Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model.
Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model.
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DOI：
10.1371/journal.pone.0156559
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Zhu Y
中科院分区：
文献类型：
--
作者：
Huang X;Xue J;Lin M;Zhu Y
活性位点预组织有助于天然酶静电稳定过渡态比基态更好地为他们的主要底物，并实现显着的速率提高。在这份报告中，我们假设，一个复杂的活性位点模型的活性位点预组织建模应有助于创建预组织的活性位点设计，并提供更高的起始活动对目标反应。我们的匹配算法ProdaMatch通过调用有效的修剪策略进行了改进，并在基准测试集中再现了十个支架的天然活性位点。10个骨架的匹配过渡态与晶体结构的均方根偏差均< 1.0 μ m，重排计算结果表明活性中心内91%的氢键得以恢复，表明活性中心可以根据预测的过渡态位置进行预组装.应用复杂的活性位点模型从头酶的设计进行了评估，通过支架选择使用一个经典的催化三联体基序的水解对硝基苯基乙酸酯。从具有1，491个蛋白质的支架文库中鉴定出80个支架，并且4个支架是天然酯酶。此外，复杂的底物的酶设计进行了研究的水解头孢氨苄使用支架选择基于两个不同的催化模体。通过经典的基于催化三联体的基序，从支架文库中仅鉴定出三个支架。相比之下，使用更灵活但仍预组织的催化基序鉴定了40个支架，其中一个支架对应于催化头孢氨苄水解和合成的α-氨基酸酯水解酶。因此，在改进的ProdaMatch程序的帮助下从头酶设计的复杂活性位点建模方法是一种有前途的方法，用于产生对靶反应具有高催化效率的活性位点。
Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic efficiencies towards target reactions.