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

在这个项目中，我们希望使用热力学积分类型的分子动力学模拟来计算蛋白质中热诱导电子转移的两个特征能量，热力学驱动力G和重组能lambda。为了定量地纠正这种方法的一个严重的概念问题，我们计划用有限差分介质连续体计算对结果进行数值后处理。使用类似的策略，电荷转移在大蛋白质聚集体将接近。作为广泛研究的基准系统，我们将使用细菌光反应中心的细胞色素亚基。此外，我们计划研究两个目前生物化学领域感兴趣的系统，一个由6个亚基组成的细菌亚硝酸盐还原酶，包含24个血红素，以及细菌呼吸链的复合物I。

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.