Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force

J Mol Biol. 1990 Nov 5;216(1):167-80. doi: 10.1016/S0022-2836(05)80068-3.

Abstract

We present an approach that is able to detect native folds amongst a large number of non-native conformations. The method is based on the compilation of potentials of mean force of the interactions of the C beta atoms of all amino acid pairs from a database of known three-dimensional protein structures. These potentials are used to calculate the conformational energy of amino acid sequences in a number of different folds. For a substantial number of proteins we find that the conformational energy of the native state is lowest amongst the alternatives. Exceptions are proteins containing large prosthetic groups, Fe-S clusters or polypeptide chains that do not adopt globular folds. We discuss briefly potential applications in various fields of protein structural research.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA-Binding Proteins / chemistry
  • Hemerythrin / chemistry
  • Immunoglobulin Light Chains
  • Immunoglobulin Variable Region
  • Mice
  • Models, Molecular*
  • Models, Theoretical*
  • Protein Conformation*
  • Proteins / chemistry*
  • Thermodynamics

Substances

  • DNA-Binding Proteins
  • Hemerythrin
  • Immunoglobulin Light Chains
  • Immunoglobulin Variable Region
  • Proteins