Computational Enzyme Design

描述(由申请人提供)： 这项提议涉及到通过计算方法创造新的酶。在设计的金属结合位点、广泛配体的受体结合和从头蛋白质的成功基础上，在缺乏先前催化特性的蛋白质支架中设计了酶活性。尽管获得了足够强的生物功能酶活性，这种通过计算设计的新型酶并没有达到天然酶观察到的催化效率。在这里，我们建议通过提高酶设计方法的准确性和初步成功的范围来扩展该方法，并用互补的定向进化技术来增强这一设计过程。这些方法将允许我们开发酶设计来测试特定的机制假说。我们建议探索和提高酶设计的准确性，以提高先前设计的TIM酶的催化效率，通过计算设计不同进化的酶甲基乙醛合成酶来检验模型中的立体电子控制，并通过设计I类(Schiff碱)缩醛酶来扩大这种计算方法所接近的反应范围。

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.