从晶体学多元变形模型的集合中,绘制相关蛋白质结构中的全性重新连接
bioRxiv : the preprint server for biology
|June 12, 2025
概括
具有共同结构的相关蛋白质通过交替形状来实现多种功能. 新的算法揭示了蛋白氨酸酸酶 (PTP) 中的共享和独特的全性网络,解释了功能多样性并使新的研究工具成为可能.
科学领域:
- 结构生物学是结构生物学.
- 生物化学 生物化学
- 生物信息学是一种生物信息学.
背景情况:
- 具有相似结构的相关蛋白质经常执行不同的生物功能.
- 这种功能多样性可能来自结构动力学和全调节的微妙差异.
- 研究这些替代形状一直在实验上具有挑战性.
研究的目的:
- 为了建模和分析相关家族内的替代蛋白质构造.
- 了解结构灵活性如何促进蛋白氨酸酸酶 (PTPs) 的功能分歧.
- 开发用于分析多元变形器模型中的全网络的计算工具.
主要方法:
- 利用qFit算法,从221个PTP结构的电子密度图中建模替代形状.
- 开发了RINFAIRE算法,用于分析相互作用网络.
- 在PTP家族中量化比较了全性网络.
主要成果:
- 确定了一种在PTP中共享的通用全性网络,该网络可以动态重新连接.
- 证明了个别的PTP具有独特的全特征.
- 表明高度连接的残留物中的突变调节了酶催化,有时会增强活性.
结论:
- 进化已经重新使用了模块化蛋白质结构,通过动态的全重连接来实现功能多样性.
- 开发的工具 (qFit和RINFAIRE) 提供了对蛋白质功能和调节的新见解.
- 这些发现为了解微妙的结构变异如何导致独特的生物学作用提供了一个框架.
相关概念视频
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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...
Cooperative Allosteric Transitions
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...
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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 pathway,...
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 pathway,...
Cooperative Allosteric Transitions
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...
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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...


