Molecular Dynamics Simulation Of Ion Transmembrane Conduction In ChR2

Channelrhodopsin-2(Ch R2)is a light-activated and non-selective cationic channel protein that can be easily expressed in specific neurons to control neuronal activity by light.Although Ch R2 has been extensively used as an optogenetic tool in neuroscience research,the molecular mechanism of cation channel formation following retinal photoisomerization in Ch R2 and the structural basis of completely different ion selectivity in anion conduction are not well understood.In this paper,the closed state of Ch R2 and the structure of Ch R2 after retinal isomerization were studied.The formation of the cationic channel is elucidated in atomic detail using molecular dynamics simulations on the all-trans-retinal(Ch R2-trans)configuration of Ch R2 and its isomerization products,13-cis-retinal(Ch R2-cis)configuration,respectively.Photoisomerization of the retinal-chromophore causes the destruction of interactions among the crucial residues(e.g.,E90,E82,N258,and R268)around the channel and the extended H-bond network mediated by numerous water molecules,which in faver of the ion channel formation.Steering molecular dynamics(SMD)simulations show that the electrostatic interactions at the binding sites in intracellular gate(ICG)and central gate(CG)can influence the transmembrane transport of Na+ in Ch R2-cis obviously.Potential of mean force(PMF)constructed by SMD and umbrella sampling also found the existing energy wells at these two binding sites during the transportation of Na+.These wells partly hinder the penetration of Na+ into cytoplasm through the ion channel.That means the ion channel is not fully open.Furthermore,The anion channel properties of EK-TC,ER-TC and i Chlo C were investigated by molecular dynamics simulation,umbrella sampling and WHAM analysis.The transport capacity of chloride ion through ion channel and the curve of PMF were compared.The results show that the five-fold mutation(i Chlo C)increases the flexibility of the transmembrane channel protein better than the double mutations in EK-TC and ER-TC,and results in an expanded ion channel pore size and decreased steric resistance.The i Chlo C mutant was also found to have a higher affinity for chloride ions and,based on surface electrostatic potential analysis,provides a favorable electrostatic environment for anion conduction.The PMF free energy curves revealed that the energy barriers for the EK-TC and ER-TC were found to be much higher than that of i Chlo C.The results suggest that the transmembrane ion channel of i Chlo C protein is better at facilitating the capture and transport of chloride ions.It indicates that the five-fold mutants are more favorable for the formation of anion channels.This investigation provides a theoretical insight on the formation mechanism of ion channels and the mechanism of ion permeation,so that we have a deeper understanding of channelrhodopsin pores.