Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination.
Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination.
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DOI：
10.1021/ja804040s
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发表时间：
2008-11-26
影响因子：
15
通讯作者：
Jorgensen, William L.
中科院分区：
文献类型：
--
作者：
Alexandrova, Anastassia N.;Roethlisberger, Daniela;Baker, David;Jorgensen, William L.
最近设计并测试了一系列消除5-硝基苯并异恶唑Kemp的酶。在设计过程中，进行了广泛的计算分析，以评估其中四种设计的潜在性能，如下所示。在蒙特卡罗(MC)统计力学模拟的背景下，利用量子力学和分子力学(QM/MM)的混合计算对酶催化反应进行了模拟。自由能微扰(FEP)计算被用来表征水中催化反应和参比过程的自由能表面。模拟得到了有关反应过程中催化机理、活化势垒和活性中心结构演变的详细信息。所设计的酶KE07、KE10(V131N)和KE15的催化机理与质子转移相一致，在过渡状态下通常比异恶唑基N-O键的断裂更快。根据自由能结果，预计所有三种酶都是活性的。还出现了进一步改进酶设计的想法。在技术方面，QM/MM并行和实验工作在人工酶设计中的协同作用得到了很好的说明。
A series of enzymes for Kemp elimination of 5-nitrobenzisoxazole have been recently designed and tested. In conjunction with the design process, extensive computational analyses were carried out to evaluate the potential performance of four of the designs, as presented here. The enzyme-catalyzed reactions were modeled using mixed quantum and molecular mechanics (QM/MM) calculations in the context of Monte Carlo (MC) statistical mechanics simulations. Free energy perturbation (FEP) calculations were used to characterize the free-energy surfaces for the catalyzed reactions as well as for reference processes in water. The simulations yielded detailed information about the catalytic mechanisms, activation barriers, and structural evolution of the active sites over the course of the reactions. The catalytic mechanism for the designed enzymes KE07, KE10(V131N), and KE15 was found to be concerted with proton transfer generally more advanced in the transition state than breaking of the isoxazolyl N-O bond. On the basis of the free-energy results, all three enzymes were anticipated to be active. Ideas for further improvement of the enzyme designs also emerged. On the technical side, the synergy of parallel QM/MM and experimental efforts in the design of artificial enzymes is well illustrated.
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DOI：
10.1073/pnas.0404387101
发表时间：
2004-08-10
影响因子：
11.1
作者：
Kaplan, J;DeGrado, WF
通讯作者：
DeGrado, WF
DOI：
10.1073/pnas.251555398
发表时间：
2001-12-04
影响因子：
11.1
作者：
Bolon, DN;Mayo, SL
通讯作者：
Mayo, SL
影响因子：
8
作者：
Dahiyat, BI;Mayo, SL
通讯作者：
Mayo, SL
影响因子：
5.6
作者：
Hennig, M;Darimont, BD;Kirschner, K
通讯作者：
Kirschner, K
影响因子：
4.4
作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
KLEIN, ML