The Mechanism of the Channel Opening in Channelrhodopsin-2: A Molecular Dynamics Simulation

Channelrhodopsin-2 (ChR2) has been one of the most important objects in the study of optogenetics. The retinal chromophore molecule absorbs photons and undergoes an isomerization reaction, which triggers the photocycle, resulting in a series of conformational changes. In this study, a series of intermediate structures (including D470, P500, P390-early, P390-late, and P520 states) of ChR2 in the photocycle were modeled, and molecular dynamics (MD) simulations were performed to elucidate the mechanism of ion channel opening of ChR2. The maximum absorption wavelength of these intermediates calculated by time-dependent density function theory (TD-DFT) is in general agreement with the experimental values, the distribution of water density gradually increases in the process of photocycle, and the radius of the ion channel is larger than 6 Å. All these results indicate that our structural models of the intermediates are reasonable. The evolution of protonation state of E90 during the photocycle is explained. E90 will deprotonate when the P390-early transforms into P390-late, in which the two conformations of P390-early and P390-late obtained from the simulations are consistent with the experimental descriptions. To validate the conductive P520 state, the potential mean force (PMF) of Na+ ions passing through the P520 intermediate was calculated by using steered molecular dynamics (SMD) simulation combined with umbrella sampling. The result shows that the Na+ ions passing through the channel with a very low energy barrier, especially in the central gate, is almost barrierless. This indicates that the channel is open in the P520 state.