Xu Z, Chai Y, Han P, Gao GF, Oricchio E, Fierz B, Trono D, Stahlberg H, Bronstein M, Correia BE. De novo design of protein interactions with learned surface fingerprints. Nature 2023; 617:176-184. [PMID: 37100904 PMCID: PMC10131520 DOI: 10.1038/s41586-023-05993-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 03/21/2023] [Indexed: 04/28/2023]
Abstract
Physical interactions between proteins are essential for most biological processes governing life1. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This knowledge gap has been a major obstacle for the comprehensive understanding of cellular protein-protein interaction networks and for the de novo design of protein binders that are crucial for synthetic biology and translational applications2-9. Here we use a geometric deep-learning framework operating on protein surfaces that generates fingerprints to describe geometric and chemical features that are critical to drive protein-protein interactions10. We hypothesized that these fingerprints capture the key aspects of molecular recognition that represent a new paradigm in the computational design of novel protein interactions. As a proof of principle, we computationally designed several de novo protein binders to engage four protein targets: SARS-CoV-2 spike, PD-1, PD-L1 and CTLA-4. Several designs were experimentally optimized, whereas others were generated purely in silico, reaching nanomolar affinity with structural and mutational characterization showing highly accurate predictions. Overall, our surface-centric approach captures the physical and chemical determinants of molecular recognition, enabling an approach for the de novo design of protein interactions and, more broadly, of artificial proteins with function.
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Affiliation(s)
- Pablo Gainza
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Monte Rosa Therapeutics, Basel, Switzerland
| | - Sarah Wehrle
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra Van Hall-Beauvais
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Anthony Marchand
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Scheck
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zander Harteveld
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stephen Buckley
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Science, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Shuguang Tan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Freyr Sverrisson
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Casper Goverde
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Priscilla Turelli
- Laboratory of Virology and Genetics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Charlène Raclot
- Laboratory of Virology and Genetics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandra Teslenko
- Laboratory of Biophysical Chemistry of Macromolecules, School of Basic Sciences, Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stéphane Rosset
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jane Marsden
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Aaron Petruzzella
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, School of Basic Sciences, Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Didier Trono
- Laboratory of Virology and Genetics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Science, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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6
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Narayanan KK, Amaya M, Tsang N, Yin R, Jays A, Broder CC, Shukla D, Procko E. The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins: Selective Ephrin-B2 Decoys for Nipah and Hendra Virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538420. [PMID: 37162958 PMCID: PMC10168364 DOI: 10.1101/2023.04.26.538420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and functions as a cell entry receptor for several henipaviruses including Nipah virus (NiV), a pathogenic zoonotic virus with pandemic potential. To understand the sequence basis of promiscuity for EFNB2 binding to the attachment glycoprotein of NiV (NiV-G) and Eph receptors, we performed deep mutagenesis on EFNB2 to identify mutations that enhance binding to NiV-G over EphB2, one of the highest affinity Eph receptors. The mutations highlight how different EFNB2 conformations are selected by NiV-G versus EphB2. Specificity mutations are enriched at the base of the G-H binding loop of EFNB2, especially surrounding a phenylalanine hinge upon which the G-H loop pivots, and at a phenylalanine hook that rotates away from the EFNB2 core to engage Eph receptors. One EFNB2 mutant, D62Q, possesses pan-specificity to the attachment glycoproteins of closely related henipaviruses and has markedly diminished binding to the six Eph receptors. However, EFNB2-D62Q has high residual binding to EphB3 and EphB4. A second deep mutational scan of EFNB2 identified combinatorial mutations to further enhance specificity to NiV-G. A triple mutant of soluble EFNB2, D62Q-Q130L-V167L, has minimal binding to Eph receptors but maintains binding, albeit reduced, to NiV-G. Soluble EFNB2 decoy receptors carrying the specificity mutations were potent neutralizers of chimeric henipaviruses. These findings demonstrate how specific residue changes at the shared binding interface of a promiscuous ligand (EFNB2) can influence selectivity for multiple receptors, and may also offer insight towards the development of henipavirus therapeutics and diagnostics.
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Affiliation(s)
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
| | - Natalie Tsang
- Department of Biochemistry, University of Illinois, Urbana IL, USA
| | - Randy Yin
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD, USA
| | - Alka Jays
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD, USA
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois, Urbana IL, USA
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana IL, USA
- Cancer Center at Illinois, University of Illinois, Urbana IL, USA
- Cyrus Biotechnology, Seattle WA, USA
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7
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Tam C, Kukimoto-Niino M, Miyata-Yabuki Y, Tsuda K, Mishima-Tsumagari C, Ihara K, Inoue M, Yonemochi M, Hanada K, Matsumoto T, Shirouzu M, Zhang KYJ. Targeting Ras-binding domain of ELMO1 by computational nanobody design. Commun Biol 2023; 6:284. [PMID: 36932164 PMCID: PMC10023680 DOI: 10.1038/s42003-023-04657-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
The control of cell movement through manipulation of cytoskeletal structure has therapeutic prospects notably in the development of novel anti-metastatic drugs. In this study, we determine the structure of Ras-binding domain (RBD) of ELMO1, a protein involved in cytoskeletal regulation, both alone and in complex with the activator RhoG and verify its targetability through computational nanobody design. Using our dock-and-design approach optimized with native-like initial pose selection, we obtain Nb01, a detectable binder from scratch in the first-round design. An affinity maturation step guided by structure-activity relationship at the interface generates 23 Nb01 sequence variants and 17 of them show enhanced binding to ELMO1-RBD and are modeled to form major spatial overlaps with RhoG. The best binder, Nb29, inhibited ELMO1-RBD/RhoG interaction. Molecular dynamics simulation of the flexibility of CDR2 and CDR3 of Nb29 reveal the design of stabilizing mutations at the CDR-framework junctions potentially confers the affinity enhancement.
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Affiliation(s)
- Chunlai Tam
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Mutsuko Kukimoto-Niino
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
| | - Yukako Miyata-Yabuki
- Drug Discovery Structural Biology Platform Unit, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kengo Tsuda
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Chiemi Mishima-Tsumagari
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kentaro Ihara
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Mio Inoue
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Mayumi Yonemochi
- Drug Discovery Structural Biology Platform Unit, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuharu Hanada
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Takehisa Matsumoto
- Drug Discovery Structural Biology Platform Unit, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan.
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8
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Okwei E, Smith ST, Bender BJ, Allison B, Ganguly S, Geanes A, Zhang X, Ledwitch K, Meiler J. Rosetta's Predictive Ability for Low-Affinity Ligand Binding in Fragment-Based Drug Discovery. Biochemistry 2023; 62:700-709. [PMID: 36626571 DOI: 10.1021/acs.biochem.2c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fragment-based drug discovery begins with the identification of small molecules with a molecular weight of usually less than 250 Da which weakly bind to the protein of interest. This technique is challenging for computational docking methods as binding is determined by only a few specific interactions. Inaccuracies in the energy function or slight deviations in the docking pose can lead to the prediction of incorrect binding or difficulties in ranking fragments in in silico screening. Here, we test RosettaLigand by docking a series of fragments to a cysteine-depleted variant of the TIM-barrel protein, HisF (UniProtKB Q9X0C6). We compare the computational results with experimental NMR spectroscopy screens. NMR spectroscopy gives details on binding affinities of individual ligands, which allows assessment of the ligand-ranking ability using RosettaLigand and also provides feedback on the location of the binding pocket, which serves as a reliable test of RosettaLigand's ability to identify plausible binding poses. From a library screen of 3456 fragments, we identified a set of 31 ligands with intrinsic affinities to HisF with dissociation constants as low as 400 μM. The same library of fragments was blindly screened in silico. RosettaLigand was able to rank binders before non-binders with an area under the curve of the receiver operating characteristics of 0.74. The docking poses observed for binders agreed with the binding pocket identified by NMR chemical shift perturbations for all fragments. Taken together, these results provide a baseline performance of RosettaLigand in a fragment-based drug discovery setting.
