Brownian dynamics study of cytochrome f / Rieske interactions with cytochrome c6 and plastocyanin
Abstract (Summary)All of the charged residues in Chlamydomonas reinhardtii (C. reinhardtii) cytochrome c6 (cyt c6) and plastocyanin (PC) were mutated to alanine and their interactions with cytochrome f (cyt f) were modeled using Brownian Dynamics simulations. Systematic mutation of charged residues on both PC and cyt c6 confirmed that electrostatic interactions 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. We observed a difference between the two acidic clusters on PC and cyt c6. Availability of seven different structures of cyt f from C. reinhardtii allowed us to model interactions between these molecules and PC and cyt c6 in the same species to study the effect of cyt f structure on its function. Different cyt f structures, which are very similar, produced different reaction rates. This was attributed to structural differences among these molecules, particularly to a small flexible loop between A184- G191. It was also showed that deletion of the cyt f small domain affected cyt c6 more than PC, due to their different binding positions on cyt f. The availability of C. reinhardtii cytochrome b6f complex, PC, and cyt c6 structures allowed us to model electron transfer interactions between the extramembrane segments of this complex and its redox partners in the same species. Also, the interactions between the extramembrane domains of cytochrome b6f complex from cyanobacterium Mastigocladus laminosus with Phormidium and Prochlorothrix PC’s were modeled. The Rieske protein in the both available crystal structures of cytochrome b6f complex did not interfere with binding of PC or cyt c6 on cyt f. When Rieske was moved close to the cyt f in C. reinhardtii, it even enhanced the interactions. PC docked on cyt f with the same orientation in the presence or the absence of Rieske. The structural studies on cyt f showed that the cyt f structure is a more important factor in complex formations than is the presence or the absence of Rieske, or its position.
School:The Ohio State University
School Location:USA - Ohio
Source Type:Master's Thesis
Date of Publication:01/01/2005