Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition

Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12467-72. doi: 10.1073/pnas.0401786101. Epub 2004 Aug 11.

Abstract

Antigen-binding fragments (Fabs) with synthetic antigen-binding sites were isolated from phage-displayed libraries with restricted complementarity-determining region (CDR) diversity. Libraries were constructed such that solvent-accessible CDR positions were randomized with a degenerate codon that encoded for only four amino acids (tyrosine, alanine, aspartate, and serine). Nonetheless, high-affinity Fabs (K(d) = 2-10 nM) were isolated against human vascular endothelial growth factor (hVEGF), and the crystal structures were determined for two distinct Fab-hVEGF complexes. The structures revealed that antigen recognition was mediated primarily by tyrosine side chains, which accounted for 71% of the Fab surface area that became buried upon binding to hVEGF. In contrast, aspartate residues within the CDRs were almost entirely excluded from the binding interface. Alanine and serine residues did not make many direct contacts with antigen, but they allowed for space and conformational flexibility and thus played an auxiliary role in facilitating productive contacts between tyrosine and antigen. Tyrosine side chains were capable of mediating most of the contacts necessary for high-affinity antigen recognition, and, thus, it seems likely that the overabundance of tyrosine in natural antigen-binding sites is a consequence of the side chain being particularly well suited for making productive contacts with antigen. The findings shed light on the basic principles governing the evolution of natural immune repertoires and should also aid the development of improved synthetic antibody libraries.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Antigens / immunology
  • Antigens / metabolism*
  • Binding Sites
  • Binding Sites, Antibody
  • Codon*
  • Complementarity Determining Regions
  • Crystallography, X-Ray
  • Epitopes
  • Humans
  • Immunoglobulin Fab Fragments / chemistry*
  • Immunoglobulin Fab Fragments / genetics
  • Immunoglobulin Fab Fragments / immunology*
  • Models, Molecular
  • Molecular Sequence Data
  • Peptide Library
  • Protein Binding
  • Protein Conformation
  • Sequence Alignment
  • Tyrosine / genetics
  • Tyrosine / metabolism*
  • Vascular Endothelial Growth Factor A / immunology

Substances

  • Antigens
  • Codon
  • Complementarity Determining Regions
  • Epitopes
  • Immunoglobulin Fab Fragments
  • Peptide Library
  • Vascular Endothelial Growth Factor A
  • Tyrosine

Associated data

  • PDB/1TZH
  • PDB/1TZI