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Projekt
Computer simulation of anion pumping by retinal proteins
Antragsteller
Stefan Fischer, Ph.D.
Fachliche Zuordnung
Bioinformatik und Theoretische Biologie
Förderung
Förderung von 2005 bis 2010
Projektkennung
Deutsche Forschungsgemeinschaft (DFG) - Projektnummer 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-Verfahren
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