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Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening.

Takemoto M, Kato HE, Koyama M, Ito J, Kamiya M, Hayashi S, Maturana AD, Deisseroth K, Ishitani R, Nureki O - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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.

No MeSH data available.


Related in: MedlinePlus

Correlation analysis for the 13-cisR-122Δp-129p simulation.(A) The matrix of correlation coefficients for the pairs of Cα atoms. (B) Mapping of the correlation coefficients to the structure. The black dashed circle represents the pair of Cα atoms with a correlation coefficient greater than 0.7. The red dashed circle represents the pair of Cα atoms in TM2 and TM7 that has a negative correlation coefficient.
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pone.0131094.g007: Correlation analysis for the 13-cisR-122Δp-129p simulation.(A) The matrix of correlation coefficients for the pairs of Cα atoms. (B) Mapping of the correlation coefficients to the structure. The black dashed circle represents the pair of Cα atoms with a correlation coefficient greater than 0.7. The red dashed circle represents the pair of Cα atoms in TM2 and TM7 that has a negative correlation coefficient.

Mentions: In addition to the movement of TM6, the outward movement of the cytoplasmic half of TM7 was observed in the 13-cisR-E122Δp-E129p simulation (Fig 6B and 6D). To visualize the correlated motions of TM6 and TM7, we calculated the correlation coefficient between each Cα atom in the TM domains. The correlation matrix showed that the cytoplasmic halves of TM6 and TM7 have a strong correlation, with a coefficient greater than 0.7 (Fig 7; black dashed circle in panel A). Moreover, in this correlation matrix, we found that the cytoplasmic half of TM2 has a negative correlation coefficient with TM7 (Fig 7A; red dashed circle), indicating that the cytoplasmic halves of TM2 and TM7 move in opposite directions (Fig 6B and 6E). These movements of TM2 and TM7 facilitate the disruption of the salt bridge between Glu121 and Arg307 in the intracellular constriction (Fig 6F). Taken together, the results of the 13-cisR-E122Δp-E129p simulation suggested that retinal isomerization induces the series of conformational changes of Trp262, followed by those of TM6, TM7, and TM2, toward channel opening. This is consistent with previous results obtained by cryo-electron microscopy and DEER spectroscopy, which suggested the movements of TM2, 6 and 7 in ChR2 during the photocycle, based on projection difference maps [41–43].


Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening.

Takemoto M, Kato HE, Koyama M, Ito J, Kamiya M, Hayashi S, Maturana AD, Deisseroth K, Ishitani R, Nureki O - PLoS ONE (2015)

Correlation analysis for the 13-cisR-122Δp-129p simulation.(A) The matrix of correlation coefficients for the pairs of Cα atoms. (B) Mapping of the correlation coefficients to the structure. The black dashed circle represents the pair of Cα atoms with a correlation coefficient greater than 0.7. The red dashed circle represents the pair of Cα atoms in TM2 and TM7 that has a negative correlation coefficient.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482709&req=5

pone.0131094.g007: Correlation analysis for the 13-cisR-122Δp-129p simulation.(A) The matrix of correlation coefficients for the pairs of Cα atoms. (B) Mapping of the correlation coefficients to the structure. The black dashed circle represents the pair of Cα atoms with a correlation coefficient greater than 0.7. The red dashed circle represents the pair of Cα atoms in TM2 and TM7 that has a negative correlation coefficient.
Mentions: In addition to the movement of TM6, the outward movement of the cytoplasmic half of TM7 was observed in the 13-cisR-E122Δp-E129p simulation (Fig 6B and 6D). To visualize the correlated motions of TM6 and TM7, we calculated the correlation coefficient between each Cα atom in the TM domains. The correlation matrix showed that the cytoplasmic halves of TM6 and TM7 have a strong correlation, with a coefficient greater than 0.7 (Fig 7; black dashed circle in panel A). Moreover, in this correlation matrix, we found that the cytoplasmic half of TM2 has a negative correlation coefficient with TM7 (Fig 7A; red dashed circle), indicating that the cytoplasmic halves of TM2 and TM7 move in opposite directions (Fig 6B and 6E). These movements of TM2 and TM7 facilitate the disruption of the salt bridge between Glu121 and Arg307 in the intracellular constriction (Fig 6F). Taken together, the results of the 13-cisR-E122Δp-E129p simulation suggested that retinal isomerization induces the series of conformational changes of Trp262, followed by those of TM6, TM7, and TM2, toward channel opening. This is consistent with previous results obtained by cryo-electron microscopy and DEER spectroscopy, which suggested the movements of TM2, 6 and 7 in ChR2 during the photocycle, based on projection difference maps [41–43].

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

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.

No MeSH data available.


Related in: MedlinePlus