在二氧化酶中活性位点循环的 conformational 动力学突出显示了用于抑制剂对接的循环结构的局限性
Yen-Hua Huang1, Tsai-Ying Huang1,2, Man-Cheng Wang1
1Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan.
International journal of molecular sciences
|October 16, 2025
概括
氨酶 (DHOase) 循环的灵活性会影响抑制剂的结合. 了解这些结构变化对于有效的基于结构的药物设计和查至关重要.
科学领域:
- 生物化学 生物化学
- 结构生物学 结构生物学
- 酶学 是一种酶学.
背景情况:
- 氨酸酶 (DHOase) 对于新一代金胺生物合成至关重要.
- 在DHOase中,一个灵活的活性位点循环会影响基质结合,催化和抑制剂识别.
- 循环形态交换 (循环入/循环出) 影响了酶的功能.
研究的目的:
- 调查活性位点循环构成在DHO酶功能和抑制剂结合中的作用.
- 分析不同DHOase类型和物种的循环灵活性.
- 评估循环形状对基于结构的抑制剂查的影响.
主要方法:
- 鉴定了5-酸 (5-FOA) 和myricetin作为*Saccharomyces cerevisiae* DHOase的抑制剂.
- 对97个晶体结构和16个物种的DHOases的AlphaFold 3.0模型进行了系统分析.
- 计算对接实验,以评估不同循环形状中的抑制剂结合.
主要成果:
- DHOase 循环构造并不普遍依赖于连接体,并且在 DHOase 类型 (I,II,III) 中显著变化.
- 类型II DHO 酶具有最大的循环灵活性.
- *Saccharomyces cerevisiae* DHOase 主要采用循环状态,阻碍了对接的活跃站点可访问性.
结论:
- *S. cerevisiae* DHOase 的循环形状阻止了已识别的抑制剂 (5-FOA,myricetin) 的生产性对接.
- 对于有效的基于结构的药物设计和抑制剂选,必须考虑循环动态.
- 选择合适的循环形状对于成功发现向DHOase的药物至关重要.
相关概念视频
Induced-fit Model
88.7K
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...
88.7K
Enzymes
93.8K
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...
93.8K
Ligand Binding and Linkage
5.5K
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...
5.5K
Allosteric Proteins-ATCase
6.5K
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...
6.5K
Ligand Binding Sites
14.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
14.9K
Ligand Binding Sites
8.6K
8.6K


