类视黄醇的构象分析及其与类视黄醇结合蛋白结合时动力学的受限情况
Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins.
作者信息
van Aalten D M, de Groot B L, Berendsen H J, Findlay J B
机构信息
Department of Biochemistry and Molecular Biology, University of Leeds, U.K.
出版信息
Biochem J. 1996 Oct 15;319 ( Pt 2)(Pt 2):543-50. doi: 10.1042/bj3190543.
An exhaustive sampling of the configurational space of all-trans retinol using a 0.1 microsecond molecular-dynamics simulation is presented. The essential dynamics technique is used to describe the conformational changes in retinol using only three degrees of freedom. The different conformational states of retinol are analysed, and differences in free energy are calculated. The essential dynamics description allows a detailed comparison of free retinol and retinoids bound to retinoid-binding proteins and opens new possibilities in the small-molecule docking field. The dynamics of retinoids when complexed with their binding proteins are restricted, and they are forced into strained conformations. A "spring' model for retinoid binding is proposed. This model is extended to a hypothesis for retinoid binding to visual pigments and bacteriorhodopsin.
本文介绍了使用0.1微秒分子动力学模拟对全反式视黄醇的构象空间进行的详尽采样。采用主成分动力学技术仅用三个自由度来描述视黄醇的构象变化。分析了视黄醇的不同构象状态，并计算了自由能差异。主成分动力学描述使得游离视黄醇与结合视黄醇结合蛋白的类视黄醇之间能够进行详细比较，并为小分子对接领域开辟了新的可能性。类视黄醇与其结合蛋白复合时的动力学受到限制，并被迫进入应变构象。提出了一种类视黄醇结合的“弹簧”模型。该模型扩展为类视黄醇与视觉色素和细菌视紫红质结合的假说。
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