Computer Simulation of Conformation-Coupled Proton Transfer in Bacteriorhodopsin

• Applicant: Professor Dr. Sandor Suhai
• Subject Area: Biophysics
• Term: from 2002 to 2007
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 5469831

Computer simulations will be performed of the bacteriorhodopsin photocycle starting from the photoisomerized state. These simulations will use as starting geometries recently determined experimental structures of the protein in a number of intermediate states. The calculations will use "molecular kinematics" methodology that determines minimum-energy pathways in configurational space between known end-state structures, in combination with hybrid quantum mechanical/molecular mechanical modeling. Pathways for proton transfer and for structural change will be determined, and it will be of particular interest to gain insight into how the two are coupled. Additional calculations will be performed to understand chloride ion pumping in halorhodopsin.

• DFG Programme: Research Units
• Subproject of: FOR 490: Molecular Mechanisms of Retinal Protein Action: A Combination of Theoretical Approaches
• Participating Persons: Professor Dr. Marcus Elstner; Dr. Stefan Fischer, Ph.D.; Professor Dr. Jeremy Christopher Smith