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Molecular dynamics simulation accurately predicts the experimentally‐observed distributions of the (C, N, O) protein atoms around water molecules and sodium ions
Author(s) -
Kombo David C.,
Young Matthew A.,
Beveridge David L.
Publication year - 2000
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/(sici)1097-0134(20000515)39:3<212::aid-prot30>3.0.co;2-c
Subject(s) - molecular dynamics , ion , molecule , force field (fiction) , operator (biology) , chemical physics , chemistry , crystal (programming language) , repressor , crystallography , sodium , water model , physics , atomic physics , computational chemistry , computer science , quantum mechanics , programming language , biochemistry , organic chemistry , transcription factor , gene
A molecular dynamics simulation of the operator binding domain of the lambda repressor protein has been carried out. The protein was embedded in explicit waters, Na + and CL − ions. The Amber 4.1 computer package and the Cornell et al. Force field were used for energy‐minimization and molecular dynamics simulation. We find that the atoms distributions in the environment of waters and Na + ions are in excellent agreement with those derived from the analysis of water molecules in crystal structures and ion‐binding proteins. We also find that, on the whole, both distributions are similar to each other. Proteins 2000;39:212–215. © 2000 Wiley‐Liss, Inc.