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Wu NC, Yuan M, Liu H, Lee CCD, Zhu X, Bangaru S, Torres JL, Caniels TG, Brouwer PJM, van Gils MJ, Sanders RW, Ward AB, Wilson IA. An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain. Cell Rep 2020; 33:108274. [PMID: 33027617 PMCID: PMC7522650 DOI: 10.1016/j.celrep.2020.108274] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022] Open
Abstract
IGHV3-53-encoded neutralizing antibodies are commonly elicited during SARS-CoV-2 infection and target the receptor-binding domain (RBD) of the spike (S) protein. Such IGHV3-53 antibodies generally have a short CDR H3 because of structural constraints in binding the RBD (mode A). However, a small subset of IGHV3-53 antibodies to the RBD contain a longer CDR H3. Crystal structures of two IGHV3-53 neutralizing antibodies here demonstrate that a longer CDR H3 can be accommodated in a different binding mode (mode B). These two classes of IGHV3-53 antibodies both target the ACE2 receptor binding site, but with very different angles of approach and molecular interactions. Overall, these findings emphasize the versatility of IGHV3-53 in this common antibody response to SARS-CoV-2, where conserved IGHV3-53 germline-encoded features can be combined with very different CDR H3 lengths and light chains for SARS-CoV-2 RBD recognition and virus neutralization.
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Affiliation(s)
- Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sandhya Bangaru
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tom G Caniels
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105AZ Amsterdam, the Netherlands
| | - Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105AZ Amsterdam, the Netherlands
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105AZ Amsterdam, the Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105AZ Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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Song X, Zhang F, Bu Y. Dynamic relaying properties of a β-turn peptide in long-range electron transfer. J Comput Chem 2019; 40:988-996. [PMID: 30451309 DOI: 10.1002/jcc.25541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/30/2018] [Accepted: 07/03/2018] [Indexed: 11/05/2022]
Abstract
The relay stations play a significant role in long-range charge hopping transfer in proteins. Although studies have clarified that many more protein structural motifs can function as relays in charge hopping transfers by acting as intermediate charge carriers, the relaying properties are still poorly understood. In this work, taking a β-turn oligopeptide as an example, we report a dynamic character of a relay with tunable relaying properties using the density functional theory calculations. Our main finding is that a β-turn peptide can serve as an effective electron relay in facilitating long-range electron migration and its relay properties is vibration-tunable. The vibration-induced structural transient distortions remarkably affect the lowest occupied molecular orbital (LUMO) energy, vertical electron affinity and electron-binding mode of the β-turn oligopeptide and the singly occupied molecular orbital (SOMO) energy of the corresponding electron adduct and thus the relaying properties. Different vibration modes lead to different structural distortions and thus have different effects on the relaying properties and ability of the β-turn peptide. For the relaying properties, there approximately is a linear negative correlation of electron affinity with the LUMO energy of the β-turn or the SOMO energy of its electron adduct. Besides, such relaying properties also vary in the vibration evolution process, and the electron-binding modes may be tunable. As an important addition to the known static charge relaying properties occurring in various protein structural motifs, this work reports the dynamic electron-relaying characteristics of a β-turn oligopeptide with variable relaying properties governed by molecular vibrations which can be applied to different proteins in mediating long-range charge transfers. Clearly, this work reveals molecular vibration effects on the electron relaying properties of protein structural motifs and provides new insights into the dynamics of long-range charge transfers in proteins. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiufang Song
- School of Chemistry &Chemical Engineering, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China
| | - Fengying Zhang
- School of Chemistry &Chemical Engineering, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China
| | - Yuxiang Bu
- School of Chemistry &Chemical Engineering, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People's Republic of China
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Joy S, Sureshbabu VV, Periyasamy G. Computational studies on ground and excited state charge transfer properties of peptidomimetics. Faraday Discuss 2018; 207:77-90. [PMID: 29359767 DOI: 10.1039/c7fd00183e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical modifications at various peptide positions result in peptidomimetics with unique physical and chemical properties that can be used for a range of applications. Among many peptidomimetics, ureidopeptides are interesting due to their ability to act as donor-bridge-acceptor systems through which charge transfer occurs in one direction and can be triggered by an electrochemical pulse without perturbing the nuclear position. In this regard, some UP mimetics with different chromophoric units are studied in this work to understand their role using DFT based methods. Computational results and natural charge analysis provide evidence for the extensive contribution of the substituents to the excitation and hole migration dynamics. Further, the results show that the UP backbone preserves its uni-directional charge transfer phenomenon from the ureido to carboxylate terminal irrespective of the terminal groups and position. However, the substituent affects the excitation energies and the time scales of the hole migration. Among the substituents studied here, fluorine migrates to the hole within a shorter time scale while phenyl groups take longer.
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Affiliation(s)
- Sherin Joy
- Department of Chemistry, Central College, Bangalore University, Bangalore, India.
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Monney NPA, Bally T, Giese B. Electronic Structure of Hole-Conducting States in Polyprolines. J Phys Chem B 2015; 119:6584-90. [DOI: 10.1021/acs.jpcb.5b02580] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Thomas Bally
- University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Bernd Giese
- University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
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