Biomaterial Database

Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins. 1996

D M van Aalten, and B L de Groot, and H J Berendsen, and J B Findlay

Department of Biochemistry and Molecular Biology, University of Leeds, U.K.

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.

UI	MeSH Term	Description	Entries
D008956	Models, Chemical	Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.	Chemical Models,Chemical Model,Model, Chemical
D011487	Protein Conformation	The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).	Conformation, Protein,Conformations, Protein,Protein Conformations
D003198	Computer Simulation	Computer-based representation of physical systems and phenomena such as chemical processes.	Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D012176	Retinoids	A group of tetraterpenes, with four terpene units joined head-to-tail. Biologically active members of this class are used clinically in the treatment of severe cystic ACNE; PSORIASIS; and other disorders of keratinization.	Retinoid
D012177	Retinol-Binding Proteins	Proteins which bind with RETINOL. The retinol-binding protein found in plasma has an alpha-1 mobility on electrophoresis and a molecular weight of about 21 kDa. The retinol-protein complex (MW	Retinoid Binding Protein,Retinol Binding Protein,Retinoid Binding Protein, F-Type,Retinoid Binding Proteins,Retinol Binding Proteins,Binding Protein, Retinoid,Binding Protein, Retinol,Binding Proteins, Retinoid,Binding Proteins, Retinol,Protein, Retinoid Binding,Protein, Retinol Binding,Retinoid Binding Protein, F Type