Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Yokohama 230-0045, Japan.
J Mol Biol. 2011 May 6;408(3):568-84. doi: 10.1016/j.jmb.2011.02.058. Epub 2011 Mar 3.
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 α-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.
将蛋白质结构变化与配体结合的因果关系进行了分类和注释，涉及蛋白质数据库中 839 对非冗余的晶体结构，其中一对有结合的低分子量配体分子，另一对没有。蛋白质结构变化首先根据移动蛋白质片段的大小分为域运动或局部运动。然后根据配体结合位点的位置和蛋白质结构变化的线性响应理论来评估蛋白质运动是否与配体结合有关。与配体结合的蛋白质运动进一步分为闭合或打开运动。这种分类揭示了以下几点：（i）与配体结合的域运动主要是闭合运动，可以用线性响应理论来描述；（ii）局部运动经常伴随着有序-无序或α-螺旋-卷曲构象转变；（iii）转移酶活性（酶委员会编号 2）是耦合域闭合运动中的主要功能。这可以解释为闭合运动将这些酶的反应位点与环境水隔离开来。
