A central core structure in an antibody variable domain determines antigen specificity

Protein Eng. 2001 Jan;14(1):67-74. doi: 10.1093/protein/14.1.67.


Antibody binding sites provide an adaptable surface capable of interacting with essentially any molecular target. Using CDR shuffling, residues important for the assembly of mucin-1 specific paratopes were defined by random recombination of the complementarity determining regions derived from a set of mucin-1 specific clones, previously selected from an antibody fragment library. It was found that positions 33 and 50 in the heavy chain and 32, 34, 90, 91 and 96 in the light chain were conserved in many of the clones. These particular residues seem to be located centrally in the binding site as indicated by a structure model analysis. The importance of several of these conserved residues was supported by their presence in a mouse monoclonal antibody with a known structure and the same epitope specificity. Several of these corresponding residues in the mouse monoclonal antibody are known to interact with the antigen. In conclusion, critical residues important for maintaining a human antigen-specific binding site during the process of in vitro antibody evolution were defined. Furthermore, an explanation for the observed restricted germline gene usage in certain antibody responses against protein epitopes is provided.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antibodies, Monoclonal / chemistry
  • Antibodies, Monoclonal / genetics*
  • Antibodies, Monoclonal / metabolism
  • Binding Sites
  • Binding Sites, Antibody
  • Complementarity Determining Regions / chemistry*
  • Conserved Sequence
  • Epitopes / chemistry
  • Evolution, Molecular
  • Humans
  • Immunoglobulin Heavy Chains / genetics
  • Immunoglobulin Light Chains / genetics
  • Immunoglobulin Variable Region / chemistry
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • Mucin-1 / chemistry*
  • Peptide Library
  • Protein Binding
  • Sequence Homology, Amino Acid
  • Tandem Repeat Sequences


  • Antibodies, Monoclonal
  • Complementarity Determining Regions
  • Epitopes
  • Immunoglobulin Heavy Chains
  • Immunoglobulin Light Chains
  • Immunoglobulin Variable Region
  • Mucin-1
  • Peptide Library

Associated data

  • GENBANK/X03398