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Computational analysis of the transient movement of helices in sensory rhodopsin II

Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan

(RECEIVED July 6, 2004; FINAL REVISION September 10, 2004; ACCEPTED September 13, 2004)

MD simulation of sensory rhodopsin II was executed for three intermediates (ground-state, K-state, M-state) appearing in its photocycle. We observed a large displacement of the cytoplasmic side of helixF only in M-state among the three intermediates. This displacement was transmitted to TM2, and the cytoplasmic side of TM2 rotated clockwise. These transient movements are in agreement with the results of an EPR experiment. That is, the early stage of signal transduction in a sRII–HtrII complex was successfully reproduced by the in silico MD simulation. By analyzing the structure of the sRII–HtrII complex, the following findings about the photocycle of sRII were obtained: (1) The hydrogen bonds between helixF and other helices determine the direction of the movement of helixF; (2) three amino acids (Arg162, Thr189, Tyr199) are essential for sRII–HtrII binding and contribute to the motion transfer from sRII to HtrII; (3) after the isomerization of retinal, a major conformational change of retinal was caused by proton transfer from Schiff base to Asp75, which, in turn, triggers the steric collision of retinal with Trp171. This is the main reason for the movement of the cytoplasmic side of helixF.

Keywords: sensory rhodopsin II; molecular dynamics simulation; signal transduction; transducer; movement of helixF

Abbreviations: sRII, sensory rhodopsin II • HtrII, transducer molecule • TM, transmembrane • BR, bacteriorhodopsin • MD, molecular dynamics • RMSD, root mean square deviation • VDW, van der Waals

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04973805.

Reprint requests to: T. Hoshino, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan; e-mail: hoshi{at}p.chiba-u.ac.jp; fax: +81-43-290-2925.

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