Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling

Abstract

The three-dimensional structures of 41 homologous proteins (belonging to eight families) were compared by pairwise superposition. A subset of “core” residues was defined as those whose side chains have <7% of their surface exposed to solvent. This subset has significantly higher sequence identity and lower root mean square (RMS) α carbon separation than for all topologically equivalent residues in the structure, when members of a protein family are superposed. For such superpositions the relationship between RMS distance and percentage sequence identity of this subset of residues is similar to that for all equivalent residues, although some variation is observed between families of proteins which are predominantly β sheet and those which are mainly α helix. The definition of a structurally more conserved core may be ueful in model building proteins from an homologous family. The RMS differences of coordinates of structures of proteins with identical sequences are found to be related to the resolutions of the structures.