title: A Brownian dynamics study of the interaction of Phormidium laminosum plastocyanin with Phormidium laminosum cytochrome f.
abstract: The interaction of Phormidium laminosum plastocyanin (PC) with P. laminosum cytochrome f (cyt f) was studied using Brownian dynamics (BD) simulations. Few complexes and a low rate of electron transfer were observed for wild-type PC. Increasing the positive electrostatic field on PC by the addition of a Zn(2+) ion in the neighborhood of D44 and D45 on PC (as found in crystal structure of plastocyanin) increased the number of complexes formed and the calculated rates of electron transfer as did PC mutations D44A, D45A, E54A, and E57A. Mutations of charged residues on Phormidium PC and Phormidium cyt f were used to map binding sites on both proteins. In both the presence and absence of the Zn(2+) ion, the following residues on PC interact with cyt f: D44, D45, K6, D79, R93, and K100 that lie in a patch just below H92 and Y88 and D10, E17, and E70 located on the upper portion of the PC molecule. In the absence of the Zn(2+) ion, K6 and K35 on the top of the PC molecule also interact with cyt f. Cyt f residues involved in binding PC, in the absence of the Zn(2+) ion, include E165, D187, and D188 that are located on the small domain of cyt f. The orientation of PC in the complexes was quite random in accordance with NMR results. In the presence of the Zn(2+) ion, K53 and E54 in the lower patch of the PC molecule also interact with cyt f and PC interacts with E86, E95, and E123 on the large domain of cyt f. Also, the orientation of PC in the complexes was much more uniform than in the absence of the Zn(2+) ion. The difference may be due to both the larger electrostatic field and the greater asymmetry of the charge distribution on PC observed in the presence of the Zn(2+) ion. Hydrophobic interactions were also observed suggesting a model of cyt f-PC interactions in which electrostatic forces bring the two molecules together but hydrophobic interactions participate in stabilizing the final electron-transfer-active dock.
authors.affiliation: Department of Biochemistry, The Ohio State University, Columbus, Ohio 34210, USA. gross.3@osu.edu
authors.forename: Elizabeth L
authors.initials: EL
authors.lastname: Gross
mesh_terms: D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D003300:Copper / Q000737:chemistry; D018360:Crystallography, X-Ray; D000458:Cyanobacteria / Q000378:metabolism*; D045348:Cytochromes f / Q000737:chemistry*; D019992:Databases as Topic; D004579:Electron Transport; D007477:Ions; D009682:Magnetic Resonance Spectroscopy; D008954:Models, Biological; D008958:Models, Molecular; D009154:Mutation; D010970:Plastocyanin / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D055672:Static Electricity; D015032:Zinc / Q000737:chemistry
chemical_list: D007477:Ions; D003300:Copper; D010970:Plastocyanin; D045348:Cytochromes f; D015032:Zinc