1
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Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE. Computational design of soluble and functional membrane protein analogues. Nature 2024; 631:449-458. [PMID: 38898281 PMCID: PMC11236705 DOI: 10.1038/s41586-024-07601-y] [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: 05/09/2023] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
De novo design of complex protein folds using solely computational means remains a substantial challenge1. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors2, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses demonstrate the high thermal stability of the designs, and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, as a proof of concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we have designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.
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Affiliation(s)
- Casper A Goverde
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Goldbach
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lars J Dornfeld
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Petra E M Balbi
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stéphane Rosset
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Srajan Kapoor
- Department of Structural Biology, University at Buffalo, Buffalo, NY, USA
| | - Jagrity Choudhury
- Department of Structural Biology, University at Buffalo, Buffalo, NY, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Christian Schellhaas
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Simon Kozlov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Sergey Ovchinnikov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex J Vecchio
- Department of Structural Biology, University at Buffalo, Buffalo, NY, USA
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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2
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Simpson MS, De Luca H, Cauthorn S, Luong P, Udeshi ND, Svinkina T, Schmieder SS, Carr SA, Grey MJ, Lencer WI. IRE1α recognizes a structural motif in cholera toxin to activate an unfolded protein response. J Cell Biol 2024; 223:e202402062. [PMID: 38578285 PMCID: PMC10996581 DOI: 10.1083/jcb.202402062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
IRE1α is an endoplasmic reticulum (ER) sensor that recognizes misfolded proteins to induce the unfolded protein response (UPR). We studied cholera toxin (CTx), which invades the ER and activates IRE1α in host cells, to understand how unfolded proteins are recognized. Proximity labeling colocalized the enzymatic and metastable A1 segment of CTx (CTxA1) with IRE1α in live cells, where we also found that CTx-induced IRE1α activation enhanced toxicity. In vitro, CTxA1 bound the IRE1α lumenal domain (IRE1αLD), but global unfolding was not required. Rather, the IRE1αLD recognized a seven-residue motif within an edge β-strand of CTxA1 that must locally unfold for binding. Binding mapped to a pocket on IRE1αLD normally occupied by a segment of the IRE1α C-terminal flexible loop implicated in IRE1α oligomerization. Mutation of the CTxA1 recognition motif blocked CTx-induced IRE1α activation in live cells, thus linking the binding event with IRE1α signal transduction and induction of the UPR.
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Affiliation(s)
- Mariska S. Simpson
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
- Graduate School of Life Sciences, Utrecht University, Utrecht, Netherlands
| | - Heidi De Luca
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
| | - Sarah Cauthorn
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Phi Luong
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
| | | | | | - Stefanie S. Schmieder
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | | | - Michael J. Grey
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Harvard Digestive Disease Center, Boston, MA, USA
| | - Wayne I. Lencer
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Harvard Digestive Disease Center, Boston, MA, USA
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3
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Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE. Computational design of soluble functional analogues of integral membrane proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.09.540044. [PMID: 38496615 PMCID: PMC10942269 DOI: 10.1101/2023.05.09.540044] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
De novo design of complex protein folds using solely computational means remains a significant challenge. Here, we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from GPCRs, are not found in the soluble proteome and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses reveal high thermal stability of the designs and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, standing as a proof-of-concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.
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4
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Svilenov HL, Delhommel F, Siebenmorgen T, Rührnößl F, Popowicz GM, Reiter A, Sattler M, Brockmeyer C, Buchner J. Extrinsic stabilization of antiviral ACE2-Fc fusion proteins targeting SARS-CoV-2. Commun Biol 2023; 6:386. [PMID: 37031320 PMCID: PMC10082628 DOI: 10.1038/s42003-023-04762-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
The angiotensin-converting enzyme 2 (ACE2) is a viral receptor used by sarbecoviruses to infect cells. Fusion proteins comprising extracellular ACE2 domains and the Fc part of immunoglobulins exhibit high virus neutralization efficiency, but the structure and stability of these molecules are poorly understood. We show that although the hinge between the ACE2 and the IgG4-Fc is highly flexible, the conformational dynamics of the two ACE2 domains is restricted by their association. Interestingly, the conformational stability of the ACE2 moiety is much lower than that of the Fc part. We found that chemical compounds binding to ACE2, such as DX600 and MLN4760, can be used to strongly increase the thermal stability of the ACE2 by different mechanisms. Together, our findings reveal a general concept for stabilizing the labile receptor segments of therapeutic antiviral fusion proteins by chemical compounds.
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Affiliation(s)
- Hristo L Svilenov
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany.
- Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | - Till Siebenmorgen
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | - Florian Rührnößl
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | | | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, 85748, Munich, Germany
| | | | - Johannes Buchner
- Center for Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of Bioscience, Technical University of Munich, 85748, Garching, Germany.
