title: Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening.
abstract: Channelrhodopsin (ChR) is a light-gated cation channel that responds to blue light. Since ChR can be readily expressed in specific neurons to precisely control their activities by light, it has become a powerful tool in neuroscience. Although the recently solved crystal structure of a chimeric ChR, C1C2, provided the structural basis for ChR, our understanding of the molecular mechanism of ChR still remains limited. Here we performed electrophysiological analyses and all-atom molecular dynamics (MD) simulations, to investigate the importance of the intracellular and central constrictions of the ion conducting pore observed in the crystal structure of C1C2. Our electrophysiological analysis revealed that two glutamate residues, Glu122 and Glu129, in the intracellular and central constrictions, respectively, should be deprotonated in the photocycle. The simulation results suggested that the deprotonation of Glu129 in the central constriction leads to ion leakage in the ground state, and implied that the protonation of Glu129 is important for preventing ion leakage in the ground state. Moreover, we modeled the 13-cis retinal bound; i.e., activated C1C2, and performed MD simulations to investigate the conformational changes in the early stage of the photocycle. Our simulations suggested that retinal photoisomerization induces the conformational change toward channel opening, including the movements of TM6, TM7 and TM2. These insights into the dynamics of the ground states and the early photocycle stages enhance our understanding of the channel function of ChR.
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Mizuki
authors.initials: M
authors.lastname: Takemoto
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Hideaki E
authors.initials: HE
authors.lastname: Kato
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Michio
authors.initials: M
authors.lastname: Koyama
authors.affiliation: Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
authors.forename: Jumpei
authors.initials: J
authors.lastname: Ito
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
authors.forename: Motoshi
authors.initials: M
authors.lastname: Kamiya
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Hayashi
authors.affiliation: Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
authors.forename: Andrés D
authors.initials: AD
authors.lastname: Maturana
authors.affiliation: Department of Bioengineering and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States of America.
authors.forename: Karl
authors.initials: K
authors.lastname: Deisseroth
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Ryuichiro
authors.initials: R
authors.lastname: Ishitani
authors.affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Osamu
authors.initials: O
authors.lastname: Nureki
mesh_terms: D001436:Bacteriorhodopsins / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D004224:Diterpenes; D004594:Electrophysiology; D005973:Glutamine / Q000737:chemistry / Q000235:genetics; D057809:HEK293 Cells; D006801:Humans; D015640:Ion Channel Gating; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D054730:Protein Interaction Domains and Motifs; D012172:Retinaldehyde / Q000737:chemistry / Q000378:metabolism*; D012243:Rhodopsin / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D004224:Diterpenes; D005973:Glutamine; C031338:13-cis-retinal; D001436:Bacteriorhodopsins; D012243:Rhodopsin; D012172:Retinaldehyde