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首页> 外文期刊>Journal of Molecular Biology >Classification and annotation of the relationship between protein structural change and ligand binding.
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Classification and annotation of the relationship between protein structural change and ligand binding.

机译：分类和注释蛋白质结构变化与配体结合之间的关系。

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摘要

The causal relationship between protein structural change and ligand binding was classified and annotated for 839 nonredundant pairs of crystal structures in the Protein Data Bank-one with and the other without a bound low-molecular-weight ligand molecule. Protein structural changes were first classified into either domain or local motions depending on the size of the moving protein segments. Whether the protein motion was coupled with ligand binding was then evaluated based on the location of the ligand binding site and by application of the linear response theory of protein structural change. Protein motions coupled with ligand binding were further classified into either closure or opening motions. This classification revealed the following: (i) domain motions coupled with ligand binding are dominated by closure motions, which can be described by the linear response theory; (ii) local motions frequently accompany order-disorder or alpha-helix-coil conformational transitions; and (iii) transferase activity (Enzyme Commission number 2) is the predominant function among coupled domain closure motions. This could be explained by the closure motion acting to insulate the reaction site of these enzymes from environmental water.
机译：在蛋白质数据库中对839个非冗余的晶体结构对进行了分类，并注释了蛋白质结构变化与配体结合之间的因果关系，一个对有低分子量配体分子，一个对不对。首先根据移动的蛋白质片段的大小将蛋白质的结构变化分为区域运动或局部运动。然后基于配体结合位点的位置并通过蛋白质结构变化的线性响应理论的应用来评估蛋白质运动是否与配体结合有关。结合配体结合的蛋白质运动进一步分为闭合运动或开放运动。这种分类揭示了以下内容：（i）结合配体结合的结构域运动主要由闭合运动决定，这可以用线性响应理论来描述; （ii）局部运动经常伴随着无序或α-螺旋-螺旋构象转变; （iii）转移酶活性（酶促委员会第2号）是偶联域闭合运动中的主要功能。这可以通过封闭运动来解释，以将这些酶的反应部位与环境水隔离开来。

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