Combinatorial Approach for Exploring Conformational Space and Activation Barriers in Computer-Aided Enzyme Design.
Combinatorial Approach for Exploring Conformational Space and Activation Barriers in Computer-Aided Enzyme Design.
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DOI：
10.1021/acscatal.0c01206
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发表时间：
2020-06-05
期刊：
影响因子：
12.9
通讯作者：
Warshel A
中科院分区：
文献类型：
--
作者：
Mondal D;Kolev V;Warshel A
计算机辅助酶设计对于生物技术的应用、医学的进步以及对酶作用的基本理解都具有重要的潜在意义。然而，在这个方向上达到预测能力是极具挑战性的。它既需要在已知结构和序列的情况下定量预测激活障碍的能力，也需要预测不同突变的影响的能力。在这项工作中，我们提出了一种预测已知结构蛋白质突变体的合理起始结构和计算产生的突变体的激活势垒的方案。我们的方法还允许我们使用所产生的突变体的预测结构来预测后续突变集的结构和激活障碍。该方案被用于检测Kemp消除酶和卤代烷脱卤酶的电子定向进化的可靠性。我们还使用单突变和双突变的结果作为预测多个并发突变对过渡状态稳定的影响的基础。这一策略似乎有助于创建一个活性漏斗，提供不同突变体的催化能力的定性排名。
Computer-aided enzyme design is a field of great potential importance for biotechnological applications, medical advances, and a fundamental understanding of enzyme action. However, reaching a predictive ability in this direction is extremely challenging. It requires both the ability to predict quantitatively the activation barriers in cases where the structure and sequence are known and the ability to predict the effect of different mutations. In this work, we propose a protocol for predicting reasonable starting structures of mutants of proteins with known structures and for calculating the activation barriers of the generated mutants. Our approach also allows us to use the predicted structures of the generated mutant to predict structures and activation barriers for subsequent set of mutations. This protocol is used to examine the reliability of the in silico directed evolution of Kemp eliminase and haloalkane dehalogenase. We also used the results of single and double mutations as a base for predicting the effect of transition-state stabilization by multiple concurrent mutations. This strategy seems to be useful in creating an activity funnel that provides a qualitative ranking of the catalytic power of different mutants.
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