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Theoretical study of volume changes associated with the helix–coil transition of an alanine‐rich peptide in aqueous solution
Author(s) -
Imai Takashi,
Takekiyo Takahiro,
Kovalenko Andriy,
Hirata Fumio,
Kato Minoru,
Taniguchi Yoshihiro
Publication year - 2005
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.20337
Subject(s) - chemistry , random coil , electromagnetic coil , van der waals force , peptide , volume (thermodynamics) , helix (gastropod) , alanine , crystallography , preprint , aqueous solution , thermodynamics , chemical physics , molecule , physics , amino acid , circular dichroism , organic chemistry , quantum mechanics , ecology , biochemistry , biology , snail
The changes in the partial molar volume (PMV) associated with the conformational transition of an alanine‐rich peptide AK16 from the α‐helix structure to various random coil structures are calculated by the three‐dimensional interaction site model (3D‐RISM) theory coupled with the Kirkwood–Buff theory. The volume change is analyzed by decomposing it into contributions from geometry and hydration: the changes in the van der Waals, void, thermal, and interaction volume. The total change in the PMV is positive. This is primarily due to the growth of void space within the peptide, which is canceled in part by the volume reduction resulting from the increase in the electrostatic interaction between the peptide and water molecules. The changes in the void and thermal volume of the coil structures are widely distributed and tend to compensate each other. Additionally, the relations between the hydration volume components and the surface properties are investigated. We categorize coil structures into extended coils with the PMV smaller than helix and general coils with the PMV larger than helix. The pressure therefore can both stabilize and destabilize the coil structures. The latter seems to be a more proper model of random coil structures of the peptide. © 2005 Wiley Periodicals, Inc. Biopolymers 79: 97–105, 2005 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com