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相关概念视频

Ligand Binding Sites02:40

Ligand Binding Sites

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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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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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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:
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Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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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...
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Ligand Binding and Linkage00:49

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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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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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Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
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联结过渡状态有多强?

Samik Bose1, Samuel D Lotz1, Indrajit Deb1

  • 1Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States.

Journal of the American Chemical Society
|November 9, 2023
PubMed
概括
此摘要是机器生成的。

计算模型使用结合动力学预测药物的有效性. 研究人员模拟了可溶性环氧化酶 (sEH) 抑制剂的联体解结,揭示了基于动态的药物设计的挑战.

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科学领域:

  • 计算化学
  • 生物物理
  • 药理学

背景情况:

  • 药物的有效性通常可以通过药物结合动力学 (按速率,离速率) 来预测,而不是单独使用热力学.
  • 优化药物化合物需要基于动力学的预测计算模型.
  • 对于这些模型来说,尽管它们的寿命很短,但了解结过渡状态至关重要.

研究的目的:

  • 用可溶性环氧化酶 (sEH) 抑制剂进行联体解结事件的计算模型.
  • 分析具有不同停留时间的抑制剂的连体结合过渡状态组合 (TSEs).
  • 确定基于动态的药物设计的挑战和机遇.

主要方法:

  • 使用权重组合方法REVO (通过变异优化重新采样组合).
  • 五种sEH抑制剂的模拟解结路径,停留时间为14. 25至31. 75分钟.
  • 分析解结合体,专注于过渡状态组合体特征和蛋白质-连接体相互作用.

主要成果:

  • 在居住时间的数量范围内达到平均预测准确度.
  • 对于具有相似结合姿势的体,观察到TSE (空间分布,蛋白质-体相互作用) 的显著差异.
  • 在考虑像连接体自由度这样的一般特征时,确定了TSE的共同点.

结论:

  • 联结过渡状态组合表现出复杂的行为,即使在相似的结合姿势中也存在差异.
  • 一般特征,如连接体自由度,在不同的TSE中显示相似性.
  • 由于过渡状态的复杂性,基于动态的合理药物设计仍然存在重大挑战.