蛋白质的定向进化优化了酶电场
Shobhit S Chaturvedi1, Santiago Vargas1, Pujan Ajmera1
1Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States.
Journal of the American Chemical Society
|June 7, 2024
概括
定向进化 (DE) 在酶的计算设计失败的地方取得了成功. 我们的研究表明,DE改变了酶的电场,通过影响反应机制,实现了高效的碳转移.
科学领域:
- 生物化学
- 蛋白质工程
- 计算生物学
背景情况:
- 计算性酶设计往往难以创建功能性酶,与实验室指导进化 (DE) 的成功形成鲜明对比.
- 定向进化成功地适应了原蛋白以催化碳转移反应,但确切的机制尚不清楚.
- 之前的解释主要集中在基质接入和结合上,这些单独无法完全解释产量增加.
研究的目的:
- 阐明酶工程中定向进化的成功背后的分子机制.
- 研究活性部位3D电场在酶功能和适应中的作用.
- 为了比较计算设计与定向进化在创造功能性酶中的有效性.
主要方法:
- 对于碳转移催化物的原蛋白的实验室演变.
- 在酶活性部位内追踪和分析3D电场动态.
- 在电场数据上应用亲和传播聚类和主要组件分析.
主要成果:
- 定向进化显著改变了原蛋白活性部位内的电场拓.
- 确定了增强过渡状态能量和影响反应机制的特定电场配置.
- 在DE过程中出现了一个重要的化学意义上的电场组件,促进了碳转移.
结论:
- 动态3D电场是酶功能和催化效率的关键决定因素.
- 酶的活性位点可以在电场动态的影响下切换催化机制.
- 了解和操纵电场对于成功的酶设计和工程至关重要.
更多相关视频
09:01Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli
Published on: March 16, 2011
30.5K
10:31Residue-Specific Exchange of Proline by Proline Analogs in Fluorescent Proteins: How "Molecular Surgery" of the Backbone Affects Folding and Stability
Published on: February 3, 2022
2.9K
相关概念视频
Introduction to Mechanisms of Enzyme Catalysis
8.1K
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes...
8.1K
Catalytically Perfect Enzymes
4.0K
The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
Most enzymes...
Most enzymes...
4.0K
Protein Dynamics in Living Cells
2.1K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
2.1K
Protein Folding
8.0K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
8.0K
Gene Families
8.8K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
8.8K
