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相关概念视频

Enzyme Inhibition01:30

Enzyme Inhibition

Inhibitors are molecules that reduce enzyme activity by binding to the enzyme. In a normally functioning cell, enzymes are regulated by a variety of inhibitors. Drugs and other toxins can also inhibit enzymes. Some inhibitors bind to the enzyme’s active site, while others inhibit enzymatic activity by binding to other sites on the protein structure.
Enzymes02:34

Enzymes

Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Ligand Binding Sites02:40

Ligand Binding Sites

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-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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 the...

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基于模板的对接使用EnzyDock的自动化最大常见子结构识别:机械和抑制器对接.

Renana Schwartz1, Amit Hadar-Volk1, Kwangho Nam2

  • 1Department of Chemistry, Israel National Institute of Energy Storage (INIES) and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel.

Journal of chemical information and modeling
|May 19, 2025
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概括

现在EnzyDock使用最大常见子结构 (MCS) 进行增强的机械对接,模拟从基质到产品的酶反应. 这一策略可以提高多种连接体和反应中间体的对接精度.

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科学领域:

  • 计算化学计算化学
  • 结构生物学 结构生物学
  • 酶学 是一种酶学.

背景情况:

  • 机械对接需要在酶的活性部位内建模多个连接体状态 (基质,中间体,产物).
  • 现有的对接程序往往难以准确地表示完整的反应坐标.
  • 此前EnzyDock已经启用了基于CHARMM的多状态,多规模对接,包括共识对接.

研究的目的:

  • 在EnzyDock.Dock中实施和评估一个以最大共同子结构 (MCS) 为指导的对接策略.
  • 为了实现连接物相似性的自动检测,以便在酶反应坐标上高效地对接.
  • 为了证明MCS引导对接对机械酶研究和抑制剂设计的实用性.

主要方法:

  • 在EnzyDock程序中集成的MCS多状态方法的实施.
  • 应用于复杂的酶反应级联 (CotB2,LepI) 进行机械对接.
  • 酶抑制剂与二叶酸减少酶和SARS-CoV-2 Mpro的对接,使用共价对接和QM/MM评分.

主要成果:

  • 通过MCS策略,可以在酶反应坐标上有效和稳健地对接连体.
  • 为了实现机械的一致性而不是对接各种抑制剂,确定了不同的MCS协议是必要的.
  • 成功应用于复杂的酶系统和抑制剂对接,包括共价相互作用.

结论:

  • MCS引导对接是强大的机械酶对接和抑制剂设计的有效策略.
  • 开发的方法增强了EnzyDock对模拟酶反应和各种连接物的能力.
  • 预计这些发现可以转移到其他分子对接程序.