通过氨基酸保护分析增强机器学习预测酶催化剂温度的最佳值
Yinyin Cao1,2, Boyu Qiu2,3, Xiao Ning2,4
1College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
International journal of molecular sciences
|June 19, 2024
概括
预测酶的最佳催化温度 (T_opt) 对工业应用至关重要. 一个新的机器学习模型,不包括保存的氨基酸,改善了T_opt对酸酶的预测准确性,有助于对工业过程的酶选择.
科学领域:
- 生物化学和分子生物学
- 计算生物学 计算生物学
- 酵素工程是什么意思 酵素工程
背景情况:
- 酶是关键的工业催化剂,但确定它们的最佳催化温度 (T_opt) 是具有挑战性的.
- 现有的T_opt实验数据有限,计算预测方法缺乏足够的准确性.
- 精确的T_opt预测对于优化酶驱动的工业过程和制药开发至关重要.
研究的目的:
- 开发一种准确的计算方法来预测酶T_opt.
- 调查删除保存的氨基酸对T_opt预测准确性的影响.
- 为工业应用提供快速酶选择的基础.
主要方法:
- 开发了一个机器学习模型,使用氨基酸频率和蛋白质分子量作为特征.
- 对于T_opt预测,使用了K-最近邻近回归算法.
- 该模型应用于酸酶序列,既完整又删除了保存的氨基酸,用于比较分析.
主要成果:
- 机器学习模型在完整的酸酶序列中获得了0.599的平均确定系数 (R2).
- 删除保存的氨基酸显著改善了模型的预测性能,R2增加到0.755.5.
- 实验验证证证实,T_opt对缺乏保存氨基酸的酸酶的预测更接近实验确定值.
结论:
- 排除保存的氨基酸可以提高基于机器学习的T_opt对酶的预测的准确性.
- 这种方法有助于为工业应用选择具有最佳热稳定的酶.
- 这项研究为加速酶工程和过程优化提供了宝贵的工具.
相关概念视频
01:13Introduction 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
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
01:07Catalytically 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
01:13Induced-fit Model
80.7K
Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
80.7K
02:34Enzymes
81.4K
Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
81.4K
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