Structure-based design of a protein immunogen that displays an HIV-1 gp41 neutralizing epitope

J Mol Biol. 2011 Dec 2;414(3):460-76. doi: 10.1016/j.jmb.2011.10.014. Epub 2011 Oct 15.


Antibody Z13e1 is a relatively broadly neutralizing anti-human immunodeficiency virus type 1 antibody that recognizes the membrane-proximal external region (MPER) of the human immunodeficiency virus type 1 envelope glycoprotein gp41. Based on the crystal structure of an MPER epitope peptide in complex with Z13e1 Fab, we identified an unrelated protein, interleukin (IL)-22, with a surface-exposed region that is structurally homologous in its backbone to the gp41 Z13e1 epitope. By grafting the gp41 Z13e1 epitope sequence onto the structurally homologous region in IL-22, we engineered a novel protein (Z13-IL22-2) that contains the MPER epitope sequence for use as a potential immunogen and as a reagent for the detection of Z13e1-like antibodies. The Z13-IL22-2 protein binds Fab Z13e1 with a K(d) of 73 nM. The crystal structure of Z13-IL22-2 in complex with Fab Z13e1 shows that the epitope region is faithfully replicated in the Fab-bound scaffold protein; however, isothermal calorimetry studies indicate that Fab binding to Z13-IL22-2 is not a lock-and-key event, leaving open the question of whether conformational changes upon binding occur in the Fab, in Z13-IL-22, or in both.

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
  • Calorimetry / methods
  • Crystallography, X-Ray / methods
  • Epitopes / chemistry
  • HIV Envelope Protein gp41 / chemistry*
  • HIV-1 / metabolism*
  • Humans
  • Immunoglobulin Fab Fragments / chemistry
  • Interleukin-22
  • Interleukins / chemistry
  • Interleukins / metabolism
  • Kinetics
  • Models, Molecular
  • Molecular Sequence Data
  • Neutralization Tests
  • Peptides / chemistry*
  • Protein Engineering / methods
  • Sequence Homology, Amino Acid
  • Surface Properties
  • Thermodynamics


  • Epitopes
  • HIV Envelope Protein gp41
  • Immunoglobulin Fab Fragments
  • Interleukins
  • Peptides

Associated data

  • PDB/3Q1S