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Populations of hydrophobic amino acids within protein globular domains: Identification of conserved “topohydrophobic” positions
Author(s) -
Poupon Anne,
Mor JeanPaul
Publication year - 1998
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19981115)33:3<329::aid-prot3>3.0.co;2-e
Subject(s) - amino acid , globular protein , crystallography , sequence (biology) , globular cluster , peptide sequence , hydrophobic effect , protein structure , lattice protein , protein superfamily , chemistry , biology , stereochemistry , biochemistry , physics , quantum mechanics , galaxy , gene
The 3D structural comparison of families of divergent homologous domains revealed two main populations of hydrophobic amino acids, one with a low and the other with a significantly higher mean solvent accessibility, allowing two regions of the core of protein globular domains to be distinguished. The side chains of hydrophobic amino acids in topologically conserved positions (positions in the structural alignment where only hydrophobic amino acids are found), which we call topohydrophobic positions, are considerably less dispersed than those of the other amino acids (hydrophobic or not). Mean distances between gravity centers of amino acids in topohydrophobic positions are significantly shorter than those for non‐topohydrophobic positions and show that the corresponding amino acids are almost all in direct contact in the inner core of globular domains. This study also showed that the small number of topohydrophobic positions is a characteristic of the structural differences between proteins of a family. This criterion is independent of the sequence identity between the sequences and of the root‐mean‐square distance between their corresponding structures. Using sensitive sequence alignment processes it will be possible, for many protein families, to identify topohydrophobic positions from sequences only. Proteins 33:329–342, 1998. © 1998 Wiley‐Liss, Inc.