Molecular Simulation Study For The Formation Mechanism Of Light-gated Ion Channels In Channelrhodopsin

Channelrhodopsin can induce ion transmembrane conduction to excite cells after absorbing light.Channelrhodopsin-2(ChR2)is a representative tool for researching Channelrhodopsin and has been widely used in neuroscience.and it produces different photocycles by different time scales of illumination,i.e.the dark-adapted photocycle excited from the dark state and the light-adapted photocycle excited by long-term illumination.After absorbsing light,the all-trans,15-anti configuration of the retinal chromophore undergoes different isomerization reactions to enter two photocycles,i.e.,the dark-adapted photocycle with the a 13-cis,15-anti configuration of retinal and the light adapted photocycle with 13-cis,15-syn configuration.But the principles of opening ion channel in different photocycles are still unclear.Therefore,the photocycle intermediates for ChR2 in dark-adapted state and light-adapted state are established to study by molecular dynamics simulation(MD)and steered molecular dynamics simulation(SMD).In dark-adapted state,the intermediates containing E90 with different protonation states were established to study the mechanism of channel opening in photocycle.The results revealed that different protonation states of E90 will affect the hydrogen bond network in the central gate(CG)to change the hydrogen bond between retinal and proton acceptors(i.e.E123 and D253).Therefore,when E90 remains protonated,the proton acceptor of retinal is E123,forming a new narrow channel along TM3.But it displayed that the channel has an obvious block,and the energy is relatively high when ion pass through the channel.When E90 is deprotonated,the proton acceptor of retinal is D253 and forms a nearly open channel along TM2.In addition,the intermediates of photocycle were also established to research the mechanism of open channel in light-adapted state.The results exhibited that the isomerization of retinal opens CG by inducing rearrangement of the hydrogen bond network.The hydrogen bond between E90 and K93 in CG induces TM2 displacement,increases the cavity of CG and opens the intracellular gate(ICG).The ion channel forms along TM2.It was found that the hydrogen bond network which originally blocked the passage of ions was destroyed and the CG and ICG are the binding sites of sodium ion in the channel.In this thesis,the main channels in both photocycles are formed along TM2,but the ion channel in the light-adapted state is not as open as in dark-adapted state.Even if these two photocycles are similar,they cannot be completely equal.It was also found that the C=N-syn isomerization of retinal restricts the orientation of proton in light-adapted state.It is impossible for the deprotonation of retinal to produce the P390~*state which is homologous with P390 state in dark-adapted cycle,because the proton cannot form interaction with polar residues around here.In this thesis,the theoretical mechanisms of ion channel opening are provided in different photocycles,and a better ion penetration pathway and structure of photocycle intermediates are qualitatively determined.