QM/MM free energy Simulations of an efficient Gluten Hydrolase (Kuma030) Implicate for a Reactant-State Based Protein-Design Strategy for General Acid/Base Catalysis.
QM/MM free energy Simulations of an efficient Gluten Hydrolase (Kuma030) Implicate for a Reactant-State Based Protein-Design Strategy for General Acid/Base Catalysis.
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高效麸质水解酶 (Kuma030) 的 QM/MM 自由能模拟涉及一般酸/碱催化的基于反应物状态的蛋白质设计策略
DOI：
10.1038/s41598-018-25471-z
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发表时间：
2018-05-04
影响因子：
4.6
通讯作者：
Yao J
中科院分区：
文献类型：
--
作者：
Wang X;Li R;Cui W;Li Q;Yao J
通过计算机设计酶来实现新的化学转化或提高催化效率是当代生物化学家的一大兴趣。Baker等人开发的Rosetta无疑是蛋白质设计领域的领先软件。通常，过渡态（TS）的优化是Rosetta方案的一部分，以增强靶酶的催化效率，因为TS稳定性是基于TS理论（TST）的催化效率的决定因素。然而，令人困惑的是，在某些情况下，反应物状态（RS）的优化也会导致催化效率的显着提高，例如谷蛋白水解酶（Kuma 030）的设计。因此，揭示RS中更好的结合导致kcat增加的根本原因是有趣的。在这项研究中，结合量子力学/分子力学（QM/MM）的分子动力学（MD）和自由能（PMF）模拟，pKa计算，统计分析，如方差分析测试进行阐明有趣的，但难以捉摸的问题。通过将计算结果与一般酸碱理论相结合，我们回答了为什么在一般酸碱催化中RS稳定化的优化会导致TS稳定化更好的问题。此外，一个新的和简化的蛋白质设计策略，提出了一般的酸/碱催化。将传统的酶作用机制应用于蛋白质设计策略，将有助于蛋白质设计方法学的发展。
It is a grand attraction for contemporary biochemists to computationally design enzymes for novel chemical transformation or improved catalytic efficiency. Rosetta by Baker et al. is no doubt the leading software in the protein design society. Generally, optimization of the transition state (TS) is part of the Rosetta’s protocol to enhance the catalytic efficiency of target enzymes, since TS stabilization is the determining factor for catalytic efficiency based on the TS theory (TST). However, it is confusing that optimization of the reactant state (RS) also results in significant improvement of catalytic efficiency in some cases, such as design of gluten hydrolase (Kuma030). Therefore, it is interesting to uncover underlying reason why a better binding in the RS leading to an increased kcat. In this study, the combined quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy (PMF) simulations, pKa calculation, and the statistical analysis such as the ANOVA test were carried out to shed light on the interesting but elusive question. By integration of our computational results and general acid/base theory, we answered the question why optimization of RS stabilization leads to a better TS stabilization in the general acid/base catalysis. In addition, a new and simplified protein-design strategy is proposed for the general acid/base catalysis. The idea, that application of traditional well-defined enzyme mechanism to protein design strategy, would be a great help for methodology development of protein design.
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DOI：
10.1002/prot.340040208
发表时间：
1988-01-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
BRUNGER, AT;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
15
作者：
Gordon, Sydney R.;Stanley, Elizabeth J.;Wolf, Sarah;Toland, Angus;Wu, Sean J.;Hadidi, Daniel;Mills, Jeremy H.;Baker, David;Pultz, Ingrid Swanson;Siegel, Justin B.
通讯作者：
Siegel, Justin B.
影响因子：
5.5
作者：
Gaus, Michael;Cui, Qiang;Elstner, Marcus
通讯作者：
Elstner, Marcus
影响因子：
16.6
作者：
EIGEN, M
通讯作者：
EIGEN, M
影响因子：
4.4
作者：
ADELMAN, SA;DOLL, JD
通讯作者：
DOLL, JD