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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 deprotonation of both Glu122 and Glu129 in the ground state.Structural comparison of the intracellular constrictions between the ATR-E122p-E129p and ATR-E122Δp-E129Δp simulations. (A) Overall structures of snapshots from the last frame of both simulations. Key residues are highlighted in orange and magenta. (B) Magnified view of the intracellular and central constrictions (left and right panels, respectively). Double arrows indicate the possible motions of Glu121-Arg307 (red), Glu122-His173 (cyan), Glu122-Arg307 (green) and Glu129-Asn297 (magenta). (C-F) Distances between (C) Glu121-Arg307, (D) Glu122-His173, (E) Glu122-Arg307, and (F) Glu129-Asn297. (G, H) Distribution of water molecules in the (G) ATR-E122p-E129p and (H) ATR-E122Δp-E129Δp simulations. The distribution maps are 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.g003: Effects of deprotonation of both Glu122 and Glu129 in the ground state.Structural comparison of the intracellular constrictions between the ATR-E122p-E129p and ATR-E122Δp-E129Δp simulations. (A) Overall structures of snapshots from the last frame of both simulations. Key residues are highlighted in orange and magenta. (B) Magnified view of the intracellular and central constrictions (left and right panels, respectively). Double arrows indicate the possible motions of Glu121-Arg307 (red), Glu122-His173 (cyan), Glu122-Arg307 (green) and Glu129-Asn297 (magenta). (C-F) Distances between (C) Glu121-Arg307, (D) Glu122-His173, (E) Glu122-Arg307, and (F) Glu129-Asn297. (G, H) Distribution of water molecules in the (G) ATR-E122p-E129p and (H) ATR-E122Δp-E129Δp simulations. The distribution maps are 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: We first performed the ATR-E122p-E129p simulation (Table 1). In this simulation, the overall structure was stable, and no large structural changes were observed (Fig 3A; gray). The interactions in both the central and intracellular constrictions were also preserved during the 150-ns simulation. The salt bridge between Glu121 and Arg307 in the intracellular constriction, and the hydrogen bond between Glu129 and Asn297 in the central constriction, were stable (Fig 3C and 3F; gray line). The hydrogen bond between Glu122 and His173 in the intracellular constriction was disrupted and reformed again during the 150-ns simulation (Fig 3D). As a result, a small number of water molecules entered through the intracellular constriction (Fig 3G). The extracellular side of the channel pathway, especially the extracellular vestibule observed in the crystal structure, was filled with water molecules (Fig 3G). However, no water channel was formed between the intra- and extracellular sides of the membrane, due to the stable hydrogen-bonds of the central constriction.


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 deprotonation of both Glu122 and Glu129 in the ground state.Structural comparison of the intracellular constrictions between the ATR-E122p-E129p and ATR-E122Δp-E129Δp simulations. (A) Overall structures of snapshots from the last frame of both simulations. Key residues are highlighted in orange and magenta. (B) Magnified view of the intracellular and central constrictions (left and right panels, respectively). Double arrows indicate the possible motions of Glu121-Arg307 (red), Glu122-His173 (cyan), Glu122-Arg307 (green) and Glu129-Asn297 (magenta). (C-F) Distances between (C) Glu121-Arg307, (D) Glu122-His173, (E) Glu122-Arg307, and (F) Glu129-Asn297. (G, H) Distribution of water molecules in the (G) ATR-E122p-E129p and (H) ATR-E122Δp-E129Δp simulations. The distribution maps are 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.g003: Effects of deprotonation of both Glu122 and Glu129 in the ground state.Structural comparison of the intracellular constrictions between the ATR-E122p-E129p and ATR-E122Δp-E129Δp simulations. (A) Overall structures of snapshots from the last frame of both simulations. Key residues are highlighted in orange and magenta. (B) Magnified view of the intracellular and central constrictions (left and right panels, respectively). Double arrows indicate the possible motions of Glu121-Arg307 (red), Glu122-His173 (cyan), Glu122-Arg307 (green) and Glu129-Asn297 (magenta). (C-F) Distances between (C) Glu121-Arg307, (D) Glu122-His173, (E) Glu122-Arg307, and (F) Glu129-Asn297. (G, H) Distribution of water molecules in the (G) ATR-E122p-E129p and (H) ATR-E122Δp-E129Δp simulations. The distribution maps are 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: We first performed the ATR-E122p-E129p simulation (Table 1). In this simulation, the overall structure was stable, and no large structural changes were observed (Fig 3A; gray). The interactions in both the central and intracellular constrictions were also preserved during the 150-ns simulation. The salt bridge between Glu121 and Arg307 in the intracellular constriction, and the hydrogen bond between Glu129 and Asn297 in the central constriction, were stable (Fig 3C and 3F; gray line). The hydrogen bond between Glu122 and His173 in the intracellular constriction was disrupted and reformed again during the 150-ns simulation (Fig 3D). As a result, a small number of water molecules entered through the intracellular constriction (Fig 3G). The extracellular side of the channel pathway, especially the extracellular vestibule observed in the crystal structure, was filled with water molecules (Fig 3G). However, no water channel was formed between the intra- and extracellular sides of the membrane, due to the stable hydrogen-bonds of the central constriction.

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