Preprint of "Environmental Modulation of Retinal Excited States in Schizorhodopsin-4"

Schizorhodopsins are a recently identified family of microbial rhodopsins that, in contrast to canonical Type I, exhibit inward proton pumping function. Here, we investigate the photophysics of Schizorhodopsin-$4$ using microsecond molecular dynamics of the full trimer embedded in an explicit double-leaflet membrane, combined with high-level QM/MM excited-state simulations, including polarization and dispersion effects. The ground-state dynamics reveal a distinct preorganization of the retinal binding pocket, characterized by a strongly stabilized retinal protonated Schiff base–counterion interaction and a dynamically hydrated intracellular aspartic acid. Vertical excitation energies computed at the XMS-CASPT$2$ and TD-DFT levels quantitatively reproduce the experimental absorption maximum. Analysis of environmental fluctuations using spectral density formalism shows that protein–chromophore dynamics dominate inhomogeneous broadening of the absorption band. These results point out a ground-state electrostatic and hydration asymmetry of the chromophore pocket that is markedly different from that of canonical outward proton-pumping rhodopsins and is consistent with inward proton pumping.