Wennmohs F, Schindler M
Ruhr-Universität Bochum, Germany.
J Comput Chem. 2005 Feb;26(3):283-93. doi: 10.1002/jcc.20163.
To properly represent weak hydrogen bonds to sulfur in biological systems, a new multipoint model of atomic sulfur for the amino acid methionine is introduced. This is of particular importance for the description of ligand-protein interactions. The parametrization is performed by fitting the nonbonding parameters of dimethyl sulfide to high level ab initio interaction energy surfaces of the dimethyl sulfide-methanol system and incorporating them in the GROMACS force field. Two examples demonstrate the performance of the new model, the molecular dynamics simulations of the hRAR receptor and of alpha-lytic protease. In hRAR the origin of the discrimination between the R- and S-enantiomers of the synthetic ligand BMS 184394 is explained, and in the simulation of the alpha-lytic protease it is shown that no artificial long range disorders are introduced by the new parametrization.
为了在生物系统中恰当地表示与硫形成的弱氢键，引入了一种针对氨基酸甲硫氨酸的新型原子硫多点模型。这对于描述配体 - 蛋白质相互作用尤为重要。通过将二甲基硫醚的非键参数拟合到二甲基硫醚 - 甲醇体系的高水平从头算相互作用能表面，并将其纳入GROMACS力场来进行参数化。两个例子展示了新模型的性能，即人视黄酸受体（hRAR）和α - 裂解蛋白酶的分子动力学模拟。在hRAR中解释了合成配体BMS 184394的R - 和S - 对映体之间区分的起源，并且在α - 裂解蛋白酶的模拟中表明新的参数化没有引入人为的长程紊乱。
