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In bacteriorhodopsin, the order of molecular events that control the cytoplasmic or extracellular accessibility of the Schiff bases (SB) are not well understood. We use molecular dynamics simulations to study a process involved in the second accessibility switch of SB that occurs after its reprotonation in the N intermediate of the photocycle. We find that once protonated, the SB C15 = NZ bond switches from a cytoplasmic facing ( 13-cis ,  15-anti ) configuration to an extracellular facing (13- cis, 15-syn ) configuration on the pico to nanosecond timescale. Significantly, rotation about the retinal’s C13 = C14 double bond is not observed. The dynamics of the isomeric state transitions of the protonated SB are strongly influenced by the surrounding charges and dielectric effects of other buried ions, particularly D96 and D212. Our simulations indicate that the thermal isomerization of retinal from  13-cis  back to  all-trans  likely occurs independently from and after the SB C15 = NZ rotation in the N-to-O transition.

Schiff Base Switch II Precedes the Retinal Thermal Isomerization in the Photocycle of Bacteriorhodopsin