ISSN:
0887-3585
Keywords:
trp-repressor
;
TIP3P water
;
hydrophobic shell
;
hydrogen bond
;
AMBER
;
diffusion coefficient
;
radial distribution
;
Chemistry
;
Biochemistry and Biotechnology
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Medicine
Notes:
The solvent structure and behavior around a protein were examined by analyzing a trajectory of molecular dynamics simulation of thetrp-holorepressor in a periodic box of water. The calculated selfdiffusion coefficient indicated that the solvent within 10 Å of the protein had lower mobility. Examination of the solvent diffusion around different atoms of different kinds of residues showed no general tendency. Thisfact suggested that the solvent mobility is not influenced significantly bythe kind of the atom or residue they solvated. Distribution analysis aroundthe protein revealed two peaks of water oxygen: a sharp one at 2.8 Å around polar and charged atoms and a broad one at ∼3.4 Å aroundapolar atoms. The former was stabilized by water-protein hydrogen bonds, and the latter was stabilized by water-lwater hydrogen bonds, suggesting the existence of a hydrophobic shell. An analysis of protein atom-water radial distribution functions confirmed these shell structures around polar or charged atoms and apolar ones. © 1993 Wiley-Liss, Inc.
Additional Material:
4 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/prot.340160305
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