The Allosteric Effect in Antibody-Antigen Recognition

Jun Zhao, Ruth Nussinov, Buyong Ma*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


We studied the molecular details of the recognition of antigens by the variable domain of their cognate antibodies in as well as those elicited by the constant domains, which do not directly interact with antigens. Such effects are difficult to study experimentally; however, molecular dynamics simulations and subsequent residue interaction network analysis provide insight into the allosteric communication between the antigen-binding CDR region and the constant domain. We performed MD simulations of the complex of Fab and prion-associated peptide in the apo and bound forms and follow the conformational changes in the antibody and cross-talk between its subunits and with antigens. These protocols could be generally applied for studies of other antigens-antibody recognition systems.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages9
StatePublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Allosteric effect
  • Antibody-antigen interaction
  • Community analysis
  • Disulfide bond
  • Dynamic network
  • Motion correlation


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