PSI photosyntethic network: The PSI network describes the Excitation Energy Transfer (EET) of PhotoSystem I (PSI) of the common pea plant Pisum sativum. The magnitude of the link energy transfer between nodes/chromophores is computed by Forster resonant energy transfer (FRET) using the pairwise physical distances between chromophores from the PDB 5L8R (Protein Data Bank). The PSI network is directed and weighted. The links in the PSI network are associated with different FRET efficiencies as a function of the nodes’ pairwise distance. The closer the nodes, the higher the link weight (FRET efficiency) joining them. We defined the cut-off distance (CD) as the distance between two nodes over which we assume the link between them absent because the associated FRET efficiency is too low. We created 10 networks using the following CD:
NO cut-off, 90, 80, 70, 60, 50, 40, 30, 20, 10 Å. Networks with lower CD presents less links.
Reference:
Daniele Montepietra, Michele Bellingeri, Francesco Scotognella, Davide Cassi (2020), Modeling the photosynthetic system I as a complex interacting network.
Journal of the Royal Society Interface 17: 20200813. http://dx.doi.org/10.1098/rsif.2020.081
The source files are NxN weighted adjacency matrix of the PSI network.
Each element i and j indicates the energy transfer value from column/chromophore i to row/chromophore j.