LAUSR

Abstract The final step of photosynthetic electron transfer from ferredoxin to NADP+ is catalysed by ferredoxin: NADP+ oxidoreductase (FNR). Localization of the FNR on the chloroplastic membrane is attained both, by the dynamic interaction via thylakoid rhodanese-like protein (TROL) and with the lasting interaction with the Tic62 protein. In such interactions, FNR forms a homodimeric complex in the presence of the FNR interacting domain from either TROL or Tic62 protein. Starting from crystal structure of FNR homodimeric complex, various systems consisting of the FNR proteins and/or the FNR binding domains from TROL and Tic62 proteins at the different pH were subjected to molecular dynamics simulations. Results of simulations enabled identification of the most important regions of non-covalent interactions between involved proteins and their detailed mapping. In silico mutations were introduced and simulated to investigate their influence to the structural properties, dynamics and stability of the protein complex. The interface regions between the FNR proteins, consisting mostly of hydrophobic interactions, were identified and shown to be under strong influence of the ITEPs conserved prolines and serines (PPSS region). Five functionally important hydrogen bond networks that span over the major structural elements of the involved proteins were identified and characterized. Three of them show pH dependence and might serve as the pH regulated switches for conformational changes of the protein complex. Presented computational results provide strong base for in vitro experiments on TROL, Tic62 and FNR proteins that should enable understanding of their behavior in the fluctuating environmental conditions.