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関連する概念動画

Ligand Binding Sites02:40

Ligand Binding Sites

12.8K
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

4.8K
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

4.2K
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...
4.2K
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

20.7K
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...
20.7K
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:
12.9K
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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関連する実験動画

Updated: Jun 26, 2025

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
08:35

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

5.2K

AlphaFold2構造は,将来のリガンド発見を導く

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
まとめ
この要約は機械生成です。

AlphaFold2モデルは,リガンド結合部位を正確に予測することで,薬剤発見の有望性を示しています. この研究は,重要な受容体に対する新薬候補の潜在的ドッキングの有効性を示しています.

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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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関連する実験動画

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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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Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

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科学分野:

  • 計算生物学
  • 構造生物学
  • 薬物の発見

背景:

  • AlphaFold2 (AF2) モデルは,リガンド認識に関する遡及的な研究において,広範な有用性を示しているが,成功度は変動している.
  • 構造ベースの薬剤設計は,効果的なリガンドドッキングのために正確なタンパク質標的構造に依存しています.

研究 の 目的:

  • σ2およびセロトニン2A (5-HT2A) 受容体に対するリガンド認識のための未精製のAlphaFold2モデルの有用性を将来的に評価する.
  • 大型複合ライブラリをドッキングする実験構造とAF2モデルのパフォーマンスを比較する.

主な方法:

  • σ2および5-HT2A受容体の未精製AF2モデルに対する大型化合物ライブラリの将来的な分子ドッキング.
  • AF2モデルと実験構造との対比でドッキングから得られたヒット率とリガンド親和度の比較.
  • AF2ドッキングで特定された強力な5-HT2Aリガンドの冷凍電子顕微鏡構造の決定.

主要な成果:

  • 実験的構造とAF2派生構造の両方を用いて高い,比較可能なヒット率と親和性を達成した.
  • AF2モデルに対するリガンドの成功ドッキングは,実験構造と比較して異なるオーステリック残留形状でも発生した.
  • トップリガンドの冷凍-EM分析は,AF2の予測と一致する残留物収納を明らかにした.

結論:

  • 精製されていないAlphaFold2モデルは,実験構造からの構成的差異であっても,リガンド結合を正確に予測できます.
  • AF2モデルは,構造ベースの薬剤設計とリガンド発見に適した低エネルギー,関連する形状を表しています.
  • これらの発見は,薬剤設計におけるAF2モデルの適用性を拡大し,従来の構造ベースの方法を補完します.