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相关概念视频

Ligand Binding Sites02:40

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...
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Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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Allosteric Regulation01:08

Allosteric Regulation

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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...
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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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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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...
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Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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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...
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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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深度学习的盲对接方法可以用来预测体化合物吗?

Eric A Chen1, Yingkai Zhang1,2,3

  • 1Department of Chemistry, New York University, New York, New York 10003, United States.

Journal of chemical information and modeling
|April 1, 2025
PubMed
概括
此摘要是机器生成的。

对全抑制剂的基于结构的药物设计很复杂. 数据驱动的最小距离矩阵表示 (MDMR) 和像DiffDock + LRD这样的对接方法可以预测全结合模式,但需要特定的蛋白质构造.

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科学领域:

  • 计算化学和结构生物学
  • 药物发现和药物化学

背景情况:

  • 阿洛斯特抑制剂比奥托斯特抑制剂具有优势,包括选择性和非竞争性结合.
  • 基于结构的药物设计 (SBDD) 对全性化合物是具有挑战性的,因为它具有多个结合点和蛋白质构成灵活性.
  • 像DiffDock这样的深度学习方法显示出对蛋白质连接体复合体预测的希望,其性能优于传统的对接工具.

研究的目的:

  • 评估最小距离矩阵表示 (MDMR) 以预测循环素依赖性激酶2 (CDK2) 的全抑制剂.
  • 评估对接方法能够预测orthosteric和allosteric结合模式的能力.
  • 为了确定蛋白质受体构造选择对接成功的影响.

主要方法:

  • 使用最小距离矩阵表示法 (MDMR),这是一个以数据为导向的方法,重点关注最小的残留-残留/连接器距离.
  • 采用了盲目对接和深度学习方法,包括DiffDock和Vina.
  • 设计的自我和交叉对接基准来评估对orthosteric和allosteric结合模式的预测准确性.
  • 研究了特定蛋白质构造的影响,包括中间状态,对对接性能.

主要成果:

  • MDMR分析揭示了多样化的蛋白质构造和连接体结合模式,确定了一个关键的中间CDK2构造.
  • DiffDock的综合方法,其次是Lin_F9局部重新对接 (DiffDock + LRD),成功地预测了orthosteric和allosteric结合姿势.
  • 准确预测全性姿势取决于选择已识别的中间蛋白质构造.

结论:

  • 像MDMR这样的数据驱动方法对于探索SBDD中的蛋白质构造格局和连接体相互作用是有价值的.
  • 预测全性姿势需要仔细考虑蛋白质受体构造,特别是中间状态.
  • DiffDock + LRD联合方法显示了预测orthosteric和allosteric抑制剂的潜力,有助于药物发现工作.