Yang Kun, Liu Xinli, Wang Xicheng, Jiang Hualiang
Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian 116024, China.
Biochem Biophys Res Commun. 2009 Feb 6;379(2):494-8. doi: 10.1016/j.bbrc.2008.12.099. Epub 2008 Dec 30.
In this paper, a new steered molecular dynamics (SMD) method with adjusting pulling direction is proposed to search an optimum trajectory of ligand dissociation. A multiobjective model and a searching technique based on information entropy with multi-population are developed to optimize the pulling direction. The improved method has been used to dissociate the substrate-bound complex structure of cytochrome P450 3A4-metyrapone. A more favorable dissociation pathway can be gained. The results show that the new pathway obtained by the proposed method has less dissociation time, smaller rupture force and lower energy barrier than that by the conventional SMD.
本文提出了一种具有调整拉力方向的新型引导分子动力学（SMD）方法，以搜索配体解离的最优轨迹。构建了一个多目标模型和一种基于多群体信息熵的搜索技术来优化拉力方向。该改进方法已用于解离细胞色素P450 3A4-美替拉酮的底物结合复合物结构，可得到更有利的解离途径。结果表明，与传统SMD方法相比，该方法获得的新途径具有更短的解离时间、更小的断裂力和更低的能垒。
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