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Affiliation(s)
- Elleansar Okwei
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee37235, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee37240, United States
| | - Shannon T Smith
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee37240, United States.,Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee37240, United States
| | - Brian J Bender
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee37240, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee37240, United States
| | - Brittany Allison
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee37235, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee37240, United States
| | - Soumya Ganguly
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee37235, United States
| | - Alexander Geanes
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee37235, United States
| | - Xuan Zhang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee37235, United States
| | - Kaitlyn Ledwitch
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee37235, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee37240, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee37235, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee37240, United States.,Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee37240, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee37240, United States.,Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103Leipzig, Germany
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9
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Marchand A, Van Hall-Beauvais AK, Correia BE. Computational design of novel protein–protein interactions – An overview on methodological approaches and applications. Curr Opin Struct Biol 2022; 74:102370. [DOI: 10.1016/j.sbi.2022.102370] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
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10
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Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease. Curr Opin Struct Biol 2022; 74:102358. [PMID: 35344834 DOI: 10.1016/j.sbi.2022.102358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/13/2022] [Accepted: 02/21/2022] [Indexed: 11/21/2022]
Abstract
T cell receptors (TCRs) orchestrate cellular immunity by recognizing peptide antigens bound and presented by major histocompatibility complex (MHC) proteins. Due to the TCR's central role in immunity and tight connection with human health, there has been significant interest in modulating TCR properties through protein engineering methods. Complicating these efforts is the complexity and vast diversity of TCR-peptide/MHC interfaces, the interdependency between TCR affinity, specificity, and cross-reactivity, and the sophisticated relationships between TCR binding properties and T cell function, many aspects of which are not well understood. Here we review TCR engineering, starting with a brief historical overview followed by discussions of more recent developments, including new efforts and opportunities to engineer TCR affinity, modulate specificity, and develop novel TCR-based constructs.
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11
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Sharma P, Procko E, Kranz DM. Engineering Proteins by Combining Deep Mutational Scanning and Yeast Display. Methods Mol Biol 2022; 2491:117-142. [PMID: 35482188 DOI: 10.1007/978-1-0716-2285-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein engineering using display platforms such as yeast display and phage display has allowed discovery of proteins with therapeutic and industrial applications. Antibodies and T cell receptors developed for therapeutic applications are often engineered by constructing libraries of mutations in loops of five to ten residues called complementarity determining regions that are in proximity to the antigen. In the past decade, deep mutational scanning has become a powerful tool in a protein engineer's toolbox, as it allows one to compare the impact of all 20 amino acids at each position, across the length of the protein. Thus, a single experiment can provide a sequence-activity landscape with information about hotspots or suboptimal binding sites in the original proteins. These residues or regions may be overlooked by engineering methods that are driven solely by structures or directed evolution of error-prone PCR libraries. Here, we describe experimental methods to engineer proteins by combining yeast display and deep mutational scanning mutagenesis, using T cell receptors as an example.
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Affiliation(s)
- Preeti Sharma
- Department of Biochemistry, University of Illinois, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - David M Kranz
- Department of Biochemistry, University of Illinois, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois, Urbana, IL, USA.
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12
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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13
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Opening of a cryptic pocket in β-lactamase increases penicillinase activity. Proc Natl Acad Sci U S A 2021; 118:2106473118. [PMID: 34799442 PMCID: PMC8617505 DOI: 10.1073/pnas.2106473118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
A protein is a shape-shifter, but it is currently unclear which of the many structures a protein can adopt are relevant for its function. Here, we examine conformations that contain a “cryptic” pocket (i.e., a pocket absent in ligand-free structures). Cryptic pockets have potential utility in drug discovery efforts because they provide a means to target “undruggable” proteins (i.e., proteins lacking known pockets) or enhance rather than inhibit protein function. In this study, we use a combination of thiol-labeling and kinetic assays, NMR, and molecular dynamic simulations to identify the function of the Ω-loop cryptic pocket in β-lactamase enzymes. We find that an open pocket population is beneficial for hydrolysis of the substrate benzylpenicillin. Understanding the functional role of protein-excited states has important implications in protein design and drug discovery. However, because these states are difficult to find and study, it is still unclear if excited states simply result from thermal fluctuations and generally detract from function or if these states can actually enhance protein function. To investigate this question, we consider excited states in β-lactamases and particularly a subset of states containing a cryptic pocket which forms under the Ω-loop. Given the known importance of the Ω-loop and the presence of this pocket in at least two homologs, we hypothesized that these excited states enhance enzyme activity. Using thiol-labeling assays to probe Ω-loop pocket dynamics and kinetic assays to probe activity, we find that while this pocket is not completely conserved across β-lactamase homologs, those with the Ω-loop pocket have a higher activity against the substrate benzylpenicillin. We also find that this is true for TEM β-lactamase variants with greater open Ω-loop pocket populations. We further investigate the open population using a combination of NMR chemical exchange saturation transfer experiments and molecular dynamics simulations. To test our understanding of the Ω-loop pocket’s functional role, we designed mutations to enhance/suppress pocket opening and observed that benzylpenicillin activity is proportional to the probability of pocket opening in our designed variants. The work described here suggests that excited states containing cryptic pockets can be advantageous for function and may be favored by natural selection, increasing the potential utility of such cryptic pockets as drug targets.
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14
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Qin YT, Ma YJ, Feng YS, He XW, Li WY, Zhang YK. Targeted Mitochondrial Fluorescence Imaging-Guided Tumor Antimetabolic Therapy with the Imprinted Polymer Nanomedicine Capable of Specifically Recognizing Dihydrofolate Reductase. ACS APPLIED MATERIALS & INTERFACES 2021; 13:40332-40341. [PMID: 34412467 DOI: 10.1021/acsami.1c11388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As we all know, inhibiting the activity of dihydrofolate reductase (DHFR) has always been an effective strategy for folate antimetabolites to treat tumors. In the past, it mainly relied on chemical drugs. Here, we propose a new strategy, (3-propanecarboxyl)triphenylphosphonium bromide (CTPB)-modified molecularly imprinted polymer nanomedicine (MIP-CTPB). MIP-CTPB prepared by imprinting the active center of DHFR can specifically bind to the active center to block the catalytic activity of DHFR, thereby inhibiting the synthesis of DNA and ultimately inhibiting the tumor growth. The modification of CTPB allows the nanomedicine to be targeted and enriched in mitochondria, where DHFR is abundant. The confocal laser imaging results show that MIP-CTPB can target mitochondria. Cytotoxicity experiments show that MIP-CTPB inhibits HeLa cell proliferation by 42.2%. In vivo experiments show that the tumor volume of the MIP-CTPB-treated group is only one-sixth of that of the untreated group. The fluorescent and paramagnetic properties of the nanomedicine enable targeted fluorescence imaging of mitochondria and T2-weighted magnetic resonance imaging of tumors. This research not only opens up a new direction for the application of molecular imprinting, but also provides a new idea for tumor antimetabolic therapy guided by targeted mitochondrial imaging.
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Affiliation(s)
- Ya-Ting Qin
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yao-Jia Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Sheng Feng
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xi-Wen He
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Wen-You Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Kui Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
- National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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15
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Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Nat Commun 2021; 12:3384. [PMID: 34099674 PMCID: PMC8185074 DOI: 10.1038/s41467-021-23609-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 05/04/2021] [Indexed: 01/07/2023] Open
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.
