Molecular modeling techniques will be employed to investigate the mechanisms underlying the light-activated anion pumping by halorhodopsin (hR) and mutants of bacteriorhodopsin (bR). The proposed calculations will exploit the information furnished by very recent experimentally-determined structures of bR ground-state mutants crystallized with various bound anions, as well as the knowledge obtained from our previous all-classical simulations of chloride transport by hR (previous TP2). Here we propose to use the molecular kinematics techniques that we have developed to compute minimum-energy pathways of the anion transfer steps in the protein. This time, the polarizability effects in the retinal binding pocket will be included by utilizing the combined quantum-mechanical/molecularmechanical (QM/MM) approach that we applied successfully to proton transfer in bR (see TP2). The calculations aim towards a detailed structural understanding of the non-equilibrium process inherent to the photocycle that results in the step-wise translocation of an anion across the membrane.
DFG Programme
Research Units
