title: All-atom molecular dynamics simulation of a photosystem i/detergent complex.
abstract: 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-β-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 fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications 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 c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.
authors.affiliation: Department of Chemical and Biomolecular Engineering, ‡Department of Biochemistry and Cellular and Molecular Biology, §Sustainable Energy Education and Research Center, and ∥Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee , Knoxville, Tennessee 37996, United States.
authors.forename: Bradley J
authors.initials: BJ
authors.lastname: Harris
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Cheng
authors.forename: Paul
authors.initials: P
authors.lastname: Frymier
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D003902:Detergents / Q000737:chemistry*; D005960:Glucosides / Q000737:chemistry*; D008823:Micelles; D056004:Molecular Dynamics Simulation; D045331:Photosystem I Protein Complex / Q000737:chemistry*; D055503:Protein Multimerization; D055550:Protein Stability; D046940:Synechococcus / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D003902:Detergents; D005960:Glucosides; D008823:Micelles; D045331:Photosystem I Protein Complex; C040358:dodecyl maltoside