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16
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McShan AC, Devlin CA, Morozov GI, Overall SA, Moschidi D, Akella N, Procko E, Sgourakis NG. TAPBPR promotes antigen loading on MHC-I molecules using a peptide trap. Nat Commun 2021; 12:3174. [PMID: 34039964 PMCID: PMC8154891 DOI: 10.1038/s41467-021-23225-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/16/2021] [Indexed: 11/08/2022] Open
Abstract
Chaperones Tapasin and TAP-binding protein related (TAPBPR) perform the important functions of stabilizing nascent MHC-I molecules (chaperoning) and selecting high-affinity peptides in the MHC-I groove (editing). While X-ray and cryo-EM snapshots of MHC-I in complex with TAPBPR and Tapasin, respectively, have provided important insights into the peptide-deficient MHC-I groove structure, the molecular mechanism through which these chaperones influence the selection of specific amino acid sequences remains incompletely characterized. Based on structural and functional data, a loop sequence of variable lengths has been proposed to stabilize empty MHC-I molecules through direct interactions with the floor of the groove. Using deep mutagenesis on two complementary expression systems, we find that important residues for the Tapasin/TAPBPR chaperoning activity are located on a large scaffolding surface, excluding the loop. Conversely, loop mutations influence TAPBPR interactions with properly conformed MHC-I molecules, relevant for peptide editing. Detailed biophysical characterization by solution NMR, ITC and FP-based assays shows that the loop hovers above the MHC-I groove to promote the capture of incoming peptides. Our results suggest that the longer loop of TAPBPR lowers the affinity requirements for peptide selection to facilitate peptide loading under conditions and subcellular compartments of reduced ligand concentration, and to prevent disassembly of high-affinity peptide-MHC-I complexes that are transiently interrogated by TAPBPR during editing.
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Affiliation(s)
- Andrew C McShan
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christine A Devlin
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Giora I Morozov
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah A Overall
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Danai Moschidi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Neha Akella
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA.
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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17
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Sahtoe DD, Coscia A, Mustafaoglu N, Miller LM, Olal D, Vulovic I, Yu TY, Goreshnik I, Lin YR, Clark L, Busch F, Stewart L, Wysocki VH, Ingber DE, Abraham J, Baker D. Transferrin receptor targeting by de novo sheet extension. Proc Natl Acad Sci U S A 2021; 118:e2021569118. [PMID: 33879614 PMCID: PMC8092486 DOI: 10.1073/pnas.2021569118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The de novo design of polar protein-protein interactions is challenging because of the thermodynamic cost of stripping water away from the polar groups. Here, we describe a general approach for designing proteins which complement exposed polar backbone groups at the edge of beta sheets with geometrically matched beta strands. We used this approach to computationally design small proteins that bind to an exposed beta sheet on the human transferrin receptor (hTfR), which shuttles interacting proteins across the blood-brain barrier (BBB), opening up avenues for drug delivery into the brain. We describe a design which binds hTfR with a 20 nM Kd, is hyperstable, and crosses an in vitro microfluidic organ-on-a-chip model of the human BBB. Our design approach provides a general strategy for creating binders to protein targets with exposed surface beta edge strands.
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Affiliation(s)
- Danny D Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- HHMI, University of Washington, Seattle, WA 98195
| | - Adrian Coscia
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Nur Mustafaoglu
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115
| | - Lauren M Miller
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Daniel Olal
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Ivan Vulovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Ta-Yi Yu
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Yu-Ru Lin
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Lars Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Florian Busch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115
- Department of Surgery and Vascular Biology Program, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02539
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- HHMI, University of Washington, Seattle, WA 98195
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18
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Bonadio A, Shifman JM. Computational design and experimental optimization of protein binders with prospects for biomedical applications. Protein Eng Des Sel 2021; 34:gzab020. [PMID: 34436606 PMCID: PMC8388154 DOI: 10.1093/protein/gzab020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/11/2021] [Accepted: 07/11/2021] [Indexed: 11/12/2022] Open
Abstract
Protein-based binders have become increasingly more attractive candidates for drug and imaging agent development. Such binders could be evolved from a number of different scaffolds, including antibodies, natural protein effectors and unrelated small protein domains of different geometries. While both computational and experimental approaches could be utilized for protein binder engineering, in this review we focus on various computational approaches for protein binder design and demonstrate how experimental selection could be applied to subsequently optimize computationally-designed molecules. Recent studies report a number of designed protein binders with pM affinities and high specificities for their targets. These binders usually characterized with high stability, solubility, and low production cost. Such attractive molecules are bound to become more common in various biotechnological and biomedical applications in the near future.
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Affiliation(s)
- Alessandro Bonadio
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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19
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Chan KK, Tan TJC, Narayanan KK, Procko E. An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. SCIENCE ADVANCES 2021; 7:eabf1738. [PMID: 33597251 PMCID: PMC7888922 DOI: 10.1126/sciadv.abf1738] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/31/2020] [Indexed: 05/04/2023]
Abstract
The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, because of close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find that an engineered decoy receptor, sACE22v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain followed by in vitro selection, with wild-type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild-type receptor. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.
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Affiliation(s)
- Kui K Chan
- Orthogonal Biologics, Champaign, IL 61821, USA
| | - Timothy J C Tan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA
| | - Krishna K Narayanan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA.
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20
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Chan KK, Tan TJC, Narayanan KK, Procko E. An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.10.18.344622. [PMID: 33398275 PMCID: PMC7781310 DOI: 10.1101/2020.10.18.344622] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find an engineered decoy receptor, sACE2 2 .v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain (RBD) followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. Variant N501Y in the RBD, which has emerged in a rapidly spreading lineage (B.1.1.7) in England, enhances affinity for wild type ACE2 20-fold but remains tightly bound to engineered sACE22.v2.4. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.
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Affiliation(s)
- Kui K Chan
- Orthogonal Biologics, Champaign IL 61821
| | - Timothy J C Tan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
| | - Krishna K Narayanan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
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A De Novo Designed Esterase with p-Nitrophenyl Acetate Hydrolysis Activity. Molecules 2020; 25:molecules25204658. [PMID: 33066055 PMCID: PMC7587395 DOI: 10.3390/molecules25204658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/04/2020] [Accepted: 10/10/2020] [Indexed: 11/18/2022] Open
Abstract
Esterases are a large family of enzymes with wide applications in the industry. However, all esterases originated from natural sources, limiting their use in harsh environments or newly- emerged reactions. In this study, we designed a new esterase to develop a new protocol to satisfy the needs for better biocatalysts. The ideal spatial conformation of the serine catalytic triad and the oxygen anion hole at the substrate-binding site was constructed by quantum mechanical calculation. The catalytic triad and oxygen anion holes were then embedded in the protein scaffold using the new enzyme protocol in Rosetta 3. The design results were subsequently evaluated, and optimized designs were used for expression and purification. The designed esterase had significant lytic activities towards p-nitrophenyl acetate, which was confirmed by point mutations. Thus, this study developed a new protocol to obtain novel enzymes that may be useful in unforgiving environments or novel reactions.
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22
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Procko E. Deep mutagenesis in the study of COVID-19: a technical overview for the proteomics community. Expert Rev Proteomics 2020; 17:633-638. [PMID: 33084449 PMCID: PMC7594187 DOI: 10.1080/14789450.2020.1833721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The spike (S) of SARS coronavirus 2 (SARS-CoV-2) engages angiotensin-converting enzyme 2 (ACE2) on a host cell to trigger viral-cell membrane fusion and infection. The extracellular region of ACE2 can be administered as a soluble decoy to compete for binding sites on the receptor-binding domain (RBD) of S, but it has only moderate affinity and efficacy. The RBD, which is targeted by neutralizing antibodies, may also change and adapt through mutation as SARS-CoV-2 becomes endemic, posing challenges for therapeutic and vaccine development. AREAS COVERED Deep mutagenesis is a Big Data approach to characterizing sequence variants. A deep mutational scan of ACE2 expressed on human cells identified mutations that increase S affinity and guided the engineering of a potent and broad soluble receptor decoy. A deep mutational scan of the RBD displayed on the surface of yeast has revealed residues tolerant of mutational changes that may act as a source for drug resistance and antigenic drift. EXPERT OPINION Deep mutagenesis requires a selection of diverse sequence variants; an in vitro evolution experiment that is tracked with next-generation sequencing. The choice of expression system, diversity of the variant library and selection strategy have important consequences for data quality and interpretation.
