All-Atom Molecular Dynamics Simulation of a Photosystem I/Detergent Complex

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-beta-D-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square flucturation (RMSF) analysis indicates that regions of high mobility correspond to solvent-exposed regions such as turns in the transmembrane alpha-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implication for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly we find that the docking of soluble electron mediators such as cytochrome c(6) and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.