title: Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f.
abstract: The oxidation of cytochrome f by the soluble cupredoxin plastocyanin is a central reaction in the photosynthetic electron transfer chain of all oxygenic organisms. Here, two different computational approaches are used to gain new insights into the role of molecular recognition and protein-protein association processes in this redox reaction. First, a comparative analysis of the computed molecular electrostatic potentials of seven single and multiple point mutants of spinach plastocyanin (D42N, E43K, E43N, E43Q/D44N, E59K/E60Q, E59K/E60Q/E43N, Q88E) and the wt protein was carried out. The experimentally determined relative rates (k(2)) for the set of plastocyanin mutants are found to correlate well (r(2) = 0.90 - 0.97) with the computed measure of the similarity of the plastocyanin electrostatic potentials. Second, the effects on the plastocyanin/cytochrome f association rate of these mutations in the plastocyanin "eastern site" were evaluated by simulating the association of the wild type and mutant plastocyanins with cytochrome f by Brownian dynamics. Good agreement between the computed and experimental relative rates (k(2)) (r(2) = 0.89 - 0.92) was achieved for the plastocyanin mutants. The results obtained by applying both computational techniques provide support for the fundamental role of the acidic residues at the plastocyanin eastern site in the association with cytochrome f and in the overall electron-transfer process.
authors.affiliation: Università di Modena e Reggio Emilia, Dipartimento di Chimica, Via Campi, 183-41100 Modena, Italy.
authors.forename: F
authors.initials: F
authors.lastname: De Rienzo
authors.forename: R R
authors.initials: RR
authors.lastname: Gabdoulline
authors.forename: M C
authors.initials: MC
authors.lastname: Menziani
authors.forename: P G
authors.initials: PG
authors.lastname: De Benedetti
authors.forename: R C
authors.initials: RC
authors.lastname: Wade
mesh_terms: D003198:Computer Simulation; D003580:Cytochromes / Q000737:chemistry*; D045348:Cytochromes f; D004579:Electron Transport; D006863:Hydrogen-Ion Concentration; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D009154:Mutation; D010084:Oxidation-Reduction; D010100:Oxygen / Q000378:metabolism; D010970:Plastocyanin / Q000737:chemistry* / Q000235:genetics; D017354:Point Mutation; D011485:Protein Binding; D011487:Protein Conformation; D018724:Spinacia oleracea / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D003580:Cytochromes; D008024:Ligands; D010970:Plastocyanin; D045348:Cytochromes f; D010100:Oxygen