Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins

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 st...

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Bibliographic Details
Published in:Biochemical journal 1996-10, Vol.319 ( Pt 2) (2), p.543-550
Main Authors: van Aalten, D M, de Groot, B L, Berendsen, H J, Findlay, J B
Format: Article
Language:English
Subjects:
Computer Simulation
Models, Chemical
Protein Conformation
Retinoids - chemistry
Retinoids - metabolism
Retinol-Binding Proteins - metabolism
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Summary: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.
ISSN:0264-6021
1470-8728
DOI:10.1042/bj3190543