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序列相似的蛋白质域对具有结构或拓差异的结构或拓差异

¹Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.

|October 11, 2024

概括

具有相似序列的蛋白质结构可以具有不同的拓. BCAlign识别了这些拓变异,对于理解蛋白质功能和进化至关重要,特别是在X射线和NMR结构之间.

科学领域:

结构生物学是结构生物学.
生物信息学是一种生物信息学.
计算化学是一种计算化学.

背景情况:

蛋白质结构分析通常根据序列相似性进行聚类,抛弃冗余结构.
序列相似性通常意味着结构上的相似性,但存在显著的差异,通常具有功能上的影响.
脊柱运动可以改变蛋白质链拓和折叠路径.

研究的目的:

在序列家族内识别具有替代链拓的蛋白质域.
开发一种方法 (BCAlign) 来对准蛋白质骨干曲线,以考虑结构和基于序列的衍生.
研究蛋白质结构中的序列相似性,结构变异和拓差异之间的关系.

主要方法:

使用CATH4.2数据库搜索具有替代链拓的域.
开发了BCAlign,通过结合结构和基于序列的衍生来优化对齐.
采用一个算法来检测曲线变形期间的固态和拓障碍.
对高度序列相似的域进行了基于序列和基于结构的对齐比较.

主要成果:

在CATH4.2序列家族中识别了具有替代链拓的域,在很大程度上独立于序列身份或RMSD.
BCAlign有效地对齐蛋白质脊柱曲线,揭示结构和拓变异.
与基于结构的对齐相比,基于序列的对齐在高度序列相似的域中突出显示了更大的结构和拓变异.
在X射线和NMR结构之间最频繁地观察到替代链的拓.

结论:

代表性蛋白质结构集应包括表现出拓变异的序列相似域.
BCAlign为分析蛋白质骨干灵活性和拓变化提供了一种新的方法.
了解拓变异对于全面的蛋白质结构-功能关系研究至关重要.
在X射线和NMR结构之间发生变化的拓的普遍性表明,这些变异在数据库中的代表性不足.

关键词:

链条拓学链条拓学关于序列对齐的度量表.非冗余的非冗余的结构对齐结构对齐结构比较结构比较

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