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Literature DB >> 8912693

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

D M van Aalten¹, B L de Groot, H J Berendsen, J B Findlay.

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.

Entities: Chemical Disease

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Year: 1996 PMID： 8912693 PMCID： PMC1217802 DOI： 10.1042/bj3190543

Source DB: PubMed Journal: Biochem J ISSN： 0264-6021 Impact factor: 3.857

35 in total

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

1. WHAT IF: a molecular modeling and drug design program.

2. Essential dynamics of the cellular retinol-binding protein--evidence for ligand-induced conformational changes.

3. An efficient method for sampling the essential subspace of proteins.

4. Distorted structure of the retinal chromophore in bacteriorhodopsin resolved by 2H-NMR.

5. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy.

6. Crystal structures of holo and apo-cellular retinol-binding protein II.

7. Visual-pigment spectra: implications of the protonation of the retinal Schiff base.

8. A novel retinol-binding protein from rat. Purification and partial characterization.

9. Structure determination of the cyclohexene ring of retinal in bacteriorhodopsin by solid-state deuterium NMR.

10. Cellular retinol-binding protein from rat liver. Purification and characterization.

1. Functional concerted motions in the bovine serum retinol-binding protein.

2. Essential dynamics of DNA containing a cis.syn cyclobutane thymine dimer lesion.

3. Conformational Analysis of Retinoic Acids: Effects of Steric Interactions on Nonplanar Conjugated Polyenes.

4. Conformational Analysis of Free and Bound Retinoic Acid.

5. Unbinding of retinoic acid from its receptor studied by steered molecular dynamics.

6. The molecular basis of the interactions between synthetic retinoic acid analogues and the retinoic acid receptors.