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Water interaction differences determine the relative energetic stability of the polyproline II conformation of the alanine dipeptide in aqueous environments
Author(s) -
Mirkin Noemi G.,
Krimm Samuel
Publication year - 2012
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22064
Subject(s) - polyproline helix , dipeptide , chemistry , alanine , aqueous solution , peptide , amino acid , stereochemistry , crystallography , organic chemistry , biochemistry
Abstract Although subsequent studies have provided extensive support for the 1968 Tiffany and Krimm proposal (Biopolymers 6, 1379) that the polyproline II (PPII) conformation is a significant component of the structure of unordered polypeptide chains, two issues are still not fully resolved: the PPII persistence length in a chain and the source of its relative stability with respect to the β‐conformation. We examine the latter question by studying the B97‐D/6‐31++G ** energy, in the absence and presence of a reaction field, of the alanine dipeptide hydrated by various amounts of explicit waters and resolving this into its three components: the energies of the individual solvated peptides and water structures plus the interaction energy involving them. We find that the relative stability of the PPII conformation is determined mainly by the difference in the interaction energies of the water structures in the near‐peptide layers. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 789–794, 2012.