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Empirical evaluation of the influence of side chains on the conformational entropy of the polypeptide backbone
Author(s) -
Stites Wesley E.,
Pranata Julianto
Publication year - 1995
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.340220206
Subject(s) - chemistry , conformational entropy , residue (chemistry) , alanine , native state , side chain , amino acid , entropy (arrow of time) , protein structure , helix (gastropod) , proline , crystallography , stereochemistry , molecule , thermodynamics , biochemistry , organic chemistry , polymer , biology , ecology , physics , snail
Changes in amino acid side chains have long been recognized to alterthe range and distribution of ϕ, ψ angles found in the main chain of polypeptides. Altering the range and distribution of ϕ, ψ angles also alters the conformational entropy of the flexible denatured state and may thus stabilize or destabilize it relative to the comparatively conformationally rigid native state. A database of 12,320 residues from 61 nonhomologous, high resolution crystal structures was examined to determine the ϕ, ψ conformational preferences of each of the 20 amino acids. These observed distributions in the native state of proteins are assumed to also reflect the distributions found in the denatured state. The distributionswere used to approximate the energy surface for each residue, allowing the calculation of relative conformational entropies for each residue relative to glycine. In the most extreme case, replacement of glycine by proline, conformational entropy changes will stabilize the native state relative to the denatured state by −0.82 ± 0.08 kcal/mol at 20°C. Surprisingly, alanine is found to be the most ordered residue other than proline. This unexpected result is a result of the high percentage of alanines found in helical conformations. This either indicates that the observed distributions in the native state do not reflect the distributions in the denatured state, or that alanine is much more likely to adopt a helical conformation in the denatured state than residues with longer side chains. Among those residues with ϕ, ψ angles compatible with helix incorporation the percentage of alanines actually in helices is very similar to other residues. This and the consistent ordering of alanine relative to other residues regardless of secondary structure are evidence that ϕ, ψ distributions in native states reflect those in the denatured states. © 1995 Wiley‐Liss, Inc.