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Molecular dynamics study of onset of water gelation around the collagen triple helix
Author(s) -
Handgraaf JanWillem,
Zerbetto Francesco
Publication year - 2006
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.21019
Subject(s) - molecular dynamics , triple helix , diffusion , chemistry , picosecond , solvation shell , molecule , hydrogen , crystallography , hydrogen bond , chemical physics , helix (gastropod) , peptide , thermodynamics , computational chemistry , stereochemistry , physics , organic chemistry , ecology , laser , biochemistry , biology , snail , solvation , optics
The onset of water gelation around a collagen‐like triple helix peptide was studied at ambient temperature and pressure by performing Molecular Dynamics simulations. The radial distribution functions of the oxygen and hydrogen atoms of water are distorted below 4 Å from the peptide. The distortion is accompanied by the breakdown of the tetrahedral coordination of the hydrogen‐bonded network of water molecules. The water shell around the peptide consists of alternating regions of higher and lower density. In agreement with experiments we find that the first hydration shell is kinetically labile, with a residence time in the order of picoseconds for a water molecule. From the computed diffusion coefficient, a key measure of the collective dynamics, we estimate the average diffusion speed decreases by a factor of 1.5 close to the peptide compared to the liquid. Our results give new insight in gel formation and structure on a molecular level. Proteins 2006. © 2006 Wiley‐Liss, Inc.