Evaluation and ranking of enzyme designs
Evaluation and ranking of enzyme designs
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DOI：
10.1002/pro.462
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发表时间：
2010-09-01
期刊：
影响因子：
8
通讯作者：
Houk, K. N.
中科院分区：
文献类型：
--
作者：
Kiss, Gert;Roethlisberger, Daniela;Houk, K. N.
2008年，一个成功的计算设计程序被报道，产生了活性酶催化剂的肯普消除。在这里，我们研究了这些蛋白质以及一组以前未发表的非活性设计，以确定活性或缺乏活性的来源，并预测哪些设计的结构最有可能是催化的。从截断模型系统的量子力学（QM）到ONIOM QM/MM和AMBER分子动力学（MD）对全蛋白质的处理方法进行了探索。最有效的程序涉及分子动力学，并建立了一个通用的MD协议。观察到许多设计与理想的催化几何形状有很大的偏差。水渗透到催化位点和活性位点周围的残留物填充不足是导致酶设计失活的主要因素。在过去，设计的酶的计算评估对于实际考虑来说时间太长，现在已经可以在实验之前并结合实验对候选物进行计算排名和细化，从而显著提高酶设计过程的效率。
In 2008, a successful computational design procedure was' reported that yielded active enzyme catalysts for the Kemp elimination. Here, we studied these proteins together with a set of previously unpublished inactive designs to determine the sources of activity or lack thereof, and to predict which of the designed structures are most likely to be catalytic. Methods that range from quantum mechanics (QM) on truncated model systems to the treatment of the full protein with ONIOM QM/MM and AMBER molecular dynamics (MD) were explored. The most effective procedure involved molecular dynamics, and a general MD protocol was established. Substantial deviations from the ideal catalytic geometries were observed for a number of designs. Penetration of water into the catalytic site and insufficient residue-packing around the active site are the main factors that can cause enzyme designs to be inactive. Where in the past, computational evaluations of designed enzymes were too time-extensive for practical considerations, it has now become feasible to rank and refine candidates computationally prior to and in conjunction with experimentation, thus markedly increasing the efficiency of the enzyme design process.