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Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins
D M van Aalten1, B L de Groot, H J Berendsen
1Department of Biochemistry and Molecular Biology, University of Leeds, U.K.
Abstract:
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.