Computational Enzyme Design

描述（由申请人提供）： 这个提议涉及通过计算方法创造新的酶。基于设计的金属结合位点、广泛配体的受体结合和从头蛋白的成功，在缺乏先前催化特征的蛋白质支架中设计酶活性。尽管实现了足够强的酶活性的生物功能，这种新的计算设计的酶没有达到天然酶观察到的催化效率。在这里，我们建议通过提高该方法的初步成功的准确性和范围来扩展酶设计方法，并使用互补的定向进化技术来增强该设计过程。这些方法将使我们能够开发酶设计来测试特定的机制假设。我们建议探索和提高在以前设计的TIM酶的催化效率增强的酶设计的准确性，检查立体电子控制模型内通过计算设计的分歧进化的酶甲基乙二醛合酶，并通过设计一个I类（希夫碱）醛缩酶这种计算方法接近的反应范围。

DESCRIPTION (provided by applicant): This proposal concerns the creation of novel enzymes by computational methodologies. Building on successes of designed metal-binding sites, receptor binding for a wide range of ligands, and de novo proteins, enzymatic activity was designed in a protein scaffold that lacked previous catalytic character. Despite achieving strong enough enzymatic activity for biological function, this novel computationally designed enzyme did not attain the catalytic efficiencies observed for natural enzymes. Here we propose to extend the enzyme design method by improving the accuracy and scope of the method's preliminary success and augment this design process with complementary directed evolution techniques. These methods will allow us to develop enzyme designs to test specific mechanistic hypotheses. We propose to explore and improve the accuracy of the enzyme design for enhanced catalytic efficiencies in the previously designed TIM enzymes, examine stereoelectronic control within the model by computationally designing the divergently evolved enzyme methylglyoxal synthase, and extend the scope of reactions approached by this computational method by designing a class I (Schiff base) aldolase enzyme.