Analysis of classical and quantum paths for deprotonation of methylamine by methylamine dehydrogenase.
Analysis of classical and quantum paths for deprotonation of methylamine by methylamine dehydrogenase.
复制标题
甲胺脱氢酶对甲胺去质子化的经典路径和量子路径分析。
作者：
K. Ranaghan;Laura Masgrau;N. Scrutton;M. Sutcliffe;A. Mulholland
甲胺脱氢酶（MADH）催化的以甲胺（MA）为底物的氢转移反应是研究酶反应中质子隧穿的一个很好的模型系统--这是一个当前非常感兴趣的领域--原子模拟将是至关重要的。在这里，我们提出了一个详细的分析的关键去质子化步骤的MADH/MA反应，并与实验观察的结果进行比较。此外，我们比较了这个反应与相关的芳香胺脱氢酶（AADH）反应与色胺，最近我们研究，并确定可能的原因所观察到的两个系统的动力学同位素效应（KIEs）的差异。我们已经使用了结合量子力学/分子力学（QM/MM）技术在分子动力学模拟和变分过渡态理论与多维隧道计算平均在合奏的路径。结果揭示了重要的机制的复杂性。我们计算活化势垒和KIEs的两种可能的质子转移确定的催化碱（Asp 428 β）的羧酸氧原子的任何一个-和分析量子效应的贡献。两种可能的质子转移的活化能垒和隧穿贡献是相似的，导致转移到任一氧的现象学活化自由能为16.5+/-0.9 kcal mol（-1）（PM 3-CHARMM计算，应用PM 3-SRP特定反应参数），与14.4 kcal mol（-1）的实验值非常一致。相比之下，对于AADH系统，发现转移至等效OD 1是优选的。详细分析了反应过程中酶复合物的结构。Thr 474 β（MADH）/Thr 172 β（AADH）与催化羧酸基团的氢键和非保守活性位点残基Tyr 471 β（MADH）/Phe 169 β（AADH）被确定为决定优选氧受体的重要因素。蛋白质的环境有显着的影响，反应能量，因此隧道贡献和KIE。这些环境效应，以及相关的明显不同的偏好，为两个羧酸氧原子（具有不同的KIE）在MADH/MA和AADH/色胺，是可能的原因，观察到的差异，在这两个重要的酶反应之间的KIE。
The hydrogen-transfer reaction catalysed by methylamine dehydrogenase (MADH) with methylamine (MA) as substrate is a good model system for studies of proton tunnelling in enzyme reactions--an area of great current interest--for which atomistic simulations will be vital. Here, we present a detailed analysis of the key deprotonation step of the MADH/MA reaction and compare the results with experimental observations. Moreover, we compare this reaction with the related aromatic amine dehydrogenase (AADH) reaction with tryptamine, recently studied by us, and identify possible causes for the differences observed in the measured kinetic isotope effects (KIEs) of the two systems. We have used combined quantum mechanics/molecular mechanics (QM/MM) techniques in molecular dynamics simulations and variational transition state theory with multidimensional tunnelling calculations averaged over an ensemble of paths. The results reveal important mechanistic complexity. We calculate activation barriers and KIEs for the two possible proton transfers identified-to either of the carboxylate oxygen atoms of the catalytic base (Asp428beta)-and analyse the contributions of quantum effects. The activation barriers and tunnelling contributions for the two possible proton transfers are similar and lead to a phenomenological activation free energy of 16.5+/-0.9 kcal mol(-1) for transfer to either oxygen (PM3-CHARMM calculations applying PM3-SRP specific reaction parameters), in good agreement with the experimental value of 14.4 kcal mol(-1). In contrast, for the AADH system, transfer to the equivalent OD1 was found to be preferred. The structures of the enzyme complexes during reaction are analysed in detail. The hydrogen bond of Thr474beta(MADH)/Thr172beta(AADH) to the catalytic carboxylate group and the nonconserved active site residue Tyr471beta(MADH)/Phe169beta(AADH) are identified as important factors in determining the preferred oxygen acceptor. The protein environment has a significant effect on the reaction energetics and hence on tunnelling contributions and KIEs. These environmental effects, and the related clearly different preferences for the two carboxylate oxygen atoms (with different KIEs) in MADH/MA and AADH/tryptamine, are possible causes of the differences observed in the KIEs between these two important enzyme reactions.
登录
查看更多内容
影响因子：
15
作者：
Hatcher, E;Soudackov, AV;Hammes-Schiffer, S
通讯作者：
Hammes-Schiffer, S
用于模拟酶中氢转移反应的混合量子/经典路径积分方法。
DOI：
10.1063/1.2362823
发表时间：
2006
期刊：
The Journal of chemical physics
影响因子：
--
作者：
Wang,Qian;Hammes-Schiffer,Sharon
通讯作者：
Hammes-Schiffer,Sharon
大豆脂氧合酶-1 催化的氢提取中压缩增强了酶动力学和隧道效应。
DOI：
10.1021/jp066263i
发表时间：
2006
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Tejero,Ismael;Garcia-Viloca,Mireia;Gonzalez-Lafont,Angels;Lluch,JoseM;York,DarrinM
通讯作者：
York,DarrinM
芳香胺脱氢酶和天青蛋白之间的电子转移反应。
影响因子：
2.9
作者：
Hyun,YL;Davidson,VL
通讯作者：
Davidson,VL
影响因子：
2.9
作者：
Rickert, KW;Klinman, JP
通讯作者：
Klinman, JP