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.
Ghane, T., Gorriz, R. F., Wrzalek, S., Volkenandt, S., Delatieh, F., Reidelbach, M., and Imhof, P. (2018) Hydrogen-Bonded Network and Water Dynamics in the D-channel of Cytochrome c Oxidase. The Journal of Membrane Biology 251, 299-314, doi: 10.1007/s00232-018-0019-x.
Helabad, M.B., Ghane, T., Reidelbach, M., Woelke, A.L., Knapp, E.W., and Imhof, P. (2017). Protonation state-dependent communication in cytochrome c oxidase. Biophysical Journal 113, 817-828; doi: 10.1016/j.bpj.2017.07.005
Reidelbach, M. and Imhof, P. (2020) Proton transfer in the D-channel of cytochrome c oxidase modelled by a transition network approach. Biochim. Biophys. Acta; doi: 10.1016/j.bbagen.2020.129614; doi: 10.1016/j.bbagen.2020.129614
Reidelbach, M., Weber, M., and Imhof, P. (2018). Prediction of perturbed proton transfer networks. Plos ONE. doi: org/10.1371/journal.pone.0207718.
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.
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.