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Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
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The Allosteric Effect in Antibody-Antigen Recognition.

Jun Zhao1, Ruth Nussinov2,3, Buyong Ma4

  • 1Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, USA.

Methods in Molecular Biology (Clifton, N.J.)
|December 14, 2020
PubMed
Summary
This summary is machine-generated.

Antibody constant domains influence antigen recognition through allosteric communication with the antigen-binding site. Molecular dynamics simulations reveal this cross-talk, aiding the study of antibody-antigen interactions.

Keywords:
Allosteric effectAntibody-antigen interactionCommunity analysisDisulfide bondDynamic networkMotion correlation

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Area of Science:

  • Immunology
  • Structural Biology
  • Computational Biology

Background:

  • Antibody-antigen recognition is crucial for adaptive immunity.
  • The role of antibody constant domains in modulating antigen binding is not fully understood.
  • Experimental study of allosteric effects in antibodies is challenging.

Purpose of the Study:

  • To investigate the molecular mechanisms of allosteric communication between antibody constant domains and antigen-binding sites.
  • To elucidate the conformational changes and cross-talk within antibodies during antigen recognition.
  • To apply computational methods to study antibody-antigen interactions.

Main Methods:

  • Molecular dynamics (MD) simulations of antibody-antigen complexes (Fab and prion-associated peptide).
  • Analysis of apo and bound forms to capture conformational dynamics.
  • Residue interaction network analysis to map communication pathways.

Main Results:

  • MD simulations revealed conformational changes in the antibody upon antigen binding.
  • Identified allosteric communication pathways between the complementarity-determining region (CDR) and constant domains.
  • Demonstrated cross-talk between antibody subunits and with the antigen.

Conclusions:

  • Constant domains allosterically influence antigen recognition by antibodies.
  • MD simulations and network analysis provide valuable insights into antibody dynamics and interactions.
  • The developed protocols are applicable to diverse antibody-antigen systems.