A multi-scale approach to electron transfer in protein aggregates: augmenting molecular dynamics simulations by dielectric continuum theory

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In this project, we wish to use molecular dynamics simulations of the thermodynamic integration type to compute two of the characteristic energies of thermally induced electron transfer in proteins, the thermodynamic driving force, Delta G, and the reorganization energy, lambda. In order to quantitatively correct for a serious conceptual problem of this method, we plan to post-process the results numerically by finite-difference dielectric continuum computations. Using a similar strategy, charge transfer within large protein aggregates will be approached. As a benchmark system extensively studied, we will use the cytochrome subunit of a bacterial photoreaction centre. In addition, we plan to investigate two systems of current interest in biochemistry, a bacterial nitrite reductase consisting of six subunits embodying 24 hemes, and complex I of the bacterial respiratory chain.