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Affiliation(s)
- Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
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23
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Chan KK, Dorosky D, Sharma P, Abbasi SA, Dye JM, Kranz DM, Herbert AS, Procko E. Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2. Science 2020; 369:1261-1265. [PMID: 32753553 PMCID: PMC7574912 DOI: 10.1126/science.abc0870] [Citation(s) in RCA: 446] [Impact Index Per Article: 111.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/05/2020] [Accepted: 07/28/2020] [Indexed: 11/26/2022]
Abstract
For severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to enter human cells, the spike protein on the surface of the virus must bind to the host receptor protein, angiotensin-converting enzyme 2 (ACE2). A soluble version of the receptor is being explored as a therapeutic. Chan et al. used deep mutagenesis to identify ACE2 mutants that bind more tightly to the spike protein and combined mutations to further increase binding affinity (see the Perspective by DeKosky). A promising variant was engineered to be a stable dimer that has a binding affinity for the spike protein; it is comparable with neutralizing antibodies and neutralized both SARS-CoV-2 and SARS-CoV-1 in a cell-based assay. In addition, the similarity to the natural receptor may limit the possibility for viral escape. Science, this issue p. 1261; see also p. 1167 The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds angiotensin-converting enzyme 2 (ACE2) on host cells to initiate entry, and soluble ACE2 is a therapeutic candidate that neutralizes infection by acting as a decoy. By using deep mutagenesis, mutations in ACE2 that increase S binding are found across the interaction surface, in the asparagine 90–glycosylation motif and at buried sites. The mutational landscape provides a blueprint for understanding the specificity of the interaction between ACE2 and S and for engineering high-affinity decoy receptors. Combining mutations gives ACE2 variants with affinities that rival those of monoclonal antibodies. A stable dimeric variant shows potent SARS-CoV-2 and -1 neutralization in vitro. The engineered receptor is catalytically active, and its close similarity with the native receptor may limit the potential for viral escape.
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Affiliation(s)
- Kui K Chan
- Orthogonal Biologics, Champaign, IL 61821, USA
| | - Danielle Dorosky
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Preeti Sharma
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA
| | - Shawn A Abbasi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - David M Kranz
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.,The Geneva Foundation, Tacoma, WA 98402, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA.
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Sharma P, Marada VVVR, Cai Q, Kizerwetter M, He Y, Wolf SP, Schreiber K, Clausen H, Schreiber H, Kranz DM. Structure-guided engineering of the affinity and specificity of CARs against Tn-glycopeptides. Proc Natl Acad Sci U S A 2020; 117:15148-15159. [PMID: 32541028 PMCID: PMC7334454 DOI: 10.1073/pnas.1920662117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The potency of adoptive T cell therapies targeting the cell surface antigen CD19 has been demonstrated in hematopoietic cancers. It has been difficult to identify appropriate targets in nonhematopoietic tumors, but one class of antigens that have shown promise is aberrant O-glycoprotein epitopes. It has long been known that dysregulated synthesis of O-linked (threonine or serine) sugars occurs in many cancers, and that this can lead to the expression of cell surface proteins containing O-glycans comprised of a single N-acetylgalactosamine (GalNAc, known as Tn antigen) rather than the normally extended carbohydrate. Previously, we used the scFv fragment of antibody 237 as a chimeric antigen receptor (CAR) to mediate recognition of mouse tumor cells that bear its cognate Tn-glycopeptide epitope in podoplanin, also called OTS8. Guided by the structure of the 237 Fab:Tn-OTS8-glycopeptide complex, here we conducted a deep mutational scan showing that residues flanking the Tn-glycan contributed significant binding energy to the interaction. Design of 237-scFv libraries in the yeast display system allowed us to isolate scFv variants with higher affinity for Tn-OTS8. Selection with a noncognate human antigen, Tn-MUC1, yielded scFv variants that were broadly reactive with multiple Tn-glycoproteins. When configured as CARs, engineered T cells expressing these scFv variants showed improved activity against mouse and human cancer cell lines defective in O-linked glycosylation. This strategy provides CARs with Tn-peptide specificities, all based on a single scFv scaffold, that allows the same CAR to be tested for toxicity in mice and efficacy against mouse and human tumors.
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Affiliation(s)
- Preeti Sharma
- Department of Biochemistry, Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
| | - Venkata V V R Marada
- Department of Biochemistry, Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Qi Cai
- Department of Biochemistry, Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Monika Kizerwetter
- Department of Biochemistry, Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yanran He
- Department of Pathology, Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Steven P Wolf
- Department of Pathology, Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Karin Schreiber
- Department of Pathology, Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Henrik Clausen
- Copenhagen Center for Glycomics, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Hans Schreiber
- Department of Pathology, Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - David M Kranz
- Department of Biochemistry, Cancer Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
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Park J, Gill KS, Aghajani AA, Heredia JD, Choi H, Oberstein A, Procko E. Engineered receptors for human cytomegalovirus that are orthogonal to normal human biology. PLoS Pathog 2020; 16:e1008647. [PMID: 32559251 PMCID: PMC7329128 DOI: 10.1371/journal.ppat.1008647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/01/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
A trimeric glycoprotein complex on the surface of human cytomegalovirus (HCMV) binds to platelet-derived growth factor (PDGF) receptor α (PDGFRα) to mediate host cell recognition and fusion of the viral and cellular membranes. Soluble PDGFRα potently neutralizes HCMV in tissue culture, and its potential use as an antiviral therapeutic has the benefit that any escape mutants will likely be attenuated. However, PDGFRα binds multiple PDGF ligands in the human body as part of developmental programs in embryogenesis and continuing through adulthood. Any therapies with soluble receptor therefore come with serious efficacy and safety concerns, especially for the treatment of congenital HCMV. Soluble virus receptors that are orthogonal to human biology might resolve these concerns. This engineering problem is solved by deep mutational scanning on the D2-D3 domains of PDGFRα to identify variants that maintain interactions with the HCMV glycoprotein trimer in the presence of competing PDGF ligands. Competition by PDGFs is conformation-dependent, whereas HCMV trimer binding is independent of proper D2-D3 conformation, and many mutations at the receptor-PDGF interface are suitable for functionally separating trimer from PDGF interactions. Purified soluble PDGFRα carrying a targeted mutation succeeded in displaying wild type affinity for HCMV trimer with a simultaneous loss of PDGF binding, and neutralizes trimer-only and trimer/pentamer-expressing HCMV strains infecting fibroblasts or epithelial cells. Overall, this work makes important progress in the realization of soluble HCMV receptors for clinical application. Human cytomegalovirus (HCMV) causes severe disease in transplant recipients and immunocompromised patients, and infections in a fetus or neonate are responsible for life-long neurological defects. Cell entry is in part mediated by a trimeric glycoprotein complex on the viral surface, which binds tightly to the host receptor PDGFRα. The soluble extracellular region of PDGFRα can be used as an antiviral agent to potently neutralize the virus in vitro. However, PDGFRα ordinarily binds growth factors in the human body to regulate developmental programs, which will limit the in vivo efficacy and safety of soluble PDGFRα. Using saturation mutagenesis and selections in human cell culture, mutations in PDGFRα are identified that eliminate off-target growth factor interactions while preserving HCMV binding and neutralization.
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Affiliation(s)
- Jihye Park
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Kevin Sean Gill
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Ali Asghar Aghajani
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Jeremiah Dallas Heredia
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Hannah Choi
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Adam Oberstein
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, Illinois, United States of America
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
- Cancer Center at Illinois (CCIL), University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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26
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Procko E. The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32511321 PMCID: PMC7239051 DOI: 10.1101/2020.03.16.994236] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The rapid and escalating spread of SARS coronavirus 2 (SARS-CoV-2) poses an immediate public health emergency. The viral spike protein S binds ACE2 on host cells to initiate molecular events that release the viral genome intracellularly. Soluble ACE2 inhibits entry of both SARS and SARS-2 coronaviruses by acting as a decoy for S binding sites, and is a candidate for therapeutic, prophylactic and diagnostic development. Using deep mutagenesis, variants of ACE2 are identified with increased binding to the receptor binding domain of S. Mutations are found across the interface, in the N90-glycosylation motif, and at buried sites where they are predicted to enhance local folding and presentation of the interaction epitope. When single substitutions are combined, large increases in binding can be achieved. The mutational landscape offers a blueprint for engineering high affinity proteins and peptides that block receptor binding sites on S to meet this unprecedented challenge.
