Computational Enzyme Design

计算酶设计

• 批准号: 7045980
• 负责人: KATARINA S MIDELFORT
• 金额: $ 4.88万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-04-01 至 2007-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7045980
• 关键词: aldehyde lyase; biotechnology; carbon oxygen lyase; catalyst; computational biology; directed evolution; enzyme activity; enzyme mechanism; enzyme model; enzyme structure; gene expression; model design /development; molecular cloning; postdoctoral investigator; protein engineering; protein purification; protein structure function; structural biology; triose phosphate isomerase

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.

描述（由申请人提供）： 该提案涉及通过计算方法创建新型酶。基于设计的金属结合位点、多种配体的受体结合和从头蛋白质的成功，在缺乏先前催化特性的蛋白质支架中设计了酶活性。尽管实现了足够强的生物功能酶活性，但这种新型计算设计的酶并未达到天然酶所观察到的催化效率。在这里，我们建议通过提高该方法初步成功的准确性和范围来扩展酶设计方法，并通过互补的定向进化技术增强该设计过程。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二醛合酶来检查模型内的立体电子控制，并扩展这种计算方法所涉及的反应范围通过设计 I 类（希夫碱）醛缩酶。