Computer simulation of the proton transfer pathways at the extracellular side of bacteriorhodopsin and calculation of IR spectra of the photocycle intermediates

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QM/MM techniques will be used to determine structures and IR spectra of the bR photocycle intermediates. To achieve this goal, we will use DFT methods as well as a reparameterized DFTB method and determine the infrared spectra via calculation of the Hessian matrix as well as via Fourier transform of the velocity- and dipole- autocorrelation functions. These calculations may help resolving the assignment problem of atomic (X-ray) structures to experimental IR spectra and in the determination of the later structures of the bR photocycle. Of particular interest is the identity and structure of the so-called proton release group (PRG). We will test the suggestion that this group consists of a protonated water cluster at the extracellular side, a hypothesis which would explain the experimental IR spectra. The determination of the PRG opens the way for the investigation of the second and fifth proton transfer steps, the proton release from the PRG to the bulk in the M state and the last proton transfer step between Asp85 and the PRG between the 0 and bR ground state. Here, minimum pathway search algorithms as well as umbrella sampling techniques will be applied.