Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point To Redesign New Diels-Alderases.
Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point To Redesign New Diels-Alderases.
复制标题
南极假丝酵母脂肪酶 B 的计算研究，以测试其作为重新设计新 Diels-Alderases 起点的能力。
DOI：
10.1021/acs.jpcb.5b10527
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发表时间：
2016
期刊：
影响因子：
--
通讯作者：
Moliner,Vicent
中科院分区：
文献类型：
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作者：
Świderek,Katarzyna;Moliner,Vicent
新型生物催化剂的设计正受到越来越多的关注。在这方面最流行的反应之一是Diels-Alder环加成反应，因为它在有机合成中的应用和缺乏有效的天然酶来催化它。本文通过理论量子力学/分子力学（QM/MM）分子动力学模拟，探讨了利用高度混杂的南极假丝酵母脂肪酶B作为蛋白质支架重新设计diols - alderase的可能性。计算了野生型和几种AM1/MM杂交突变体的两个反应的自由能面，修正量在M06-2X/MM水平。对溶液中对应反应的研究使得可以进行比较分析，得出有趣的结论。由于亲二烯亲和物在所有测试的蛋白质变体的氧阴离子空穴中锚定得非常好，从反应物络合物到过渡态的轻微电子变化表明，突变应该集中在有利于反应物络合物的反应构象的形成上，这反过来又会降低能量势垒。
The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels–Alder cycloaddition because of its applications in organic synthesis and the absence of efficient natural enzymes that catalyze it. In this paper, the possibilities of using the highly promiscuous Candida Antarctica lipase B as a protein scaffold to redesign a Diels–Alderase has been explored by means of theoretical quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. Free energy surfaces have been computed for two reactions in the wild-type and in several mutants with hybrid AM1/MM potentials with corrections at M06-2X/MM level. The study of the counterpart reactions in solution has allowed performing comparative analysis that render interesting conclusions. Since the dienophile anchors very well in the oxyanion hole of all tested protein variants, the slight electronic changes from reactant complex to the transition state suggest that mutations should be focused in favoring the formation of reactive conformations of a reactant complex that, in turn, would reduce the energy barrier.