De Vivo Marco, Ensing Bernd, Klein Michael L
Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
J Am Chem Soc. 2005 Aug 17;127(32):11226-7. doi: 10.1021/ja053049j.
Recently, a new branch of fatty acid metabolism has been opened by the novel phosphatase activity found in the N-terminal domain of the, hence bifunctional, soluble epoxide hydrolase (sEH). Importantly, this finding has also provided a new site for drug targeting in sEH's activity regulation. Classical MD and hybrid Car-Parrinello QM/MM calculations have been performed to investigate the reaction mechanism of the phosphoenzyme intermediate formation in the first step of the catalysis. The results support a concerted multi-event reaction mechanism: (1) a dissociative in-line nucleophilic substitution for the phosphoryl transfer reaction; (2) a double proton transfer involved in the formation of a good leaving group in the transition state. The presence of a water bridge in the substrate/enzyme complex allowed an efficient proton shuttle, showing its key role in speeding up the catalysis. The calculated free energy of the favored catalytic pathway is approximately 19 kcal/mol, in excellent agreement with experimental data.
最近，在双功能可溶性环氧化物水解酶（sEH）的N端结构域中发现的新型磷酸酶活性开启了脂肪酸代谢的一个新分支。重要的是，这一发现也为sEH活性调节中的药物靶向提供了一个新位点。已进行经典分子动力学（MD）和混合Car-Parrinello量子力学/分子力学（QM/MM）计算，以研究催化第一步中磷酸酶中间体形成的反应机制。结果支持协同多事件反应机制：（1）磷酸转移反应的解离型线性亲核取代；（2）过渡态中形成良好离去基团时涉及的双质子转移。底物/酶复合物中存在水桥允许有效的质子穿梭，表明其在加速催化中的关键作用。有利催化途径的计算自由能约为19千卡/摩尔，与实验数据高度吻合。
