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Relationships between amino acid sequence and backbone torsion angle preferences
Author(s) -
Keskin O.,
Yuret D.,
Gursoy A.,
Turkay M.,
Erman B.
Publication year - 2004
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/prot.20100
Subject(s) - dihedral angle , protein data bank , torsion (gastropod) , protein data bank (rcsb pdb) , steric effects , crystallography , chemistry , protein structure , stereochemistry , biology , molecule , hydrogen bond , biochemistry , anatomy , organic chemistry
Statistical averages and correlations for backbone torsion angles of chymotrypsin inhibitor 2 are calculated by using the Rotational Isomeric States model of chain statistics. Statistical weights of torsional states of ϕψ pairs, needed for the statistics of the full chain, are obtained in two different ways: 1) by using knowledge‐based pairwise dependent ϕψ energy maps from Protein Data Bank (PDB) and 2) by collecting torsion angle data from a large number of random coil configurations of an all‐atom protein model with volume exclusion. Results obtained by using PDB data show strong correlations between adjacent torsion angle pairs belonging to both the same and different residues. These correlations favor the choice of the native‐state torsion angles, and they are strongly context dependent, determined by the specific amino acid sequence of the protein. Excluded volume or steric clashes, only, do not introduce context‐dependent ϕψ correlations into the chain that would affect the choice of native‐state torsional angles. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.