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Affiliation(s)
- Erik Procko
- Department of Biochemistry, University of Illinois, Urbana IL 61801
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27
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Reeb J, Wirth T, Rost B. Variant effect predictions capture some aspects of deep mutational scanning experiments. BMC Bioinformatics 2020; 21:107. [PMID: 32183714 PMCID: PMC7077003 DOI: 10.1186/s12859-020-3439-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/03/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as missense mutations, or non-synonymous Single Nucleotide Variants - missense SNVs or nsSNVs) for particular proteins. We assembled SAV annotations from 22 different DMS experiments and normalized the effect scores to evaluate variant effect prediction methods. Three trained on traditional variant effect data (PolyPhen-2, SIFT, SNAP2), a regression method optimized on DMS data (Envision), and a naïve prediction using conservation information from homologs. RESULTS On a set of 32,981 SAVs, all methods captured some aspects of the experimental effect scores, albeit not the same. Traditional methods such as SNAP2 correlated slightly more with measurements and better classified binary states (effect or neutral). Envision appeared to better estimate the precise degree of effect. Most surprising was that the simple naïve conservation approach using PSI-BLAST in many cases outperformed other methods. All methods captured beneficial effects (gain-of-function) significantly worse than deleterious (loss-of-function). For the few proteins with multiple independent experimental measurements, experiments differed substantially, but agreed more with each other than with predictions. CONCLUSIONS DMS provides a new powerful experimental means of understanding the dynamics of the protein sequence space. As always, promising new beginnings have to overcome challenges. While our results demonstrated that DMS will be crucial to improve variant effect prediction methods, data diversity hindered simplification and generalization.
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Affiliation(s)
- Jonas Reeb
- Department of Informatics, Bioinformatics & Computational Biology - i12, TUM (Technical University of Munich), Boltzmannstr 3, 85748, Garching/Munich, Germany.
| | - Theresa Wirth
- Department of Informatics, Bioinformatics & Computational Biology - i12, TUM (Technical University of Munich), Boltzmannstr 3, 85748, Garching/Munich, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics & Computational Biology - i12, TUM (Technical University of Munich), Boltzmannstr 3, 85748, Garching/Munich, Germany
- Institute for Advanced Study (TUM-IAS), Lichtenbergstr 2a, 85748, Garching/Munich, Germany
- TUM School of Life Sciences Weihenstephan (WZW), Alte Akademie 8, Freising, Germany
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West, 168th Street, New York, NY, 10032, USA
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Ernst P, Zosel F, Reichen C, Nettels D, Schuler B, Plückthun A. Structure-Guided Design of a Peptide Lock for Modular Peptide Binders. ACS Chem Biol 2020; 15:457-468. [PMID: 31985201 DOI: 10.1021/acschembio.9b00928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peptides play an important role in intermolecular interactions and are frequent analytes in diagnostic assays, also as unstructured, linear epitopes in whole proteins. Yet, due to the many different sequence possibilities even for short peptides, classical selection of binding proteins from a library, one at a time, is not scalable to proteomes. However, moving away from selection to a rational assembly of preselected modules binding to predefined linear epitopes would split the problem into smaller parts. These modules could then be reassembled in any desired order to bind to, in principle, arbitrary sequences, thereby circumventing any new rounds of selection. Designed Armadillo repeat proteins (dArmRPs) are modular, and they do bind elongated peptides in a modular way. Their consensus sequence carries pockets that prefer arginine and lysine. In our quest to select pockets for all amino acid side chains, we had discovered that repetitive sequences can lead to register shifts and peptide flipping during selections from libraries, hindering the selection of new binding specificities. To solve this problem, we now created an orthogonal binding specificity by a combination of grafting from β-catenin, computational design and mutual optimization of the pocket and the bound peptide. We have confirmed the design and the desired interactions by X-ray structure determination. Furthermore, we could confirm the absence of sliding in solution by a single-molecule Förster resonance energy transfer. The new pocket could be moved from the N-terminus of the protein to the middle, retaining its properties, further underlining the modularity of the system.
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Affiliation(s)
- Patrick Ernst
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Franziska Zosel
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Christian Reichen
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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29
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Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF. MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. Genome Biol 2019; 20:223. [PMID: 31679514 PMCID: PMC6827219 DOI: 10.1186/s13059-019-1845-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/01/2019] [Indexed: 11/10/2022] Open
Abstract
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data for basic and clinical research, there is no standard resource for their discovery and distribution. Here, we present MaveDB ( https://www.mavedb.org ), a public repository for large-scale measurements of sequence variant impact, designed for interoperability with applications to interpret these datasets. We also describe the first such application, MaveVis, which retrieves, visualizes, and contextualizes variant effect maps. Together, the database and applications will empower the community to mine these powerful datasets.
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Affiliation(s)
- Daniel Esposito
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jochen Weile
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia
| | - Frederick P Roth
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
- Canadian Institute for Advanced Research, Toronto, ON, Canada.
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Canadian Institute for Advanced Research, Toronto, ON, Canada.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Alan F Rubin
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
- Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
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30
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Foight GW, Wang Z, Wei CT, Jr Greisen P, Warner KM, Cunningham-Bryant D, Park K, Brunette TJ, Sheffler W, Baker D, Maly DJ. Multi-input chemical control of protein dimerization for programming graded cellular responses. Nat Biotechnol 2019; 37:1209-1216. [PMID: 31501561 PMCID: PMC6776690 DOI: 10.1038/s41587-019-0242-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/25/2019] [Indexed: 12/11/2022]
Abstract
Chemical and optogenetic methods for post-translationally controlling protein function have enabled modulation and engineering of cellular functions. However, most of these methods only confer single-input, single-output control. To increase the diversity of post-translational behaviors that can be programmed, we built a system based on a single protein receiver that can integrate multiple drug inputs, including approved therapeutics. Our system translates drug inputs into diverse outputs using a suite of engineered reader proteins to provide variable dimerization states of the receiver protein. We show that our single receiver protein architecture can be used to program a variety of cellular responses, including graded and proportional dual-output control of transcription and mammalian cell signaling. We apply our tools to titrate the competing activities of the Rac and Rho GTPases to control cell morphology. Our versatile tool set will enable researchers to post-translationally program mammalian cellular processes and to engineer cell therapies.
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Affiliation(s)
- Glenna Wink Foight
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Zhizhi Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Cindy T Wei
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Per Jr Greisen
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Global Research, Novo Nordisk A/S, Måløv, Denmark
| | - Katrina M Warner
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | | | - Keunwan Park
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Systems Biotechnology Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
| | - T J Brunette
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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31
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Day AL, Greisen P, Doyle L, Schena A, Stella N, Johnsson K, Baker D, Stoddard B. Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold. Protein Eng Des Sel 2019; 31:375-387. [PMID: 30566669 DOI: 10.1093/protein/gzy031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/02/2018] [Accepted: 11/07/2018] [Indexed: 12/25/2022] Open
Abstract
Attempts to create novel ligand-binding proteins often focus on formation of a binding pocket with shape complementarity against the desired ligand (particularly for compounds that lack distinct polar moieties). Although designed proteins often exhibit binding of the desired ligand, in some cases they display unintended recognition behavior. One such designed protein, that was originally intended to bind tetrahydrocannabinol (THC), was found instead to display binding of 25-hydroxy-cholecalciferol (25-D3) and was subjected to biochemical characterization, further selections for enhanced 25-D3 binding affinity and crystallographic analyses. The deviation in specificity is due in part to unexpected altertion of its conformation, corresponding to a significant change of the orientation of an α-helix and an equally large movement of a loop, both of which flank the designed ligand-binding pocket. Those changes led to engineered protein constructs that exhibit significantly more contacts and complementarity towards the 25-D3 ligand than the initial designed protein had been predicted to form towards its intended THC ligand. Molecular dynamics simulations imply that the initial computationally designed mutations may contribute to the movement of the helix. These analyses collectively indicate that accurate prediction and control of backbone dynamics conformation, through a combination of improved conformational sampling and/or de novo structure design, represents a key area of further development for the design and optimization of engineered ligand-binding proteins.
