Role of Coupled Amino Acids in the Mechanisms of Enzyme Catalysis

偶联氨基酸在酶催化机制中的作用

• 批准号: 2147498
• 负责人: Mary Jo Ondrechen
• 金额: $ 81.07万
• 依托单位: Northeastern University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2147498&HistoricalAwards=false
• 关键词: Role; Coupled; Amino; Acids; Mechanisms

This project develops concepts that will improve our understanding of how enzymes work. Enzymes are nature’s catalysts that make chemical reactions happen under mild conditions. The same reactions on a laboratory bench or industrial reactor might require high temperature and/or strong acid or strong base. Yet enzymes in every living system enable reactions to happen at ambient temperature, or body temperature, and neutral conditions. This project will provide valuable new information into how enzymes achieve this feat and, in turn, inform the field of enzyme engineering. The goal is to build a knowledge base that will enable the design of enzymes that can catalyze industrial chemical reactions with less energy consumption and fewer by-products than conventional processes. Several dozen students, in research laboratories and classrooms, will be trained in computational and experimental techniques, a training vital to the high-tech economy of the region and U.S. competitiveness in the global economy. The project will include students from underserved communities. All methods and programs developed, including all code and data generated will be made freely available to the community. To achieve catalytic properties comparable to those of natural enzymes, engineered enzymes must incorporate the same kinds of electrostatic, chemical, and dynamic properties that occur in natural enzymes. This project combines theory, computation, and biochemical experiments to achieve three aims. First, a retrospective study will be performed of the pathways of evolved, designed enzymes to establish which properties are developing, as catalytic capabilities increase from the initial designs to the most recent, most effective catalysts. The human enzyme phosphoglucose isomerase (PGI) is an enzyme for which experimental results already exist to show that several of its amino acids, including some not in direct contact with the reacting molecules, participate in the catalytic process. PGI will be analyzed in detail to determine how each of these amino acids helps catalysis. Finally, starting with an enzyme of unknown function from Mycobacterium tuberculosis (Mt) with weak isomerase activity but high structural similarity to the highly active enzyme ketosteroid isomerase from Pseudomonas putida, computational engineering will be used to increase isomerase activity in the Mt enzyme and the activity of the engineered Variants will be measured through direct biochemical assay.This award was jointly funded by the Molecular Biophysics Cluster in the Molecular and Cellular Biosciences (MCB) Division and the Chemistry of Life Processes program in the Chemistry (CHE) Division.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

该项目开发了概念，可以提高我们对酶如何工作的理解。酶是自然的催化剂，使化学反应在轻度条件下发生。实验室或工业反应堆的反应可能需要高温和/或强酸或强碱。然而，每个生命系统中的酶都可以在环境温度或体温和中性条件下发生反应。该项目将为酶如何实现这一壮举提供宝贵的新信息，然后为酶工程领域提供信息。目的是建立一个知识库，该知识基础将使酶的设计比传统过程相比，能够以更少的能源消耗和更少的副产品催化工业化学反应。在研究实验室和教室中的数十名学生将接受计算和实验技术的培训，这是该地区高科技经济至关重要的培训，以及美国在全球经济中的竞争力。该项目将包括来自服务不足社区的学生。开发的所有方法和程序，包括所有生成的代码和数据，将免费提供给社区。为了实现与天然酶相当的催化特性，工程酶必须结合天然酶中发生的相同种类的静电，化学和动态特性。该项目结合了理论，计算和生化实验，以实现三个目标。首先，将对进化，设计的酶的途径进行回顾性研究，以确定哪些特性正在发展，因为催化能力从初始设计到最新的，最有效的催化剂。人酶磷酸葡萄糖异构酶（PGI）是一种酶，已经存在实验结果，以表明其几种氨基酸，包括一些与反应分子直接接触的氨基酸参与催化过程。将对PGI进行详细分析，以确定这些氨基酸中的每一个如何帮助催化剂。最后，从来自结核分枝杆菌（MT）的未知功能的酶开始，具有弱异构酶活性，但与高度活跃的酶促酮异构酶异构酶的结构相似性很高由分子和细胞生物科学（MCB）分裂（MCB）分裂和化学过程中的化学过程（CHE）分区的化学过程（CHE）划分共同资助。该奖项反映了NSF的法定任务，并被基金会的智力和更广泛的影响通过评估来诚实地通过评估来诚实地支持。

项目成果

Biochemical Activity of 17 Cancer-Associated Variants of DNA Polymerase Kappa Predicted by Electrostatic Properties

• DOI: 10.1021/acs.chemrestox.3c00233
• 发表时间: 2023-10-26
• 期刊: CHEMICAL RESEARCH IN TOXICOLOGY
• 影响因子: 4.1
• 作者: Kankanamge，Lakindu S. Pathira;Mora，Alexandra;Beuning，Penny J.
• 通讯作者: Beuning，Penny J.

Functional annotation of haloacid dehalogenase superfamily structural genomics proteins

• DOI: 10.1042/bcj20230057
• 发表时间: 2023-10-01
• 期刊: BIOCHEMICAL JOURNAL
• 影响因子: 4.1
• 作者: Kankanamge，Lakindu S. Pathira;Ruffner，Lydia A.;Ondrechen，Mary Jo
• 通讯作者: Ondrechen，Mary Jo