Three-dimensional model of sensory rhodopsin I reveals important restraints between the protein and the chromophore

A structural model is constructed for the integral membrane protein, sensory rhodopsin I (SRI), the phototaxis receptor of the archaeon Halobacterium salinarium. The model is built on the template of the homologous bacteriorhodopsin (BR), The modeling procedure includes sequence alignment, a side chain rotamer search and simulated annealing by restricted molecular dynamics, The structure is in general agreement with previous results from mutagenesis experiments, chromophore substitution and room and cryogenic temperature spectroscopy, In particular, a residue near the beta-ionone ring of the retinylidene chromophore is found to be critical in maintaining the proper isomeric conformation of the chromophore; a layer of residues lying on the cytoplasmic side of the chromophore pocket is found to modulate the restraints around the C-13 region of the chromophore, affecting the isomerizations around its 13 = 14 bond that are important to the protein's activity, The restraints in these regions are more stringent in SRI than in BR, The tightened restraints are chiefly due to van der Waals interactions, where the attractive and repulsive components play separable roles, Aromatic residues account for a majority of the restrictive interactions, It is hypothesized that the enhanced barriers due to these restrictions regulate the progress of SRI's photocycle, so that it can couple,vith the phototaxis reaction chain in the bacterium, A possibility is also suggested that conformational changes of the protein provide the signal recognized by the transducer.