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Affiliation(s)
- Austin L Day
- Departments of Bioengineering and Biochemistry, University of Washington, Molecular Engineering and Sciences, Seattle, WA, USA
| | - Per Greisen
- Departments of Bioengineering and Biochemistry, University of Washington, Molecular Engineering and Sciences, Seattle, WA, USA
| | - Lindsey Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA
| | - Alberto Schena
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nephi Stella
- Departments of Bioengineering and Biochemistry, University of Washington, Molecular Engineering and Sciences, Seattle, WA, USA
| | - Kai Johnsson
- Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - David Baker
- Departments of Bioengineering and Biochemistry, University of Washington, Molecular Engineering and Sciences, Seattle, WA, USA
| | - Barry Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA
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Conformational Engineering of HIV-1 Env Based on Mutational Tolerance in the CD4 and PG16 Bound States. J Virol 2019; 93:JVI.00219-19. [PMID: 30894475 DOI: 10.1128/jvi.00219-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/16/2019] [Indexed: 12/22/2022] Open
Abstract
HIV-1 infection is initiated by viral Env engaging the host receptor CD4, triggering Env to transition from a "closed" to "open" conformation during the early events of virus-cell membrane fusion. To understand how Env sequence accommodates this conformational change, mutational landscapes decoupled from virus replication were determined for Env from BaL (clade B) and DU422 (clade C) isolates interacting with CD4 or antibody PG16 that preferentially recognizes closed trimers. Sequence features uniquely important to each bound state were identified, including glycosylation and binding sites. Notably, the Env apical domain and trimerization interface are under selective pressure for PG16 binding. Based on this key observation, mutations were found that increase presentation of quaternary epitopes associated with properly conformed trimers when Env is expressed at the plasma membrane. Many mutations reduce electrostatic repulsion at the Env apex and increase PG16 recognition of Env sequences from clades A and B. Other mutations increase hydrophobic packing at the gp120 inner-outer domain interface and were broadly applicable for engineering Env from diverse strains spanning tiers 1, 2, and 3 across clades A, B, C, and BC recombinants. Core mutations predicted to introduce steric strain in the open state show markedly reduced CD4 interactions. Finally, we demonstrate how our methodology can be adapted to interrogate interactions between membrane-associated Env and the matrix domain of Gag. These findings and methods may assist vaccine design.IMPORTANCE HIV-1 Env is dynamic and undergoes large conformational changes that drive fusion of virus and host cell membranes. Three Env proteins in a trimer contact each other at their apical tips to form a closed conformation that presents epitopes recognized by broadly neutralizing antibodies. The apical tips separate, among other changes, to form an open conformation that binds tightly to host receptors. Understanding how Env sequence facilitates these structural changes can inform the biophysical mechanism and aid immunogen design. Using deep mutational scans decoupled from virus replication, we report mutational landscapes for Env from two strains interacting with conformation-dependent binding proteins. Residues in the Env trimer interface and apical domains are preferentially conserved in the closed conformation, and conformational diversity is facilitated by electrostatic repulsion and an underpacked core between domains. Specific mutations are described that enhance presentation of the trimeric closed conformation across diverse HIV-1 strains.
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Park J, Selvam B, Sanematsu K, Shigemura N, Shukla D, Procko E. Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits. J Biol Chem 2019; 294:4759-4774. [PMID: 30723160 DOI: 10.1074/jbc.ra118.006173] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/24/2019] [Indexed: 01/06/2023] Open
Abstract
Class C G protein-coupled receptors (GPCRs) are obligatory dimers that are particularly important for neuronal responses to endogenous and environmental stimuli. Ligand recognition through large extracellular domains leads to the reorganization of transmembrane regions to activate G protein signaling. Although structures of individual domains are known, the complete architecture of a class C GPCR and the mechanism of interdomain coupling during receptor activation are unclear. By screening a mutagenesis library of the human class C sweet taste receptor subunit T1R2, we enhanced surface expression and identified a dibasic intracellular retention motif that modulates surface expression and co-trafficking with its heterodimeric partner T1R3. Using a highly expressed T1R2 variant, dimerization sites along the entire subunit within all the structural domains were identified by a comprehensive mutational scan for co-trafficking with T1R3 in human cells. The data further reveal that the C terminus of the extracellular cysteine-rich domain needs to be properly folded for T1R3 dimerization and co-trafficking, but not for surface expression of T1R2 alone. These results guided the modeling of the T1R2-T1R3 dimer in living cells, which predicts a twisted arrangement of domains around the central axis, and a continuous folded structure between transmembrane domain loops and the cysteine-rich domains. These insights have implications for how conformational changes between domains are coupled within class C GPCRs.
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Affiliation(s)
- Jihye Park
- From the Departments of Biochemistry and
| | - Balaji Selvam
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
| | - Keisuke Sanematsu
- the Section of Oral Neuroscience, Graduate School of Dental Science, and.,the Division of Sensory Physiology-Medical Application Sensing, Research and Development Center for Five-Sense Devices, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Noriatsu Shigemura
- the Section of Oral Neuroscience, Graduate School of Dental Science, and.,the Division of Sensory Physiology-Medical Application Sensing, Research and Development Center for Five-Sense Devices, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Diwakar Shukla
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
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Zhai J, Zhao M, Cao X, Li M, Zhao M. Metal-Ion-Responsive Bionanocomposite for Selective and Reversible Enzyme Inhibition. J Am Chem Soc 2018; 140:16925-16928. [DOI: 10.1021/jacs.8b10848] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Junqiu Zhai
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Muhua Zhao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiangjian Cao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Mengyuan Li
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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35
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Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, Vaughan JC, Stoddard BL, Baker D. De novo design of a fluorescence-activating β-barrel. Nature 2018; 561:485-491. [PMID: 30209393 PMCID: PMC6275156 DOI: 10.1038/s41586-018-0509-0] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/10/2018] [Indexed: 01/07/2023]
Abstract
The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of α-helical coiled-coil structures, but to date there has been no success with β-barrels. Here we show that accurate de novo design of β-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of β-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. This de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.
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Affiliation(s)
- Jiayi Dou
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Anastassia A. Vorobieva
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Lindsey A. Doyle
- Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Matthew J. Bick
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Binchen Mao
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Glenna W. Foight
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Min Yen Lee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Lauren A. Gagnon
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Enrique Marcos
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Barry L. Stoddard
- Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA,# corresponding author
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36
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Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas. Hum Genet 2018; 137:665-678. [PMID: 30073413 PMCID: PMC6153521 DOI: 10.1007/s00439-018-1916-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/21/2018] [Indexed: 12/12/2022]
Abstract
Given the constantly improving cost and speed of genome sequencing, it is reasonable to expect that personal genomes will soon be known for many millions of humans. This stands in stark contrast with our limited ability to interpret the sequence variants which we find. Although it is, perhaps, easiest to interpret variants in coding regions, knowledge of functional impact is unknown for the vast majority of missense variants. While many computational approaches can predict the impact of coding variants, they are given a little weight in the current guidelines for interpreting clinical variants. Laboratory assays produce comparatively more trustworthy results, but until recently did not scale to the space of all possible mutations. The development of deep mutational scanning and other multiplexed assays of variant effect has now brought feasibility of this endeavour within view. Here, we review progress in this field over the last decade, break down the different approaches into their components, and compare methodological differences.
