Probing the Impact of Local Structural Dynamics of Conformational Epitopes on Antibody Recognition

Biochemistry. 2016 Apr 19;55(15):2197-213. doi: 10.1021/acs.biochem.5b01354. Epub 2016 Apr 4.


Antibody-antigen interactions are governed by recognition of specific residues and structural complementarity between the antigen epitope and antibody paratope. While X-ray crystallography has provided detailed insights into static conformations of antibody-antigen complexes, factors such as conformational flexibility and dynamics, which are not readily apparent in the structures, can also have an impact on the binding event. Here we investigate the contribution of dynamics in the HIV-1 gp120 glycoprotein to antibody recognition of conserved conformational epitopes, including the CD4- and coreceptor-binding sites, and an inner domain site that is targeted by ADCC-active antibodies. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) was used to measure local structural dynamics across a panel of variable loop truncation mutants of HIV-1 gp120, including full-length gp120, ΔV3, ΔV1/V2, and extended core, which includes ΔV1/V2 and V3 loop truncations. CD4-bound full-length gp120 was also examined as a reference state. HDX-MS revealed a clear trend toward an increased level of order of the conserved subunit core resulting from loop truncation. Combined with biolayer interferometry and enzyme-linked immunosorbent assay measurements of antibody-antigen binding, we demonstrate that an increased level of ordering of the subunit core was associated with better recognition by an array of antibodies targeting complex conformational epitopes. These results provide detailed insight into the influence of structural dynamics on antibody-antigen interactions and suggest the importance of characterizing the structural stability of vaccine candidates to improve antibody recognition of complex epitopes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Antigen-Antibody Complex / chemistry*
  • Antigen-Antibody Reactions*
  • Binding Sites, Antibody
  • CD4 Antigens / chemistry
  • CD4 Antigens / metabolism
  • Crystallography, X-Ray
  • Epitopes / chemistry*
  • Epitopes / metabolism
  • HEK293 Cells
  • HIV Antibodies / chemistry*
  • HIV Antibodies / metabolism*
  • HIV Envelope Protein gp120 / chemistry*
  • HIV Envelope Protein gp120 / immunology*
  • HIV-1 / immunology
  • Humans
  • Models, Molecular
  • Molecular Docking Simulation
  • Protein Binding
  • Protein Conformation


  • Antigen-Antibody Complex
  • CD4 Antigens
  • Epitopes
  • HIV Antibodies
  • HIV Envelope Protein gp120