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

Abstract

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.

The cytochrome f–plastocyanin complex as a model to study transient interactions between redox proteins

“…BD analyses are quite sensitive to small changes in conformation of the proteins that are being modeled. For instance, the C f –Pc complex with spinach Pc adopted two different conformations when using distinct structural data sources [50]. On the basis of such finding, it was suggested that Pc may assume distinct conformations in solution so as to yield a productive ET complex.…”

Electrostatic strain and concerted motions in the transient complex between plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum

“…The resulting kinetic data have been very useful to analyse the interaction between Pc and Cf by means of theoretical methods, including Molecular Dynamics (MD) at sub-nanosecond time scale [17], rigid-body MD [18], Molecular Modelling [19] supported by NMR data and Brownian Dynamics (BD) simulations [20][21][22][23][24][25][26][27][28]. Last computations, in particular, are in good agreement with experimentally calculated reaction rates [21,[24][25][26], thereby explaining many effects of ionic strength and mutations on the kinetics.…”

“…Recently, it has been shown that different conformations of Pc lead to different BD data [22] and that the geometry of the copper centre of Pc is perturbed upon binding to Cf [32]. In addition, the role of the small domain of Cf in Pc docking is not fully understood, and there still exist some discrepancies to reconcile structural and functional data, especially in Phormidium cyanobacterium.…”

Comparative analysis of plastocyanin–cytochrome f complex formation in higher plants, green algae and cyanobacteria

“…However, these proteins seem to be in head‐on orientation. Later Gross and co‐authors used BD simulations of Cyt f and Pc complex formation in higher plants (Gross ), green algae Chlamydomonas reinhardtii (Haddadian and Gross , b), cyanobacterium P. laminosum (Gross ) and Cyt f from P. laminosum with various cyanobacterial plastocyanins (Gross and Rosenberg ).…”