Hugosson Håkan W, Laio Alessandro, Maurer Patrick, Rothlisberger Ursula
Laboratory of Computational Chemistry and Biochemistry, Institute of Molecular and Biological Chemistry, Swiss Federal Institute of Technology EPF Lausanne, Switzerland.
J Comput Chem. 2006 Apr 15;27(5):672-84. doi: 10.1002/jcc.20360.
Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).
已对水中二肽甘氨酸 - 丙氨酸的两性离子形式进行了分子动力学研究，重点是使用一系列理论方法研究其溶剂化和静电性质，这些方法包括从纯经典力场，到量子力学/分子力学混合模拟，再到完全量子力学的Car - Parrinello计算。这些研究结果表明，对于二肽中大多数原子，所有使用的方法得到的溶剂化模式相似，但某些基团可能有很大差异；即羧基和氨基末端，以及主链酰胺NH基团。这可能对其他研究水中带有 -NH(3) (+) 和 -CO(2) (-) 侧链的肽和蛋白质的理论研究有影响。量子力学/分子力学混合模拟成功再现了完全量子力学模拟的溶剂化模式（物理和化学分类号：87.14.Ee、87.15.Aa、87.15.He、71.15.Pd）。
