Modelling photosystem I as a complex interacting network

Abstract

In this paper, we model the excitation energy transfer (EET) of photosystem I (PSI) of the common pea plant Pisum sativum as a complex interacting network. 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). We measure the global PSI network EET efficiency adopting well-known network theory indicators: the network efficiency (Eff) and the largest connected component (LCC). We also account the number of connected nodes/chromophores to P700 (CN), a new ad hoc measure we introduce here to indicate how many nodes in the network can actually transfer energy to the P700 reaction centre. We find that when progressively removing the weak links of lower EET, the Eff decreases, while the EET paths integrity (LCC and CN) is still preserved. This finding would show that the PSI is a resilient system owning a large window of functioning feasibility and it is completely impaired only when removing most of the network links. From the study of different types of chromophore, we propose different primary functions within the PSI system: chlorophyll a (CLA) molecules are the central nodes in the EET process, while other chromophore types have different primary functions. Furthermore, we perform nodes removal simulations to understand how the nodes/chromophores malfunctioning may affect PSI functioning. We discover that the removal of the CLA triggers the fastest decrease in the Eff, confirming that CAL is the main contributors to the high EET efficiency. Our outcomes open new perspectives of research, such comparing the PSI energy transfer efficiency of different natural and agricultural plant species and investigating the light-harvesting mechanisms of artificial photosynthesis both in plant agriculture and in the field of solar energy applications.