Literature DB >> 24089367

Conformational dynamics of individual antibodies using computational docking and AFM.

Rui C Chaves1, Jean-Marie Teulon, Michael Odorico, Pierre Parot, Shu-Wen W Chen, Jean-Luc Pellequer.   

Abstract

Molecular recognition between a receptor and a ligand requires a certain level of flexibility in macromolecules. In this study, we aimed at analyzing the conformational variability of receptors portrayed by monoclonal antibodies that have been individually imaged using atomic force microscopy (AFM). Individual antibodies were chemically coupled to activated mica surface, and they have been imaged using AFM in ambient conditions. The resulting topographical surface of antibodies was used to assemble the three subunits constituting antibodies: two antigen-binding fragments and one crystallizable fragment using a surface-constrained computational docking approach. Reconstructed structures based on 10 individual topographical surfaces of antibodies are presented for which separation and relative orientation of the subunits were measured. When compared with three X-ray structures of antibodies present in the protein data bank database, results indicate that several arrangements of the reconstructed subunits are comparable with those of known structures. Nevertheless, no reconstructed structure superimposes adequately to any particular X-ray structure consequence of the antibody flexibility. We conclude that high-resolution AFM imaging with appropriate computational reconstruction tools is adapted to study the conformational dynamics of large individual macromolecules deposited on mica.
Copyright © 2013 John Wiley & Sons, Ltd.

Entities:  

Keywords:  Immunoglobulin G (IgG); Protein structure reconstruction; atomic force microscopy (AFM); docking; structure dynamics

Mesh:

Substances:

Year:  2013        PMID: 24089367     DOI: 10.1002/jmr.2310

Source DB:  PubMed          Journal:  J Mol Recognit        ISSN: 0952-3499            Impact factor:   2.137


  6 in total

1.  DockAFM: benchmarking protein structures by docking under AFM topographs.

Authors:  Rui C Chaves; Jean-Luc Pellequer
Journal:  Bioinformatics       Date:  2013-09-26       Impact factor: 6.937

2.  Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular Simulations.

Authors:  Sotaro Fuchigami; Shoji Takada
Journal:  Front Mol Biosci       Date:  2022-04-29

3.  3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography.

Authors:  Xing Zhang; Lei Zhang; Huimin Tong; Bo Peng; Matthew J Rames; Shengli Zhang; Gang Ren
Journal:  Sci Rep       Date:  2015-05-05       Impact factor: 4.379

4.  The Plasma Factor XIII Heterotetrameric Complex Structure: Unexpected Unequal Pairing within a Symmetric Complex.

Authors:  Sneha Singh; Alexis Nazabal; Senthilvelrajan Kaniyappan; Jean-Luc Pellequer; Alisa S Wolberg; Diana Imhof; Johannes Oldenburg; Arijit Biswas
Journal:  Biomolecules       Date:  2019-11-21

5.  Characterization of Monoclonal Antibody-Protein Antigen Complexes Using Small-Angle Scattering and Molecular Modeling.

Authors:  Maria Monica Castellanos; James A Snyder; Melody Lee; Srinivas Chakravarthy; Nicholas J Clark; Arnold McAuley; Joseph E Curtis
Journal:  Antibodies (Basel)       Date:  2017-12-15

6.  Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure.

Authors:  Toru Niina; Yasuhiro Matsunaga; Shoji Takada
Journal:  PLoS Comput Biol       Date:  2021-07-20       Impact factor: 4.475

  6 in total

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