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5
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Xi Z, Liu X, Lin R, Persons JD, Ilina TV, Li W, Dimitrov DS, Ishima R. The reduced form of the antibody CH2 domain. Protein Sci 2021; 30:1895-1903. [PMID: 34107549 DOI: 10.1002/pro.4142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022]
Abstract
Among the immunoglobulin domains, the CH2 domain has the lowest thermal stability, which also depends on amino acid sequence and buffer conditions. To further identify factors that influence CH2 folding and stability, we characterized the domain in the reduced form using differential scanning fluorimetry and nuclear magnetic resonance. We show that the CH2 domain can fold, similarly to the disulfide-bridged form, without forming a disulfide-bridge, even though the protein contains two Cys residues. Although the reduced form exhibits thermal stability more than 15°C lower than the disulfide-bridged form, it does not undergo immediate full oxidization. To explain this phenomenon, we compared CH2 oxidization at different conditions and demonstrate a need for significant fluctuation of the folded conformation to enhance CH2 disulfide-bridge formation. We conclude that, since CH2 can be purified as a folded, semi-stable, reduced protein that can coexist with the oxidized form, verification of the level of oxidization at each step is critical in CH2 engineering studies.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Xianglei Liu
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rui Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Gastroenterology and Hepatology, Tianjin Medical University, General Hospital, Tianjin, China
| | - John D Persons
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Wei Li
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dimiter S Dimitrov
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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6
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Pastrana B, Nieves S, Li W, Liu X, Dimitrov DS. Developability Assessment of an Isolated C H2 Immunoglobulin Domain. Anal Chem 2021; 93:1342-1351. [PMID: 33325681 DOI: 10.1021/acs.analchem.0c02663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The IgG CH2 domain continues to hold promise for the development of new therapeutic entities because of its bifunctional role as a biomarker and effector protein. The need for further understanding of molecular stability and aggregation in therapeutic proteins has led to the development of a breakthrough quantum cascade laser microscope to allow for real-time comparability assessment of an array of related proteins in solution upon thermal perturbation. Our objective was to perform a comprehensive developability assessment of three similar monoclonal antibody (mAb) fragments: CH2, CH2s, and m01s. The CH2 construct consists of residues Pro238 to Lys340 of the IgG1 heavy chain sequence. CH2s has a 7-residue deletion at the N-terminus and a 16-residue C-terminal extension containing a histidine tag. The m01s construct is identical to CH2s, except for two cysteines introduced at positions 242 and 334. A series of hyperspectral images was acquired during thermal perturbation from 28 to 60 °C for all three proteins in an array. Co-distribution and two-dimensional infrared correlation spectroscopies yielded the mechanism of aggregation and stability for these three proteins. The level of detail is unprecedented, identifying the regions within CH2 and CH2s that are prone to self-association and establishing the differences in stability. Furthermore, CH2 helical segments, β-sheets, β-turns, and random coil regions were less stable than in CH2s and m01s because of the presence of the N-terminal 310-helix and β-turn type III. The engineered disulfide bridge in m01s eliminated the self-association process and rendered this mAb fragment the most stable.
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Affiliation(s)
- Belinda Pastrana
- Protein Dynamic Solutions, 9 Audubon Road, Wakefield, Massachusetts 01880-1256, United States
| | - Sherly Nieves
- Protein Dynamic Solutions, 9 Audubon Road, Wakefield, Massachusetts 01880-1256, United States
| | - Wei Li
- National Cancer Institute, Frederick, Maryland 21702-1201, United States.,Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, Pennsylvania 15261, United States
| | - Xianglei Liu
- Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, Pennsylvania 15261, United States
| | - Dimiter S Dimitrov
- National Cancer Institute, Frederick, Maryland 21702-1201, United States.,Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh, 3550 Terrace Street, Pittsburgh, Pennsylvania 15261, United States
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7
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Molecular mechanism of amyloidogenic mutations in hypervariable regions of antibody light chains. J Biol Chem 2021; 296:100334. [PMID: 33508322 PMCID: PMC7949129 DOI: 10.1016/j.jbc.2021.100334] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
Systemic light chain (AL) amyloidosis is a fatal protein misfolding disease in which excessive secretion, misfolding, and subsequent aggregation of free antibody light chains eventually lead to deposition of amyloid plaques in various organs. Patient-specific mutations in the antibody VL domain are closely linked to the disease, but the molecular mechanisms by which certain mutations induce misfolding and amyloid aggregation of antibody domains are still poorly understood. Here, we compare a patient VL domain with its nonamyloidogenic germline counterpart and show that, out of the five mutations present, two of them strongly destabilize the protein and induce amyloid fibril formation. Surprisingly, the decisive, disease-causing mutations are located in the highly variable complementarity determining regions (CDRs) but exhibit a strong impact on the dynamics of conserved core regions of the patient VL domain. This effect seems to be based on a deviation from the canonical CDR structures of CDR2 and CDR3 induced by the substitutions. The amyloid-driving mutations are not necessarily involved in propagating fibril formation by providing specific side chain interactions within the fibril structure. Rather, they destabilize the VL domain in a specific way, increasing the dynamics of framework regions, which can then change their conformation to form the fibril core. These findings reveal unexpected influences of CDR-framework interactions on antibody architecture, stability, and amyloid propensity.
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8
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Weber B, Maier A, Buchner J. Peptides in proteins. J Pept Sci 2019; 26:e3235. [PMID: 31867828 DOI: 10.1002/psc.3235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 12/18/2022]
Abstract
During evolution C-terminal peptide extensions were added to proteins on the gene level. These convey additional functions such as interaction with partner proteins or oligomerisation. IgM antibodies and molecular chaperones are two prominent examples discussed.
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Affiliation(s)
- Benedikt Weber
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Andreas Maier
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
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9
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Gao X, Conard A, Yang C, Zhan Y, Zeng F, Shi J, Li W, Dimitrov DS, Gong R. Optimization of the C-Terminus of an Autonomous Human IgG1 CH2 Domain for Stability and Aggregation Resistance. Mol Pharm 2019; 16:3647-3656. [DOI: 10.1021/acs.molpharmaceut.9b00544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xinyu Gao
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alex Conard
- Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania 15261, United States
| | - Chunpeng Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yancheng Zhan
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Zeng
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Wei Li
- Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania 15261, United States
| | - Dimiter S. Dimitrov
- Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania 15261, United States
| | - Rui Gong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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