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

Biophysics Program and Department of Biochemistry, The Ohio State University, Columbus, Ohio

Correspondence: Address reprint requests to Prof. Elizabeth L. Gross, Dept. of Biochemistry, The Ohio State University, 484 W. 12th Ave., Columbus, OH 43210. Tel.: 614-292-9480; E-mail: gross.3{at}osu.edu.

Using Brownian dynamics 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, and 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 cyt 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 Brownian dynamics simulations in mutagenesis studies.

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