A Brownian Dynamics Study of the Interaction of Phormidium Cytochrome f with Various Cyanobacterial Plastocyanins

• Published in: Biophysical journal 2006-01, Vol.90 (1), p.366-380
• Main Authors: Gross, Elizabeth L., Rosenberg, Irving
• Format: Article
• Language: English
• Subjects: Anabaena - metabolism; Bacteria; Binding sites; Bioenergetics; Biophysics - methods; Computer Simulation; Crystal structure; Cyanobacteria - metabolism; Cyanophyta; Cytochromes - chemistry; Cytochromes f - chemistry; Databases, Protein; Electron transfer; Electrostatics; Models, Molecular; Molecules; Mutation; Nostoc; Nostoc - metabolism; Phormidium; Phormidium laminosum; Photosynthetic Reaction Center Complex Proteins - chemistry; Plastocyanin - chemistry; Prochlorothrix hollandica; Protein Binding; Protein Conformation; Protein Structure, Tertiary; Software; Static Electricity; Synechococcus; Synechococcus - metabolism; Synechocystis; Zinc - chemistry
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1529/biophysj.105.065185

Brownian dynamics simulations were used to study the role of electrostatic forces in the interactions of cytochrome f from the cyanobacterium Phormidium laminosum with various cyanobacterial plastocyanins. Both the net charge on the plastocyanin molecule and the charge configuration around H92 (H87 in higher plants) are important in determining the interactions. Those plastocyanins (PCs) with a net charge more negative than −2.0, including those from Synechococcus sp. PCC7942, Synechocystis sp. 6803, and P. laminosum showed very little complex formation. On the other hand, complex formation for those with a net charge more positive than −2.0 (including Nostoc sp. PCC7119 and Prochlorothrix hollandica) as well as Nostoc plastocyanin mutants showed a linear dependence of complex formation upon the net charge on the plastocyanin molecule. Mutation of charged residues on the surface of the PC molecules also affected complex formation. Simulations involving plastocyanin mutants K35A, R93A, and K11A (when present) showed inhibition of complex formation. In contrast, D10A and E17A mutants showed an increase in complex formation. All of these residues surround the H92 (H87 in higher plant plastocyanins) ligand to the copper. An examination of the closest electrostatic contacts shows that these residues interact with D63, E123, R157, D188, and the heme on Phormidium cytochrome f. In the complexes formed, the long axis of the PC molecule lies perpendicular to the long axis of cytochrome f. There is considerable heterogeneity in the orientation of plastocyanin in the complexes formed.