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37
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Heredia JD, Park J, Brubaker RJ, Szymanski SK, Gill KS, Procko E. Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning. THE JOURNAL OF IMMUNOLOGY 2018; 200:3825-3839. [PMID: 29678950 DOI: 10.4049/jimmunol.1800343] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/30/2018] [Indexed: 02/02/2023]
Abstract
Chemokine receptors CXCR4 and CCR5 regulate WBC trafficking and are engaged by the HIV-1 envelope glycoprotein gp120 during infection. We combine a selection of human CXCR4 and CCR5 libraries comprising nearly all of ∼7000 single amino acid substitutions with deep sequencing to define sequence-activity landscapes for surface expression and ligand interactions. After consideration of sequence constraints for surface expression, known interaction sites with HIV-1-blocking Abs were appropriately identified as conserved residues following library sorting for Ab binding, validating the use of deep mutational scanning to map functional interaction sites in G protein-coupled receptors. Chemokine CXCL12 was found to interact with residues extending asymmetrically into the CXCR4 ligand-binding cavity, similar to the binding surface of CXCR4 recognized by an antagonistic viral chemokine previously observed crystallographically. CXCR4 mutations distal from the chemokine binding site were identified that enhance chemokine recognition. This included disruptive mutations in the G protein-coupling site that diminished calcium mobilization, as well as conservative mutations to a membrane-exposed site (CXCR4 residues H792.45 and W1614.50) that increased ligand binding without loss of signaling. Compared with CXCR4-CXCL12 interactions, CCR5 residues conserved for gp120 (HIV-1 BaL strain) interactions map to a more expansive surface, mimicking how the cognate chemokine CCL5 makes contacts across the entire CCR5 binding cavity. Acidic substitutions in the CCR5 N terminus and extracellular loops enhanced gp120 binding. This study demonstrates how comprehensive mutational scanning can define functional interaction sites on receptors, and novel mutations that enhance receptor activities can be found simultaneously.
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Affiliation(s)
- Jeremiah D Heredia
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jihye Park
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Riley J Brubaker
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Steven K Szymanski
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Kevin S Gill
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Erik Procko
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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38
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Yagi S, Akanuma S, Yamagishi A. Creation of artificial protein-protein interactions using α-helices as interfaces. Biophys Rev 2018; 10:411-420. [PMID: 29214605 PMCID: PMC5899712 DOI: 10.1007/s12551-017-0352-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/15/2017] [Indexed: 12/31/2022] Open
Abstract
Designing novel protein-protein interactions (PPIs) with high affinity is a challenging task. Directed evolution, a combination of randomization of the gene for the protein of interest and selection using a display technique, is one of the most powerful tools for producing a protein binder. However, the selected proteins often bind to the target protein at an undesired surface. More problematically, some selected proteins bind to their targets even though they are unfolded. Current state-of-the-art computational design methods have successfully created novel protein binders. These computational methods have optimized the non-covalent interactions at interfaces and thus produced artificial protein complexes. However, to date there are only a limited number of successful examples of computationally designed de novo PPIs. De novo design of coiled-coil proteins has been extensively performed and, therefore, a large amount of knowledge of the sequence-structure relationship of coiled-coil proteins has been accumulated. Taking advantage of this knowledge, de novo design of inter-helical interactions has been used to produce artificial PPIs. Here, we review recent progress in the in silico design and rational design of de novo PPIs and the use of α-helices as interfaces.
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Affiliation(s)
- Sota Yagi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.
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39
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Foight GW, Chen TS, Richman D, Keating AE. Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design. Methods Mol Biol 2018; 1561:213-232. [PMID: 28236241 DOI: 10.1007/978-1-4939-6798-8_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peptide reagents with high affinity or specificity for their target protein interaction partner are of utility for many important applications. Optimization of peptide binding by screening large libraries is a proven and powerful approach. Libraries designed to be enriched in peptide sequences that are predicted to have desired affinity or specificity characteristics are more likely to yield success than random mutagenesis. We present a library optimization method in which the choice of amino acids to encode at each peptide position can be guided by available experimental data or structure-based predictions. We discuss how to use analysis of predicted library performance to inform rounds of library design. Finally, we include protocols for more complex library design procedures that consider the chemical diversity of the amino acids at each peptide position and optimize a library score based on a user-specified input model.
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Affiliation(s)
- Glenna Wink Foight
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Bldg., 68-622, Cambridge, MA, 02139, USA
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - T Scott Chen
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Bldg., 68-622, Cambridge, MA, 02139, USA
- Google Inc., Mountain View, CA, 94043, USA
| | - Daniel Richman
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Bldg., 68-622, Cambridge, MA, 02139, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Bldg., 68-622, Cambridge, MA, 02139, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Bldg., 68-622, Cambridge, MA, 02139, USA.
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40
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Abstract
The immune systems protect our bodies from foreign molecules or antigens, where antibodies play important roles. Antibodies evolve over time upon antigen encounter by somatically mutating their genome sequences. The end result is a series of antibodies that display higher affinities and specificities to specific antigens. This process is called affinity maturation. Recent improvements in computer hardware and modeling algorithms now enable the rational design of protein structures and functions, and several works on computer-aided antibody design have been published. In this chapter, we briefly describe computational methods for antibody affinity maturation, focusing on methods for sampling antibody conformations and for scoring designed antibody variants. We also discuss lessons learned from the successful computer-aided design of antibodies.
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Affiliation(s)
- Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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41
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Leong SW, Lim TS, Ismail A, Choong YS. Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein. J Mol Recognit 2017; 31:e2695. [PMID: 29230887 DOI: 10.1002/jmr.2695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/13/2017] [Accepted: 11/19/2017] [Indexed: 01/10/2023]
Abstract
With the development of de novo binders for protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking "disembodied" amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural protein-antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen-based detection agents for typhoid diagnostics.
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Affiliation(s)
- Siew Wen Leong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Asma Ismail
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, Penang, Malaysia
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42
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Sharma P, Kranz DM. Subtle changes at the variable domain interface of the T-cell receptor can strongly increase affinity. J Biol Chem 2017; 293:1820-1834. [PMID: 29229779 DOI: 10.1074/jbc.m117.814152] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/03/2017] [Indexed: 11/06/2022] Open
Abstract
Most affinity-maturation campaigns for antibodies and T-cell receptors (TCRs) operate on the residues at the binding site, located within the loops known as complementarity-determining regions (CDRs). Accordingly, mutations in contact residues, or so-called "second shell" residues, that increase affinity are typically identified by directed evolution involving combinatorial libraries. To determine the impact of residues located at a distance from the binding site, here we used single-codon libraries of both CDR and non-CDR residues to generate a deep mutational scan of a human TCR against the cancer antigen MART-1·HLA-A2. Non-CDR residues included those at the interface of the TCR variable domains (Vα and Vβ) and surface-exposed framework residues. Mutational analyses showed that both Vα/Vβ interface and CDR residues were important in maintaining binding to MART-1·HLA-A2, probably due to either structural requirements for proper Vα/Vβ association or direct contact with the ligand. More surprisingly, many Vα/Vβ interface substitutions yielded improved binding to MART-1·HLA-A2. To further explore this finding, we constructed interface libraries and selected them for improved stability or affinity. Among the variants identified, one conservative substitution (F45βY) was most prevalent. Further analysis of F45βY showed that it enhanced thermostability and increased affinity by 60-fold. Thus, introducing a single hydroxyl group at the Vα/Vβ interface, at a significant distance from the TCR·peptide·MHC-binding site, remarkably affected ligand binding. The variant retained a high degree of specificity for MART-1·HLA-A2, indicating that our approach provides a general strategy for engineering improvements in either soluble or cell-based TCRs for therapeutic purposes.
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Affiliation(s)
- Preeti Sharma
- From the Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - David M Kranz
- From the Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
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43
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Chapman AM, McNaughton BR. Scratching the Surface: Resurfacing Proteins to Endow New Properties and Function. Cell Chem Biol 2017; 23:543-553. [PMID: 27203375 DOI: 10.1016/j.chembiol.2016.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 12/22/2022]
Abstract
Protein engineering is an emerging discipline that dovetails modern molecular biology techniques with high-throughput screening, laboratory evolution technologies, and computational approaches to modify sequence, structure, and, in some cases, function and properties of proteins. The ultimate goal is to develop new proteins with improved or designer functions for use in biotechnology, medicine, and basic research. One way to engineer proteins is to change their solvent-exposed regions through focused or random "protein resurfacing." In this review we explain what protein resurfacing is, and discuss recent examples of how this strategy is used to generate proteins with altered or broadened recognition profiles, improved stability, solubility, and expression, cell-penetrating ability, and reduced immunogenicity. Additionally we comment on how these properties can be further improved using chemical resurfacing approaches. Protein resurfacing will likely play an increasingly important role as more biologics enter clinical use, and we present some arguments to support this view.
