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

Diffusion
of mobile charge carriers, such as ferredoxin and plastocyanin,
often constitutes a rate-determining step in photosynthetic energy
conversion. The diffusion time scales typically exceed that of other
primary bioenergetic processes and remain beyond the reach of direct
simulation at the molecular level. We characterize the diffusive kinetics
of ferredoxin and plastocyanin upon the photosystem I-rich domain
of Prochlorococcus, the most abundant phototroph
on Earth by mass. A modeling approach for ferredoxin and plastocyanin
diffusion is presented that uses ensembles of coarse-grained molecular
dynamics simulations in Martini 2.2P with GROMACS 2021.2. The simulation
ensembles are used to construct the diffusion coefficient and drift
for ferredoxin and plastocyanin as spatial functions in the photosystem
I domain of the MIT9313 ecotype. Four separate models are constructed,
corresponding to ferredoxin and plastocyanin in reduced and oxidized
states. A single scaling constant of 0.7 is found to be sufficient
to adjust the diffusion coefficient obtained from the Martini simulation
ensemble to match the in vitro values for both ferredoxin and plastocyanin.
A comparison of Martini versions (2.2P, 2.2, 3) is presented with
respect to diffusion scaling. The diffusion coefficient and drift
together quantify the inhomogeneity of diffusive behavior. Notably,
a funnel-like convergence toward the corresponding putative binding
positions is observed for both ferredoxin and plastocyanin, even without
such a priori foreknowledge supplied in the simulation protocol. The
approach presented here is of relevance for studying diffusion kinetics
in photosynthetic and other bioenergetic processes.