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相关概念视频

Intrinsically Disordered Proteins02:18

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...
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Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

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Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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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...
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Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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相关实验视频

Updated: May 29, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

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对于内在无序的蛋白质进行集体对接.

Anjali Dhar1, Thomas R Sisk1, Paul Robustelli1

  • 1Dartmouth College, Department of Chemistry, Hanover, NH, 03755.

bioRxiv : the preprint server for biology
|February 3, 2025
PubMed
概括
此摘要是机器生成的。

内在无序蛋白 (IDP) 是关键的药物点,但对传统设计来说具有挑战性. 新的集体对接方法准确地预测了像α-synuclein这样的IDP的小分子结合亲和力和机制.

关键词:
药物发现 药物发现 药物发现整体对接的对接方式本质上有障碍的蛋白质.分子对接 分子对接分子动力学分子动力学

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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相关实验视频

Last Updated: May 29, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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科学领域:

  • 生物化学 生物化学
  • 计算生物学 计算生物学
  • 药物发现 药物发现 药物发现

背景情况:

  • 内在无序蛋白质 (IDP) 与许多人类疾病有关.
  • 国内流离失所者缺乏稳定的3D结构,这使得他们成为传统基于结构的药物设计的困难目标.
  • 针对境内流离失所者为新型治疗策略提供了一个有希望的途径.

研究的目的:

  • 开发计算效率高的集体对接方法,用于预测小分子与IDP的结合.
  • 在原子分辨率下描述具有IDP的小分子的动态和异质结合机制.
  • 为了验证ensemble对接对实验数据的预测能力.

主要方法:

  • 为内在无序的蛋白质量身定制的组合对接协议的开发.
  • 应用方法来预测小分子连接体的相对结合亲缘关系.
  • 使用NMR光谱来实验验证结合亲缘关系.
  • 与长时间分子动力学模拟进行结合模式分析的比较.

主要成果:

  • 合并对接准确地预测了α-synuclein配体的相对结合亲缘关系.
  • 计算方法产生了连接体结合模式的构造组合.
  • 结果与经过实验验证的分子动力学模拟显示出了显著的一致性.
  • 证明了在原子分辨率下表征动态结合机制的能力.

结论:

  • 集成对接方法显示出预测小分子与IDP结合的巨大潜力.
  • 这些计算方法可以有效地描述动态和异质的结合机制.
  • 开发的协议可以作为加快IDP药物发现运动的有价值工具.