Brownian dynamics computational study of the interaction of spinach plastocyanin with turnip cytochrome f: the importance of plastocyanin conformational changes

• Published in: Photosynthesis research 2007-11, Vol.94 (2-3), p.411-422
• Main Author: Gross, Elizabeth L
• Format: Article
• Language: English
• Subjects: Brassica rapa - metabolism; Brownian dynamics; Computer Simulation; Crystal structure; cytochrome f; Cytochromes f - chemistry; Cytochromes f - metabolism; electron transfer; Models, Molecular; Molecular Conformation; Plant Proteins - chemistry; Plant Proteins - metabolism; plastocyanin; Plastocyanin - chemistry; Plastocyanin - metabolism; Protein Binding; Protein Conformation; protein-protein interactions; Spinacia oleracea - metabolism
• ISSN: 0166-8595; 1573-5079
• DOI: 10.1007/s11120-007-9192-y

Brownian Dynamics (BD) computer simulations were used to study electrostatic interactions between turnip cytochrome f (cyt f) and spinach plastocyanin (PC). Three different spinach PC structures were studied: The X-ray crystal structure of Xue and coworkers [(1998) Protein Sci 7:2099-2105] and the NMR structure of Musiani et al. [(2005) J Biol Chem 280:18833-18841] and Ubbink and co-workers [(1998) Structure 6:323-335]. Significant differences exist in the backbone conformation between the PC taken from Ubbink and coworkers and the other two PC structures particularly the regions surrounding G10, E59-E60, and D51. Complexes formed in BD simulations using the PC of Ubbink and colleagues had a smaller Cu-Fe distance than the other two. These results suggest that different PC conformations may exist in solution with different capabilities of forming electron-transfer-active docks. All three types of complexes show electrostatic contacts between D42, E43, and D44 on PC and K187 on cyt f as well as between E59 on PC and K58 on cyt f. However, the PC of Ubbink and coworkers reveals additional contacts between D51 and cyt f as a result of the difference in backbone configuration. A second minor complex component was observed for the PC of Ubbink and co-workers and Xue and co-workers which had contacts between K187 on cyt f and E59 and E60 on PC rather than between K187 on cyt f and D42-D44 on PC as observed for the major components. This second type of complex may represent an earlier complex which rearranges to form a final complex capable of electron transfer.