从MD模拟中揭示PTPN11 SH2域中的Allostery
Massimiliano Anselmi1, Jochen S Hub2
1Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany. massimiliano.anselmi@uni-saarland.de.
Methods in molecular biology (Clifton, N.J.)
|September 5, 2023
概括
本研究介绍了一种主要成分分析 (PCA) 方法,用于分析Src-homology 2 (SH2) 域结构. 该方法揭示了SHP2的N-SH2和C-SH2域之间的明显的结构动态,反映了它们独特的功能作用.
科学领域:
- 生物化学 生物化学
- 结构生物学 结构生物学
- 分子动力学分子动力学
背景情况:
- Src-homology 2 (SH2) 域是关键的蛋白质相互作用模块,可以结合色胺基因.
- 氨酸酸酶SHP2利用其N-SH2和C-SH2域来调节信号通路及其自身的催化活性.
- 了解SH2域形态是阐明SHP2功能和全调节的关键.
研究的目的:
- 通过主要成分分析 (PCA) 来研究SH2域结构的新方法.
- 在各种条件下分析和合理化SH2域的结合点构造.
- 调查SHP2.2内的N-SH2和C-SH2域的独特构造动态.
主要方法:
- 将主要组件分析 (PCA) 应用于SH2域的结构数据.
- 分类和可视化不同的SH2域构造.
- 对结合部位的可访问性和潜在的全性相互作用的分析.
主要成果:
- PCA有效地区分,分组和分类SH2域结构,基于结合点构造.
- 该方法识别了可访问的构造和潜在的全相互作用.
- 在N-SH2和C-SH2域之间观察到结构动态的显著差异.
结论:
- 开发的PCA方法为分析SH2域结构合集提供了一个强大的框架.
- N-SH2和C-SH2的不同形态动态可能是它们在SHP2中的特殊功能作用的基础.
- 这种方法有助于研究SHP2信号传输中的蛋白质-连接体相互作用和全调节.
相关概念视频
Cooperative Allosteric Transitions
7.9K
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...
7.9K
Allosteric Proteins-ATCase
5.8K
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...
5.8K
Ligand 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
Conserved 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
Allosteric Regulation
58.2K
Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
58.2K
ATP Synthase: Mechanism
14.8K
In animals, the mitochondrial F1F0 ATP synthase is the key protein that synthesizes ATP molecules through a complex catalytic mechanism. While the nuclear genome encodes the majority of ATP synthase subunits, the mitochondrial genome encodes some of the enzyme's most critical components. The formation of this multi-subunit enzyme is a complex multi-step process regulated at the level of transcription, translation, and assembly. Defects in one or more of these steps can result in decreased...
14.8K


