Design of New Enzyme Catalysts

描述（由申请人提供）：本研究的目标是开发计算工具来设计自然界中不存在的反应的酶催化剂。基于共价和非共价催化机制，将设计几种类型反应的催化结合位点。对潜在侧链催化基团的组合探索，以及对最佳催化排列的量子力学测试，将导致潜在催化位点的层次结构。我们的合作者，David Baker和他的团队，将使用设计的催化位点的坐标来预测序列，这些序列将折叠成具有这种几何形状的催化位点。QM和QM/MM方法将在我们的实验室进行测试和开发，以预测哪些设计的蛋白质可能是最好的催化剂。这些蛋白质将由Baker小组用标准的分子生物学技术合成，我们将合作测试这些新蛋白质的催化活性和机制。重点是开发有效的方法来预测有效的蛋白质催化剂，这些方法将针对具有不同催化能力的酶和突变体的已知数据进行测试。

DESCRIPTION (provided by applicant): The goals of this research are to develop computational tools to design enzyme catalysts for reactions not found in nature. Catalytic binding sites for several types of reactions will be designed, based upon both covalent and noncovalent catalytic mechanisms. Combinatorial exploration of potential side-chain catalytic groups, followed by quantum mechanical testing of optimum catalytic arrangements will lead to a hierarchy of potential catalytic sites. Our collaborators, David Baker and his group, will use the coordinates of the designed catalytic sites to predict sequences that will fold into a catalytic site with this geometry. QM and QM/MM methods will be tested and developed in our lab to predict which of the designed proteins are likely to be the best catalysts. The proteins will be synthesized by the Baker group with standard molecular biological techniques, and in collaboration we will test the catalytic activity and mechanisms of these new proteins. Emphasis is on the development of efficient methods for the prediction of effective protein catalysts, and these methods will be tested against known data on enzymes and mutants that have different catalytic proficiencies. PUBLIC HEALTH RELEVANCE: During this grant period, we will develop and use the tools of computational chemistry to design novel enzymes. Our emphasis will be to demonstrate that we can do what has never been done before: design a functioning enzyme from scratch, starting with ideas about a catalytic site and ending with a fully functioning enzyme for a non-natural reaction. The initial target reactions will be of use in the synthesis of pharmaceutical targets and for the decomposition of a broad class of compounds utilized as pesticides and herbicides.