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Evaluation of short‐range interactions as secondary structure energies for protein fold and sequence recognition
Author(s) -
Miyazawa Sanzo,
Jernigan Robert L.
Publication year - 1999
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(19990815)36:3<347::aid-prot9>3.0.co;2-3
Subject(s) - protein secondary structure , chemistry , side chain , tripeptide , statistical potential , protein structure , contact order , residue (chemistry) , sequence (biology) , crystallography , stereochemistry , peptide , protein structure prediction , native state , biochemistry , organic chemistry , polymer
Short‐range interactions for secondary structures of proteins are evaluated as potentials of mean force from the observed frequencies of secondary structures in known protein structures which are assumed to have an equilibrium distribution with the Boltzmann factor of secondary structure energies. A secondary conformation at each residue position in a protein is described by a tripeptide, including one nearest neighbor on each side. The secondary structure potentials are approximated as additive contributions from neighboring residues along the sequence. These are part of an empirical potential to provide a crude estimate of protein conformational energy at a residue level. Unlike previous works, interactions are decoupled into intrinsic potentials of residues, potentials of backbone‐backbone interactions, and of side chain‐backbone interactions. Also interactions are decoupled into one‐body, two‐body, and higher order interactions between peptide backbone and side chain and between backbones. These decouplings are essential to correctly evaluate the total secondary structure energy of a protein structure without overcounting interactions. Each interaction potential is evaluated separately by taking account of the correlation in the amino acid order of protein sequences. Interactions among side chains are neglected, because of the relatively limited number of protein structures. Proteins 1999;36:347–356. Published 1999 Wiley‐Liss, Inc.