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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

Effects of the deprotonation of either Glu122 or Glu129 in the ground state.(A, B, C) Distances between (A) Glu129-Asn297, (B) Glu122-His273 and (C) Glu122-Arg307 in the ATR-E122p-E129Δp and ATR-E122Δp-E129p simulations. (D, E) Distributions of water molecules in the ATR-E122p-E129Δp and ATR-E122Δp-E129p simulations. The distribution map is contoured at the probability density of 0.0015 molecules Å-3 ns-1. The time-averaged structure of the protein over 150 ns is shown.
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pone.0131094.g004: Effects of the deprotonation of either Glu122 or Glu129 in the ground state.(A, B, C) Distances between (A) Glu129-Asn297, (B) Glu122-His273 and (C) Glu122-Arg307 in the ATR-E122p-E129Δp and ATR-E122Δp-E129p simulations. (D, E) Distributions of water molecules in the ATR-E122p-E129Δp and ATR-E122Δp-E129p simulations. The distribution map is contoured at the probability density of 0.0015 molecules Å-3 ns-1. The time-averaged structure of the protein over 150 ns is shown.

Mentions: To investigate the effect of the deprotonation of each glutamate residue, we performed simulations in which either Glu122 or Glu129 was deprotonated (ATR-E122Δp-E129p and ATR-E122p-E129Δp; Table 1). In these simulations, similar structural changes to those in the ATR-E122Δp-E129Δp simulation were observed: the Glu129-Asn297 hydrogen bond was disrupted upon Glu129 deprotonation in the ATR-E122p-E129Δp simulation (Fig 4A; cyan line), while the Glu122-His173 hydrogen bond was disrupted and the salt bridge between Glu122 and Arg307 was formed upon Glu122 deprotonation in the ATR-E122Δp-E129p simulation (Fig 4B and 4C; red line). However, the water distributions revealed that no water channels were formed in these simulations, suggesting that ion or proton leakage did not occur (Fig 4D and 4E). In the ATR-E122p-E129Δp simulation, the water permeation was disturbed by the interaction between Glu122 and His173, and a small number of water molecules entered through these constrictions, similar to the ATR-E122p-E129p simulation. In the ATR-E122Δp-E129p simulation, the hydrogen bond between Glu129 and Asn297 blocked the water permeation. In contrast to the case of the Glu122-His173 interaction, no water molecules passed through the channel pathway, because of the stable Glu129-Asn297 hydrogen bond. Therefore, we hypothesized that either Glu122 or Glu129 is protonated, to prevent the water channel formation and proton leakage.


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)

Effects of the deprotonation of either Glu122 or Glu129 in the ground state.(A, B, C) Distances between (A) Glu129-Asn297, (B) Glu122-His273 and (C) Glu122-Arg307 in the ATR-E122p-E129Δp and ATR-E122Δp-E129p simulations. (D, E) Distributions of water molecules in the ATR-E122p-E129Δp and ATR-E122Δp-E129p simulations. The distribution map is contoured at the probability density of 0.0015 molecules Å-3 ns-1. The time-averaged structure of the protein over 150 ns is shown.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131094.g004: Effects of the deprotonation of either Glu122 or Glu129 in the ground state.(A, B, C) Distances between (A) Glu129-Asn297, (B) Glu122-His273 and (C) Glu122-Arg307 in the ATR-E122p-E129Δp and ATR-E122Δp-E129p simulations. (D, E) Distributions of water molecules in the ATR-E122p-E129Δp and ATR-E122Δp-E129p simulations. The distribution map is contoured at the probability density of 0.0015 molecules Å-3 ns-1. The time-averaged structure of the protein over 150 ns is shown.
Mentions: To investigate the effect of the deprotonation of each glutamate residue, we performed simulations in which either Glu122 or Glu129 was deprotonated (ATR-E122Δp-E129p and ATR-E122p-E129Δp; Table 1). In these simulations, similar structural changes to those in the ATR-E122Δp-E129Δp simulation were observed: the Glu129-Asn297 hydrogen bond was disrupted upon Glu129 deprotonation in the ATR-E122p-E129Δp simulation (Fig 4A; cyan line), while the Glu122-His173 hydrogen bond was disrupted and the salt bridge between Glu122 and Arg307 was formed upon Glu122 deprotonation in the ATR-E122Δp-E129p simulation (Fig 4B and 4C; red line). However, the water distributions revealed that no water channels were formed in these simulations, suggesting that ion or proton leakage did not occur (Fig 4D and 4E). In the ATR-E122p-E129Δp simulation, the water permeation was disturbed by the interaction between Glu122 and His173, and a small number of water molecules entered through these constrictions, similar to the ATR-E122p-E129p simulation. In the ATR-E122Δp-E129p simulation, the hydrogen bond between Glu129 and Asn297 blocked the water permeation. In contrast to the case of the Glu122-His173 interaction, no water molecules passed through the channel pathway, because of the stable Glu129-Asn297 hydrogen bond. Therefore, we hypothesized that either Glu122 or Glu129 is protonated, to prevent the water channel formation and proton leakage.

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