Next-generation computational enzyme design for the creation of efficient artificial biocatalysts

用于创建高效人工生物催化剂的下一代计算酶设计

• 批准号: RGPIN-2021-03484
• 负责人: Chica, Roberto
• 金额: $ 5.76万
• 依托单位: University of Ottawa
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=748188
• 关键词: Next; generation; computational; enzyme; design

Enzymes are the most efficient catalysts known. They can accelerate chemical reactions by more than a billion times, display unmatched selectivity, and are completely biodegradable. If we could create, from scratch, artificial enzymes that can catalyze any chemical reaction with high efficiency, it would open the door to highly valuable biotechnologies that are currently inaccessible using natural enzymes. These include biocatalytic syntheses of fine chemicals and pharmaceuticals, treatment of metabolic disorders, and bioremediation of contaminated water and soil. In this proposed research program, we will develop next-generation enzyme design methods and use them to create efficient artificial biocatalysts for the synthesis of valuable chemicals. These methods will be based on the multistate protein design algorithms that we developed in the previous funding cycle, which allow proteins to be modeled, not as a single structure as is traditionally done, but as structural ensembles that more realistically represent the range of conformations that these molecules can sample in solution. This is important because enzymes must "move" in order to catalyze chemical reactions with extreme precision and efficiency. To date, all published examples of computational enzyme design have focussed on the design of a single structural state, not taking into account the ability of enzymes to exchange between multiple states, and thereby yielded artificial enzymes with catalytic efficiencies several orders of magnitude worse than those of their natural counterparts. The development and experimental validation of our proposed multistate enzyme design algorithms will be undertaken in the following research themes. 1) We will develop methods to design complete enzymatic catalytic cycles, instead of considering only a single state as was done previously, and use them to create efficient biocatalysts for multistep reactions of industrial interest. 2) We will develop methods to predict mutations far from the active site that will have a favorable effect on catalysis, an essential requirement for the creation of highly active enzymes that nevertheless remains elusive. 3) We will develop multistate design methods to control enzyme conformational equilibria and eventually create large conformational changes required for more complex reactions. In the long term, we will combine these methods to create biocatalysts `on-demand' for valuable biotechnological applications. The proposed research program will provide world-class research training, in both computational and experimental techniques, to a diverse group of trainees, helping them acquire skills highly sought after by the pharmaceutical, biotech, and bioproducts industries. As enzymes can be applied to a wide range of commercially and societally relevant problems, our proposed research will yield new technologies required to tackle important challenges of 21st century Canada in industry, the environment and medicine.

酶是已知的最有效的催化剂。它们可以将化学反应加速超过十亿次，表现出无与伦比的选择性，并且完全可生物降解。如果我们可以从头开始创建可以以高效率催化任何化学反应的人工酶，那么它将为当前使用天然酶无法访问的高价生物技术打开大门。其中包括精细化学物质和药物的生物催化合成，代谢性疾病的治疗以及受污染的水和土壤的生物修复。在该拟议的研究计划中，我们将开发下一代酶设计方法，并使用它们来创建有效的人工生物催化剂来综合有价值的化学物质。这些方法将基于我们在先前的资金周期中开发的多态蛋白质设计算法，该算法允许对蛋白质进行建模，而不是传统上所做的单个结构，而是像传统上所做的单一结构，而作为结构集合，这些结构集合更现实地表示这些分子可以在溶液中采样的构象范围。这很重要，因为酶必须“移动”才能以极高的精度和效率催化化学反应。迄今为止，所有已发表的计算酶设计的例子都集中在单个结构状态的设计上，而没有考虑酶在多个状态之间交换的能力，从而产生了具有催化效率的人工酶，几个比其自然对抗的质量差。我们提出的多态酶设计算法的开发和实验验证将在以下研究主题中进行。 1）我们将开发设计完整的酶促催化周期的方法，而不是像以前仅考虑一个单个状态，并使用它们来创建有效的生物催化剂来实现工业兴趣的多步反应。 2）我们将开发方法来预测远离活性部位的突变，这将对催化产生有利的影响，这是创建高度活跃酶的必不可少的要求，尽管如此，仍然难以捉摸。 3）我们将开发多态设计方法来控制酶构象平衡，并最终产生更复杂的反应所需的巨大构象变化。从长远来看，我们将结合这些方法，以创建有价值的生物技术应用的生物催化剂“按需”。拟议的研究计划将向一组不同的学员提供世界一流的研究培训，包括计算和实验技术，帮助他们获得药物，生物技术和生物生物产品行业高度追捧的技能。由于可以将酶应用于各种商业和社会相关的问题，因此我们提出的研究将产生新技术，以应对21世纪加拿大在工业，环境和医学方面的重要挑战。