将分子动力学与贝叶斯分析结合起来,以预测和评估流感血凝素中的联结突变
Peter M Kasson1, Daniel L Ensign, Vijay S Pande
1Department of Chemistry, Stanford University, Stanford, California 94305, USA.
Journal of the American Chemical Society
|July 30, 2009
概括
预测流感病毒突变是流行病监测的关键. 分子动力学模拟可以识别影响血凝素的突变.
科学领域:
- 病毒学 病毒学
- 计算生物学 计算生物学
- 生物物理学的生物物理.
背景情况:
- 流感病毒通过血凝素与细胞表面的甘氨酸结合感染细胞.
- 糖甘结合的特异性影响了物种间的流感传播,例如禽流感和猪流感.
- 预测影响甘氨酸结合的突变对于流行性流感监测至关重要.
研究的目的:
- 设计一种计算方法来预测改变流感血氨酸糖结合的突变.
- 评估分子动力学模拟对受体结合域和基突变的预测能力.
主要方法:
- 开发了一种分子动力学方法来得分潜在的血质素突变.
- 对17种不同的血凝素突变体进行了超过1毫秒的模拟.
- 采用贝叶斯模型来对影响血凝胺-连接体复合体稳定性的突变进行排序.
主要成果:
- 鉴定了七种突变,预计其分离率显著增加 (k (((off)).
- 证明了分子动力学对预测连接物结合突变的有用性,包括全突变.
- 提供了一种在实验验证之前计算评估突变者的方法.
结论:
- 分子动力学模拟为识别流感病毒联体结合突变提供了可概括的方法.
- 这种方法有助于理解血凝素对甘氨酸结合的决定因素,特别是H5N1流感.
- 对突变体的计算评估是预测和控制流行性流感菌株的重要一步.
相关概念视频
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 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...

