Molecular dynamics simulation of cocaine binding with human butyrylcholinesterase and its mutants
Molecular dynamics simulation of cocaine binding with human butyrylcholinesterase and its mutants
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DOI：
10.1021/jp0447136
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发表时间：
2005-03-17
影响因子：
3.3
通讯作者：
Zhan, CG
中科院分区：
文献类型：
--
作者：
Hamza, A;Cho, H;Zhan, CG
利用分子动力学方法模拟了可卡因与野生型人丁酰胆碱酯酶（BChE）及其突变体的结合，并基于最近报道的人BChE的X-射线晶体结构.对于每个BChE-可卡因系统，我们模拟了在水中的nonprereactive和prereactive复合物。尽管在酰基结合口袋处发现了显著差异，但模拟结构证实了从基于同源模型的野生型BChE与可卡因的早期计算研究中获得的基本结构和机制见解，例如，生物活性（-）-可卡因的BChE催化水解的速率决定步骤是活性位点中的（-）-可卡因从非预反应性BChE（-）-可卡因复合物转化为前反应复合物已经证明，对非预反应性和预反应性BChE-可卡因复合物的MD模拟可以清楚地揭示特定突变是否产生所需的BChE-（-）-可卡因结合结构，其中（-）-可卡因旋转受到较少阻碍，同时维持所需的预反应性BChE-（-）-可卡因结合。基于MD模拟，预期A328 W/Y332 A和A328 W/Y332 G BChE对（-）-可卡因水解的催化活性高于野生型BChE，并且A328 W/Y332 G BChE的活性应略高于A328 W/Y332 ABChE，这是由于突变BChE中较少阻碍的（-）-可卡因旋转.然而，较少阻碍的（-）-可卡因旋转只是一个必要条件，为更高的活性突变BChE。（-）-可卡因旋转在A328 W/Y332 A/Y 419 S BChE中也较少受阻，但（-）-可卡因以不适合催化的方式与A328 W/Y332 A/Y 419 S BChE结合。因此，预期A328 W/Y332 A/Y 419 S BChE失去催化活性。我们的实验动力学数据证实了计算预测，表明本研究中使用的基于MD模拟的计算方案在预测BChE突变体对（-）-可卡因水解的催化活性方面是可靠的。
Molecular dynamics (MD) simulations were carried out to study cocaine binding with wild-type human butyryleholinesterase (BChE) and its mutants based on a recently reported X-ray crystal structure of human BChE. For each BChE-cocaine system, we simulated both the nonprereactive and prereactive complexes in water. Despite the significant difference found at the acyl binding pocket, the simulated structures confirm the fundamental structural and mechanistic insights obtained from earlier computational studies of wild-type BChE with cocaine based on a homology model, e.g. the rate-determining step for BChE-catalyzed hydrolysis of biologically active (-)-cocaine is the (-)-cocaine rotation in the active site from the nonprereactive BChE(-)-cocaine complex to the prereactive complex. It has been demonstrated that the MD simulations on both the nonprereactive and prereactive BChE-cocaine complexes can clearly reveal whether specific mutations produce the desired BChE- (-)-cocaine binding structures in which the (-)-cocaine rotation is less hindered while the required prereactive BChE- (-)-cocaine binding is maintained. Based on the MD simulations, both A328W/Y332A and A328W/Y332G BChE ' s are expected to have catalytic activity for (-)-cocaine hydrolysis higher than that of wild-type BChE and the activity of A328W/Y332G BChE should be slightly higher than that of A328W/Y332A BChE due to the less-hindered (-)-cocaine rotation in the mutant BChE ' s. However, the less-hindered (-)-cocaine rotation is only a necessary condition for a higher activity mutant BChE. The (-)-cocaine rotation is also less hindered in A328W/Y332A/Y419S BChE, but (-)-cocaine binds with A328W/Y332A/Y419S BChE in a way that is not suitable for the catalysis. Thus, A328W/Y332A/ Y419S BChE is expected to lose the catalytic activity. The computational predictions were confirmed by our experimental kinetic data, demonstrating that the MD simulation -based computational protocol used in this study is reliable in prediction of the catalytic activity of BChE mutants for (-)-cocaine hydrolysis.