Project C5

Computation of proton transfer pathways from discrete state models

Principal Investigator: Prof. Dr. Petra Imhof (FU)

The proton transfer along the so-called D- and K- channels in cytochrome c oxidase is investigated by a combination of classical molecular dynamics simulations and quantum chemical calculations. Discrete protonation and conformational states are combined to a transition network, allowing to determine the most probable proton transfer pathways. Moreover, we investigate the communication between the two channels and the impact of a change in protonation state in one channel on the proton movement in the other one. Finally, a kinetic model will be constructed that allows for the direct comparison with experimentally-determined proton positions and transfer rates.

Publications 2016

Bagherpoor Helabad, M., Ghane, T., Reidelbach, M., Woelke, A. L., Knapp, E. W., and Imhof, P. (2016). Protonation state dependent communication in Cytochrome c Oxidase. Biophysical Journal 111, 492-503.

Helabad, M.B., Ghane, T., Reidelbach, M., Woelke, A.L., Knapp, E.W., and Imhof, P. (2016). Protonation state-dependent communication in cytochrome c oxidase. Biophysical Journal 111, 492-503.

Imhof, P. (2016). A Networks Approach to Modeling Enzymatic Reactions. In: Gregory A. Voth (ed.) Methods in Enzymology: Computational approaches for studying Enzyme Mechanism 578, 249-271.

Reidelbach, M., Betz, F., Mäusle, R. M., and Imhof, P. (2016). Proton transfer pathways in an aspartate-water cluster sampled by a network of discrete states. Chemical Physics Letters 659, 169-175.