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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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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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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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Metal-Ligand Bonds02:51

Metal-Ligand Bonds

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The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
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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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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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相关实验视频

Updated: Jun 26, 2025

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

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阿尔法Fold2结构指导潜在的连接体发现

Jiankun Lyu1,2, Nicholas Kapolka3, Ryan Gumpper3

  • 1Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.

Science (New York, N.Y.)
|May 16, 2024
PubMed
概括
此摘要是机器生成的。

AlphaFold2模型通过准确预测配体结合部位,显示出药物发现的前景. 这项研究表明它们在潜在的对抗关键受体的新药候选者的有效性.

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Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
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Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery
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相关实验视频

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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
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Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
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Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery
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科学领域:

  • 计算生物学
  • 结构生物学
  • 药物发现

背景情况:

  • 在回顾性联体识别研究中,AlphaFold2 (AF2) 模型具有广泛的实用性,但成功率可变.
  • 基于结构的药物设计依赖于精确的蛋白质标结构以实现有效的连接.

研究的目的:

  • 预期评估未精炼的AlphaFold2模型对σ2和2A (5-HT2A) 受体的联体识别的有用性.
  • 将AF2模型的性能与大型复合库对接中的实验结构进行比较.

主要方法:

  • 大型化合物库与σ2和5-HT2A受体的未精炼AF2模型的潜在分子对接.
  • 与AF2模型相比,通过对接获得的命中率和连体亲属性与实验结构的比较.
  • 通过AF2对接确定一个强大的5-HT2A连接体的冷电子显微镜结构.

主要成果:

  • 使用实验和AF2衍生结构实现了高和可比的命中率和亲和度.
  • 与实验结构相比,即使有不同的正体残留形状,也可以成功对接AF2模型.
  • 对顶部配体的冷电磁分析显示了与AF2预测一致的残留住宿.

结论:

  • 不精细的AlphaFold2模型可以准确地预测连体结合,即使与实验结构的构造差异不同.
  • AF2模型代表了低能量,适合基于结构的药物设计和配体发现的相关构造.
  • 这些发现扩大了AF2模型在药物设计中的适用性,补充了传统的基于结构的方法.