Design of New Enzyme Catalysts

描述(申请人提供)：这项研究的目标是开发计算工具，为自然界中未发现的反应设计酶催化剂。将根据共价和非共价催化机制设计几种类型的反应的催化结合部位。组合探索潜在的侧链催化基团，然后进行最优催化排列的量子力学测试，将导致潜在催化中心的层次结构。我们的合作者David Baker和他的团队将使用设计的催化位置的坐标来预测将折叠成具有这种几何形状的催化位置的序列。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，我们将在合作中测试这些新蛋白质的催化活性和机理。重点是开发预测有效蛋白质催化剂的有效方法，这些方法将与具有不同催化熟练程度的酶和突变体的已知数据进行测试。 公共卫生相关性：在这一资助期间，我们将开发和使用计算化学的工具来设计新的酶。我们的重点将是证明我们可以做以前从未做过的事情：从头开始设计起作用的酶，从关于催化部位的想法开始，以用于非自然反应的全功能酶结束。最初的目标反应将用于药物目标的合成和作为杀虫剂和除草剂的一大类化合物的分解。

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.