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Front. Immunol. | doi: 10.3389/fimmu.2018.00413

Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification

  • 1Program in Molecular Biophysics, Johns Hopkins University, United States
  • 2School of Science and Technology, Kwansei Gakuin University, Japan
  • 3Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Japan
  • 4Department of Bioengineering, School of Engineering, The University of Tokyo, Japan
  • 5School of Engineering, The University of Tokyo, Japan
  • 6The Institute of Medical Science, The University of Tokyo, Japan
  • 7Chemical & Biomolecular Engineering, Johns Hopkins University, United States
  • 8Institute for NanoBioTechnology, Johns Hopkins University, United States
  • 9Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, United States

Antibodies can rapidly evolve in specific response to antigens. Affinity maturation drives this evolution through cycles of mutation and selection leading to enhanced antibody specificity and affinity. Elucidating the biophysical mechanisms that underlie affinity maturation is fundamental to understanding B-cell immunity. An emergent hypothesis is that affinity maturation reduces the conformational flexibility of the antibody’s antigen-binding paratope to minimize entropic losses incurred upon binding. In recent years, computational and experimental approaches have tested this hypothesis on a small number of antibodies, often observing a decrease in the flexibility of the Complementarity Determining Region (CDR) loops that typically comprise the paratope and in particular the CDR-H3 loop, which contributes a plurality of antigen contacts. However, there were a few exceptions, and previous studies were limited to a small handful of cases. Here, we determined the structural flexibility of the CDR-H3 loop for thousands of recently-determined homology models of the human peripheral blood cell antibody repertoire using rigidity theory. We found no clear delineation in the flexibility of naïve and antigen-experienced antibodies. To account for possible sources of error, we additionally analyzed hundreds of human and mouse antibodies in the Protein Data Bank through both rigidity theory and B-factor analysis. By both metrics, we observed only a slight decrease in the CDR-H3 loop flexibility when comparing affinity-matured antibodies to naïve antibodies, and the decrease was not as drastic as previously reported. Further analysis, incorporating molecular dynamics (MD) simulations, revealed a spectrum of changes in flexibility. Our results suggest that rigidification may be just one of many biophysical mechanisms for increasing affinity.

Keywords: Antibody repertoires, Affinity maturation, Complementarity Determining Regions (CDRs), Conformational flexibility, Rigidity theory, Pebble Game (PG) algorithm, RosettaAntibody, Molecular dynamics (MD) simulations

Received: 06 Dec 2017; Accepted: 14 Feb 2018.

Edited by:

Gregory C. Ippolito, University of Texas at Austin, United States

Reviewed by:

Roy Mariuzza, University of Maryland, College Park, United States
Oana I. Lungu, Signature Science, LLC, United States  

Copyright: © 2018 Jeliazkov, Sljoka, Kuroda, Tsuchimura, Katoh, Tsumoto and Gray. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
PhD. Adnan Sljoka, Kwansei Gakuin University, School of Science and Technology, Nishinomiya, Japan,
Prof. Jeffrey J. Gray, Johns Hopkins University, Program in Molecular Biophysics, Baltimore, Maryland, United States,