de Groot B L, Vriend G, Berendsen H J
Department of Biophysical Chemistry, The University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands.
J Mol Biol. 1999 Mar 5;286(4):1241-9. doi: 10.1006/jmbi.1998.2568.
Conformational changes are known to play a crucial role in the function of the bacterial GroE chaperonin system. Here, results are presented from an essential dynamics analysis of known experimental structures and from computer simulations of GroEL using the CONCOORD method. The results indicate a possible direct form of inter-ring communication associated with internal fluctuations in the nucleotide-binding domains upon nucleotide and GroES binding that are involved in the allosteric mechanism of GroEL. At the level of conformational transitions in entire GroEL rings, nucleotide-induced structural changes were found to be distinct and in principle uncoupled from changes occurring upon GroES binding. However, a coupling is found between nucleotide-induced conformational changes and GroES-mediated transitions, but only in simulations of GroEL double rings, and not in simulations of single rings. This provides another explanation for the fact that GroEL functions a double ring system.
已知构象变化在细菌GroE伴侣蛋白系统的功能中起着关键作用。本文给出了对已知实验结构进行主成分分析的结果，以及使用CONCOORD方法对GroEL进行计算机模拟的结果。结果表明，在核苷酸和GroES结合时，核苷酸结合结构域的内部波动可能与环间通讯的直接形式相关，这涉及到GroEL的变构机制。在整个GroEL环的构象转变水平上，发现核苷酸诱导的结构变化是独特的，原则上与GroES结合时发生的变化无关。然而，在核苷酸诱导的构象变化和GroES介导的转变之间发现了耦合，但仅在GroEL双环模拟中存在，而在单环模拟中不存在。这为GroEL作为双环系统发挥功能这一事实提供了另一种解释。