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Affiliation(s)
- Alex M Chapman
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian R McNaughton
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA; Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.
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44
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Dou J, Doyle L, Jr Greisen P, Schena A, Park H, Johnsson K, Stoddard BL, Baker D. Sampling and energy evaluation challenges in ligand binding protein design. Protein Sci 2017; 26:2426-2437. [PMID: 28980354 PMCID: PMC5699494 DOI: 10.1002/pro.3317] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 11/06/2022]
Abstract
The steroid hormone 17α-hydroxylprogesterone (17-OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17-OHP containing an extended, nonpolar, shape-complementary binding pocket for the four-ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17-OHP with micromolar affinity. A co-crystal structure of one of the designs revealed that 17-OHP is rotated 180° around a pseudo-two-fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same "flipped" orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two-fold symmetry of the molecule.
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Affiliation(s)
- Jiayi Dou
- Department of Bioengineering, University of Washington, Seattle, Washington.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington
| | - Lindsey Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Per Jr Greisen
- Global Research, Novo Nordisk A/S, DK-2760, Måløv, Denmark
| | - Alberto Schena
- Ecole Polytechnique Federale de Lausanne, Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research (NCCR) in Chemical Biology, Lausanne, Switzerland
| | - Hahnbeom Park
- Institute for Protein Design, University of Washington, Seattle, Washington.,Department of Biochemistry, University of Washington, Seattle, Washington
| | - Kai Johnsson
- Ecole Polytechnique Federale de Lausanne, Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research (NCCR) in Chemical Biology, Lausanne, Switzerland
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, Washington.,Department of Biochemistry, University of Washington, Seattle, Washington.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington
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Ivanov SM, Cawley A, Huber RG, Bond PJ, Warwicker J. Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold. PLoS One 2017; 12:e0185928. [PMID: 29016650 PMCID: PMC5634604 DOI: 10.1371/journal.pone.0185928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/21/2017] [Indexed: 12/05/2022] Open
Abstract
An improved knowledge of protein-protein interactions is essential for better understanding of metabolic and signaling networks, and cellular function. Progress tends to be based on structure determination and predictions using known structures, along with computational methods based on evolutionary information or detailed atomistic descriptions. We hypothesized that for the case of interactions across a common interface, between proteins from a pair of paralogue families or within a family of paralogues, a relatively simple interface description could distinguish between binding and non-binding pairs. Using binding data for several systems, and large-scale comparative modeling based on known template complex structures, it is found that charge-charge interactions (for groups bearing net charge) are generally a better discriminant than buried non-polar surface. This is particularly the case for paralogue families that are less divergent, with more reliable comparative modeling. We suggest that electrostatic interactions are major determinants of specificity in such systems, an observation that could be used to predict binding partners.
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Affiliation(s)
- Stefan M. Ivanov
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Andrew Cawley
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jim Warwicker
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
- * E-mail:
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46
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Hidden Markov model and Chapman Kolmogrov for protein structures prediction from images. Comput Biol Chem 2017; 68:231-244. [DOI: 10.1016/j.compbiolchem.2017.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/11/2017] [Accepted: 04/11/2017] [Indexed: 11/20/2022]
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Abstract
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs. Future challenges also include dissemination of CPD software to the general use of life-sciences researchers and the emphasis of success within an in vivo milieu. CPD increases our understanding of protein structure and function and the relationships between the two along with the application of such know-how for the benefit of mankind. Applied aspects range from biological drugs, via healthier and tastier food products to nanotechnology and environmentally friendly enzymes replacing toxic chemicals utilized in the industry.
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Brender JR, Shultis D, Khattak NA, Zhang Y. An Evolution-Based Approach to De Novo Protein Design. Methods Mol Biol 2017; 1529:243-264. [PMID: 27914055 PMCID: PMC5667548 DOI: 10.1007/978-1-4939-6637-0_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
EvoDesign is a computational algorithm that allows the rapid creation of new protein sequences that are compatible with specific protein structures. As such, it can be used to optimize protein stability, to resculpt the protein surface to eliminate undesired protein-protein interactions, and to optimize protein-protein binding. A major distinguishing feature of EvoDesign in comparison to other protein design programs is the use of evolutionary information in the design process to guide the sequence search toward native-like sequences known to adopt structurally similar folds as the target. The observed frequencies of amino acids in specific positions in the structure in the form of structural profiles collected from proteins with similar folds and complexes with similar interfaces can implicitly capture many subtle effects that are essential for correct folding and protein-binding interactions. As a result of the inclusion of evolutionary information, the sequences designed by EvoDesign have native-like folding and binding properties not seen by other physics-based design methods. In this chapter, we describe how EvoDesign can be used to redesign proteins with a focus on the computational and experimental procedures that can be used to validate the designs.
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van Rosmalen M, Janssen BMG, Hendrikse NM, van der Linden AJ, Pieters PA, Wanders D, de Greef TFA, Merkx M. Affinity Maturation of a Cyclic Peptide Handle for Therapeutic Antibodies Using Deep Mutational Scanning. J Biol Chem 2016; 292:1477-1489. [PMID: 27974464 DOI: 10.1074/jbc.m116.764225] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/29/2016] [Indexed: 11/06/2022] Open
Abstract
Meditopes are cyclic peptides that bind in a specific pocket in the antigen-binding fragment of a therapeutic antibody such as cetuximab. Provided their moderate affinity can be enhanced, meditope peptides could be used as specific non-covalent and paratope-independent handles in targeted drug delivery, molecular imaging, and therapeutic drug monitoring. Here we show that the affinity of a recently reported meditope for cetuximab can be substantially enhanced using a combination of yeast display and deep mutational scanning. Deep sequencing was used to construct a fitness landscape of this protein-peptide interaction, and four mutations were identified that together improved the affinity for cetuximab 10-fold to 15 nm Importantly, the increased affinity translated into enhanced cetuximab-mediated recruitment to EGF receptor-overexpressing cancer cells. Although in silico Rosetta simulations correctly identified positions that were tolerant to mutation, modeling did not accurately predict the affinity-enhancing mutations. The experimental approach reported here should be generally applicable and could be used to develop meditope peptides with low nanomolar affinity for other therapeutic antibodies.
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Affiliation(s)
- Martijn van Rosmalen
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Brian M G Janssen
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Natalie M Hendrikse
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Ardjan J van der Linden
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Pascal A Pieters
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Dave Wanders
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Tom F A de Greef
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- From the Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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50
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Riley TP, Ayres CM, Hellman LM, Singh NK, Cosiano M, Cimons JM, Anderson MJ, Piepenbrink KH, Pierce BG, Weng Z, Baker BM. A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Eng Des Sel 2016; 29:595-606. [PMID: 27624308 PMCID: PMC5181382 DOI: 10.1093/protein/gzw050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 11/13/2022] Open
Abstract
T-cell receptors (TCRs) have emerged as a new class of therapeutics, most prominently for cancer where they are the key components of new cellular therapies as well as soluble biologics. Many studies have generated high affinity TCRs in order to enhance sensitivity. Recent outcomes, however, have suggested that fine manipulation of TCR binding, with an emphasis on specificity may be more valuable than large affinity increments. Structure-guided design is ideally suited for this role, and here we studied the generality of structure-guided design as applied to TCRs. We found that a previous approach, which successfully optimized the binding of a therapeutic TCR, had poor accuracy when applied to a broader set of TCR interfaces. We thus sought to develop a more general purpose TCR design framework. After assembling a large dataset of experimental data spanning multiple interfaces, we trained a new scoring function that accounted for unique features of each interface. Together with other improvements, such as explicit inclusion of molecular flexibility, this permitted the design new affinity-enhancing mutations in multiple TCRs, including those not used in training. Our approach also captured the impacts of mutations and substitutions in the peptide/MHC ligand, and recapitulated recent findings regarding TCR specificity, indicating utility in more general mutational scanning of TCR-pMHC interfaces.
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Affiliation(s)
- Timothy P Riley
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Lance M Hellman
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Nishant K Singh
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Michael Cosiano
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Jennifer M Cimons
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Michael J Anderson
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Kurt H Piepenbrink
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Brian G Pierce
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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