Project Details
Projekt
Computer simulation of anion pumping by retinal proteins
Applicant
Stefan Fischer, Ph.D.
Subject Area
Bioinformatics and Theoretical Biology
Term
from 2005 to 2010
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 5469831
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
