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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
连接体重组自由能量在蛋白质-连接体结合-亲缘关系预测中的重要性
Chao-Yie Yang1, Haiying Sun, Jianyong Chen
1Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, Michigan 48109, USA.
Journal of the American Chemical Society
|September 10, 2009
概括
预测小分子结合亲和力对于药物设计至关重要. 包括连接体重组的自由能量显著改善了Smac模拟物与XIAP蛋白结合的计算预测.
科学领域:
- 计算化学是一种计算化学.
- 结构生物学是结构生物学.
- 药物发现 药物发现
背景情况:
- 精确预测小分子连接体与生物标的结合亲和力对于基于结构的药物设计至关重要.
- 当前的计算方法往往难以可靠地预测这些结合性亲和关系,阻碍了药物开发.
- 小分子Smac (第二个线粒体衍生卡斯巴酶激活剂) 模仿剂向XIAP (X-结抑制剂) 蛋白质具有治疗意义.
研究的目的:
- 通过计算预测31个小分子Smac模仿XIAP蛋白质的结合模型和亲缘关系.
- 评估各种计算方法的性能,包括对接和MM-GBSA,用于绑定亲和力预测.
- 研究连接体重组自由能量对结合亲缘关系预测准确性的影响.
主要方法:
- 计算对接被用来预测31个Smac模拟器和XIAP的绑定模型.
- 使用经验评分,基于知识的评分函数和MM-GBSA计算了绑定亲和力.
- 用分子动力学模拟来生成组合蛋白质-连接体形状.
- 修改了MM-GBSA计算以包括连接体重组自由能量.
主要成果:
- 计算对接准确地预测了结合模型,并通过实验晶体结构验证.
- 标准计算方法对约束亲缘关系 (r(2) 的预测差到适度,在0.21和0.36之间.
- 包括MM-GBSA中的联体重组自由能量在内显著改善了结合亲和力预测 (r(2) 从0.36增加到0.66).
- 改进的预测得到了10个额外的Smac模拟器的验证.
结论:
- 配体重组自由能量是准确预测蛋白质-配体结合自由能量的一个关键因素.
- 在计算方法中包含连接体重组自由能量为药物设计提供了重大进步.
- 这项研究强调了评估其他联结蛋白系统的联结蛋白重组自由能量的重要性,并开发新的评分功能.
相关概念视频
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-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...
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-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...
Conserved Binding Sites
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 analyses the...
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 analyses the...
The Equilibrium Binding Constant and Binding Strength
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:
The Equilibrium Binding Constant and Binding Strength
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:
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...
