Modeling Diffusive Motion of Ferredoxin and Plastocyanin\non the PSI Domain of Procholorococcus marinus MIT9313

Diffusion\nof mobile charge carriers, such as ferredoxin and plastocyanin,\noften constitutes a rate-determining step in photosynthetic energy\nconversion. The diffusion time scales typically exceed that of other\nprimary bioenergetic processes and remain beyond the reach of direct\nsimulation at the molecular level. We characterize the diffusive kinetics\nof ferredoxin and plastocyanin upon the photosystem I-rich domain\nof <i>Prochlorococcus</i>, the most abundant phototroph\non Earth by mass. A modeling approach for ferredoxin and plastocyanin\ndiffusion is presented that uses ensembles of coarse-grained molecular\ndynamics simulations in Martini 2.2P with GROMACS 2021.2. The simulation\nensembles are used to construct the diffusion coefficient and drift\nfor ferredoxin and plastocyanin as spatial functions in the photosystem\nI domain of the MIT9313 ecotype. Four separate models are constructed,\ncorresponding to ferredoxin and plastocyanin in reduced and oxidized\nstates. A single scaling constant of 0.7 is found to be sufficient\nto adjust the diffusion coefficient obtained from the Martini simulation\nensemble to match the in vitro values for both ferredoxin and plastocyanin.\nA comparison of Martini versions (2.2P, 2.2, 3) is presented with\nrespect to diffusion scaling. The diffusion coefficient and drift\ntogether quantify the inhomogeneity of diffusive behavior. Notably,\na funnel-like convergence toward the corresponding putative binding\npositions is observed for both ferredoxin and plastocyanin, even without\nsuch a priori foreknowledge supplied in the simulation protocol. The\napproach presented here is of relevance for studying diffusion kinetics\nin photosynthetic and other bioenergetic processes.