非血红素铁酶的计算稳定使新功能的高效演变成为可能
Brianne R King1, Kiera H Sumida2, Jessica L Caruso1
1Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.
bioRxiv : the preprint server for biology
|August 2, 2024
概括
ProteinMPNN是一种深度学习工具,增强生物催化剂工程的酶稳定性. 稳定的酶在针对新功能的定向进化中显示出更大的改进.
科学领域:
- 生物催化和酶工程 生物催化和酶工程
- 计算生物学和蛋白质设计
- 合成生物学 合成生物学
背景情况:
- 定向进化是设计新型生物催化剂的关键.
- 酶稳定性对于成功的工程至关重要,因为新的催化功能可能会破坏稳定.
- 从稳定的酶支架开始,通常有利于定向进化.
研究的目的:
- 研究深度学习工具ProteinMPNN对重新设计Fe (II) /αKG超级酶家族的实用性.
- 提高酶的稳定性,可溶性和表达性,同时保持原生和非原生催化功能.
- 建立计算序列重新设计作为指导进化的初步步骤.
主要方法:
- 使用的蛋白MPNN用于Fe (II) /αKG酶的计算序列重新设计.
- 在野生类型和稳定酶变体上进行了位点和突变发生.
- 在非原生C-H基化反应中选增加活性.
主要成果:
- 蛋白MPNN成功地重新设计了Fe ((II) /αKG酶 (tP4H和GREE) 以提高稳定性,溶解性和表达.
- 与野生类型酶相比,稳定酶变体在非原生活性中表现出显著更大的增加.
- 简单的结构标准使得稳定,具有催化作用的变体能够产生.
结论:
- 使用ProteinMPNN进行计算序列重新设计是一种有效的策略,用于在定向进化之前稳定酶.
- 这种方法可以加速新型生物催化剂的工程,以增强的特性和功能.
- 蛋白MPNN提供了一种用户友好和可访问的方法,用于改善生物催化剂的酶支架.
![Protein Film Infrared Electrochemistry Demonstrated for Study of H2 Oxidation by a [NiFe] Hydrogenase](/_next/image?url=https%3A%2F%2Fcloudfront.jove.com%2FCDNSource%2Fteasers%2F55858.jpg&w=3840&q=50)
相关概念视频
01:07Catalytically Perfect Enzymes
3.9K
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...
3.9K
01:19Allosteric Proteins-ATCase
5.7K
Binding sites linkages can regulate a protein's function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
5.7K
00:49Ligand Binding and Linkage
4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
01:49Conserved Binding Sites
4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K
01:57Gene 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
01:19Enzyme Kinetics
96.3K
Enzymes speed up reactions by lowering the activation energy of the reactants. The speed at which the enzyme turns reactants into products is called the rate of reaction. Several factors impact the rate of reaction, including the number of available reactants. Enzyme kinetics is the study of how an enzyme changes the rate of a reaction.
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
96.3K