Molecular dynamics simulation accurately predicts the experimentally-observed distributions of the (C, N, O) protein atoms around water molecules and sodium ions
✍ Scribed by David C. Kombo; Matthew A. Young; David L. Beveridge
- Publisher
- John Wiley and Sons
- Year
- 2000
- Tongue
- English
- Weight
- 102 KB
- Volume
- 39
- Category
- Article
- ISSN
- 0887-3585
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✦ Synopsis
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.