解密结合点 基质混杂和专家酶的形式变化
Deeksha Thakur1, Paras Verma1, Shashi Bhushan Pandit1
1Bioinformatics Center, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) - Mohali, Knowledge City, Sector-81, SAS Nagar, Manauli 140306, India.
Journal of chemical information and modeling
|August 14, 2025
概括
酶基质散乱性,即处理多个基质的能力,与活性部位的灵活性有关. 构造动力学使杂交和专业酶能够结合多种基质,扩大它们的功能作用.
科学领域:
- 生物化学 生物化学
- 酶学 是一种酶学.
- 结构生物学 结构生物学
背景情况:
- 基质乱交使酶能够催化与非原生基质的反应,扩大它们的功能表,帮助进化适应或酶设计.
- 基质乱交的分子基础尚未完全理解,但越来越多地认为活性部位的结构灵活性是关键因素.
- 假设酶通过其活性位点内的先前存在的构成状态来适应替代基质.
研究的目的:
- 为了研究活性位点形状灵活性在基质乱交中的作用.
- 为了比较基质结合能力状态在杂交和专家酶中的构造动态.
主要方法:
- 采用长期的水分子动力学模拟来分析酶结构.
- 视觉评估了替代酶构成的变异性.
- 使用原生功能评分量化评估基质结合能力的形状.
主要成果:
- 在杂交和专业酶中确定了多个基质结合能力的适应体.
- 观察到限制性符合者也存在于两种类型的酶中.
- 证明,在两种类型的酶中,结构动力学对基质结合至关重要,尽管程度不同.
结论:
- 酶活性位点的 conformational 动力学在基质结合中起着重要作用.
- 杂交和专业酶都表现出结构灵活性,允许各种基质的结合.
- 形状灵活性的程度影响了在酶中观察到的基质乱交程度.
相关概念视频
Ligand Binding and Linkage
4.9K
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...
4.9K
Allosteric Proteins-ATCase
5.9K
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...
5.9K
Induced-fit Model
82.2K
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...
82.2K
Conserved Binding Sites
4.4K
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...
4.4K
Introduction to Mechanisms of Enzyme Catalysis
8.8K
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...
8.8K
Cooperative Allosteric Transitions
8.0K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
8.0K


