Brownian Dynamics Study of Cytochrome f Interactions with Cytochrome c6 and Plastocyanin in the Chlamydomonas reinhardtii, Plastocyanin and Cytochrome c6 Mutants

¹ The Ohio State University

^* To whom correspondence should be addressed. E-mail: gross.3{at}osu.edu.

Submitted on September 25, 2004
Revised on October 21, 2004
Accepted on 17 December 2004

	Abstract

Using Brownian Dynamics (BD) simulations, all of the charged residues in Chlamydomonas reinhardtii cytochrome c6 (cyt c6) and plastocyanin (PC) were mutated to alanine and their interactions with cytochrome f (cyt f) were modeled. Systematic mutation of charged residues on both PC and cyt c6 confirmed that electrostatic interactions (at least in vitro) play an important role in bringing these proteins sufficiently close to cyt f to allow hydrophobic and Van der Waals interactions to form the final electron transfer-active complex. The charged residue mutants on PC and cyt c6 displayed similar inhibition classes. Our results indicate a difference between the two acidic clusters on PC. Mutations D44A and E43A, of the lower cluster showed greater inhibition than do any of the mutations of the upper cluster residues. Replacement of acidic residues on cyt c6 that correspond to the PC's lower cluster, particularly E70 and E69, was observed to be more inhibitory than those corresponding to the upper cluster. In PC residues: D42, E43, D44, D53, D59, D61, E85; and in cyt c6 residues: D2, E54, K57, D65, R66, E70, E71, and the heme had significant electrostatic contacts with cyt f charged residues. PC and cyt c6 showed different binding sites and orientations on cyt f. As there are no experimental c6 mutation data available for algae, our results could serve as a good guide for future experimental work on this protein. The comparison between computational values and the available experimental data (for PC-cyt f interactions) showed overall good agreement, which supports the predictive power of BD simulations in mutagenesis studies.

Key Words: Brownian Dynamics, Cytochrome c6, Cytochrome f, Plastocyanin, Protein Interactions

This article has been cited by other articles:

				E. J. Haddadian and E. L. Gross A Brownian Dynamics Study of the Interactions of the Luminal Domains of the Cytochrome b6f complex with Plastocyanin and Cytochrome c6: The Effects of the Rieske FeS Protein on the Interactions Biophys. J., October 1, 2006; 91(7): 2589 - 2600. [Abstract] [Full Text] [PDF]

				E. J. Haddadian and E. L. Gross A Brownian Dynamics Study of the Effects of Cytochrome f Structure and Deletion of Its Small Domain in Interactions with Cytochrome c6 and Plastocyanin in Chlamydomonas reinhardtii Biophys. J., January 15, 2006; 90(2): 566 - 577. [Abstract] [Full Text] [PDF]

				E. L. Gross and I. Rosenberg A Brownian Dynamics Study of the Interaction of Phormidium Cytochrome f with Various Cyanobacterial Plastocyanins Biophys. J., January 1, 2006; 90(1): 366 - 380. [Abstract] [Full Text] [PDF]