介质状态的结构异质性促进了CRIPT对PDZ3的结合领域:从分子动力学和马尔科夫状态模型分析的洞察力
Xingyu Song1, Dongdong Wang2, Jie Ji1
1Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China.
Journal of chemical theory and computation
|February 21, 2025
概括
内在无序的蛋白质 (IDP) 通过探索多种构造来快速结合目标. 这项研究揭示了类似漏斗的景观和加速结合的动态相互作用,为IDP功能提供了新的见解.
科学领域:
- 生物化学 生物化学
- 结构生物学 结构生物学
- 计算生物学 计算生物学
背景情况:
- 内在无序蛋白质 (IDP) 缺乏稳定的三级结构,但对细胞功能至关重要.
- IDPs通常经历"折叠结合"机制,但快速结合的动力学和分子基础仍然不清楚.
- 克里普特和PSD-95之间的相互作用对神经元发育至关重要.
研究的目的:
- 阐明内在无序蛋白质的快速结合动力学背后的分子机制.
- 为了研究CRIPT在与PSD-95 PDZ域结合时的结构动态.
- 探讨结构异质性在国内流离失所者的约束过程中的作用.
主要方法:
- 使用广泛的分子动力学 (MD) 模拟 (67.7 μs) 来描述CRIPT-PSD-95相互作用.
- 马尔科夫状态模型 (MSM) 分析被用来剖析结合路径和结构格局.
- 该研究的重点是CRIPT的C端区域和PSD-95.5的第三个PDZ域.
主要成果:
- IDP 呈现出类似漏斗的绑定景观,允许在目标绑定之前探索多个构造.
- 形成结构异质的中间复合体,由原生和非原生相互作用的平衡稳定.
- 在与PSD-95.5结合时,CRIPT采用β-链形态.
- 结构异质性被确定为促进加速结合动学的关键因素.
结论:
- 内在的障碍通过一个涉及多样化的形状集和途径的机制促进了快速结合.
- 这些发现扩展了经典的飞模型,突出了IDP的功能优势.
- 这项研究为IDP如何在细胞过程中实现高效的分子识别和功能提供了新的见解.
相关概念视频
Intrinsically Disordered Proteins
17.7K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
17.7K
Conservation of Protein Domains Over Different Proteins
10.7K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.7K
Protein Folding
117.1K
Overview
117.1K
Conserved Binding Sites
4.1K
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...
4.1K
Protein-protein Interfaces
12.4K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.4K
Protein and Protein Structure
77.9K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
A protein's shape is critical to its function. For example, an enzyme...
77.9K


