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Exploring stereochemical specificity of phosphotriesterase by MM-PBSA and MM-GBSA calculation and steered molecular dynamics simulation

文献类型： 外文期刊

作者： Zhu, Jingxuan 1 ; Li, Xin 1 ; Zhang, Siqi 1 ; Ye, Hen 1 ; Zhao, Hui 2 ; Jin, Hanyong 1 ; Han, Weiwei 1 ;

作者机构： 1.Jilin Univ, Sch Life Sci, Key Lab Mol Enzymol & Engn, Minist Educ, Changchun 130023, Jilin, Peoples R China

2.Chinese Acad Trop Agr Sci, Inst Trop Biosci & Biotechnol, Changchun 130023, Jilin, Peoples R China

关键词： docking;MM-PBSA and MM-GBSA calculation;steered molecular dynamics simulation;stereoselectivity;phosphotriesterase

期刊名称：JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS （ 影响因子：3.31； 五年影响因子：2.689 ）

ISSN： 0739-1102

年卷期： 2017 年 35 卷 14 期

页码：

收录情况： SCI

摘要： Wild-type phosphotriesterase (PTE) prefers the S-P-enantiomers over the corresponding R-P-enantiomers by factors ranging from 10 to 90. To satisfy the binding modes of the PTE of S-P- and R-P-enantiomers, all-atom molecular dynamics simulations were carried out on two paraoxon S-P and R-P derivatives, namely, S-p-1 and R-p-1. Molecular mechanics Poisson-Boltzmann surface area and molecular mechanics generalized Born surface area (MM-PBSA and MM-GBSA) calculations indicated that His230 in S-p-1-PTE had a closer interaction with the substrate than that in R-p-1-PTE and that such interaction increased the catalytic efficiency of PTE for S-p-1. The steered molecular dynamics simulation indicated that, compared with S-p-1, R-p-1 in the unbinding (binding) may hinder some residue displacement, thus requiring more effort to escape the binding pocket of PTE. In addition, Trp131, Phe306, and Tyr309 are deemed important residues for the S-p-1 unbinding pathway via PTE, whereas Tyr309 alone is considered an important residue for the R-p-1 unbinding pathway. These results demonstrate the possibility of dramatically altering the stereoselectivity and overall reactivity of the native enzyme toward chiral substrates by modifying specific residues located within the active site of PTE.

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