PLIP 2025:将蛋白质-蛋白质相互作用引入到蛋白质-配体相互作用配置文件中
Philipp Schake1, Sarah Naomi Bolz1, Katja Linnemann1
1Biotec and scads.ai, TU Dresden, 01307 Dresden, Germany.
Nucleic acids research
|May 10, 2025
概括
蛋白质 - 连接体相互作用分析器 (PLIP) 现在分析了蛋白质 - 蛋白质相互作用,揭示了像venetoclax这样的药物如何通过重叠的结合资料来模仿自然相互作用.
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:
- 蛋白质结构含有复杂的分子相互作用,对生物功能至关重要.
- 了解这些相互作用是药物发现和开发的关键.
- 蛋白质 - 连接体相互作用分析仪 (PLIP) 工具分析了蛋白质结构内的分子相互作用.
研究的目的:
- 引入能够分析蛋白质-蛋白质相互作用的增强PLIP工具.
- 通过比较药物标和原生相互作用来证明PLIP在理解药物机制方面的实用性.
- 为PLIP提供可访问的版本,包括Web服务器,源代码和Jupyter笔记本.
主要方法:
- PLIP检测了八种类型的非共价相互作用.
- 该研究比较了癌症药物venetoclax的PLIP识别的相互作用与Bcl-2和BAX之间的原生蛋白质-蛋白质相互作用.
- 分析的重点是确定药物结合和原生蛋白质复合体之间的重叠相互作用概况.
主要成果:
- 增强的PLIP成功地纳入了蛋白质与蛋白质相互作用分析.
- 在PLIP分析中,venetoclax和原生Bcl-2/BAX相互作用的相互作用概况之间存在显著的重叠.
- 这种重叠表明,venetoclax有效地模仿了原生蛋白质与蛋白质的相互作用.
结论:
- 扩展的PLIP工具对于分析小分子和蛋白质与蛋白质相互作用都是有价值的.
- 通过模仿或破坏原生蛋白相互作用,PLIP可以阐明药物如何调节生物通路.
- 作为Web服务器和其他格式的PLIP的可用性提高了研究人员的可访问性.
更多相关视频
12:53Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics
Published on: July 6, 2014
31.4K
06:50Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
910
相关概念视频
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 Networks
3.9K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
3.9K
Ligand Binding Sites
12.6K
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...
12.6K
Protein-Protein Interfaces
3.6K
3.6K
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
The Equilibrium Binding Constant and Binding Strength
12.7K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
12.7K
