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

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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 clockwisely. These transient movements are in agreement with the results of EPR experiment. That is, the early stage of signal transduction in sRII – HtrII complex was successfully reproduced by the in silico MD simulation. By analyzing the structure of 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 the 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.

https://opac.ll.chiba-u.jp/da/curator/900020998/

https://opac.ll.chiba-u.jp/da/curator/900020998/ProteinScience_14_183_2005.pdf

Journal Article

Protein Science

14

183

192

2005

eng