Protein-Protein Interactions and Electron Transfer Associated with Cytochrome F and Plastocyanin from the Cyanobacterium Prochlorothrix Hollandica

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Protein-Protein Interactions and Electron Transfer Associated with Cytochrome F and Plastocyanin from the Cyanobacterium Prochlorothrix Hollandica PROTEIN-PROTEIN INTERACTIONS AND ELECTRON TRANSFER ASSOCIATED WITH CYTOCHROME F AND PLASTOCYANIN FROM THE CYANOBACTERIUM PROCHLOROTHRIX HOLLANDICA. Maria V. Baranova A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY August 2007 Committee: George S. Bullerjahn, Advisor J. Devin McAuley Graduate Faculty Representative Michael Y. Ogawa Neocles Leontis ii ABSTRACT George S. Bullerjahn, Advisor This dissertational work describes the minimal structural requirements of interaction surfaces between two proteins involved in photosynthetic electron transfer cyt f and PC from cyanobacterium Prochlorothrix hollandica analyzed by stopped-flow absorption spectroscopy and HSQC NMR. Two mutant P.hollandica cyt f, Y102G and Y102G/F100S, yielding a modified surface-exposed loop region, were expressed and characterized to analyze the structurally unique Prochlorothrix cyt f ‘pocket-like’ region involved in the PC-cyt f complex formation and electron transfer. Stopped-flow studies showed that altering these residues slows down ket more than one order of magnitude. We propose that Tyr102 and Phe100 are actively involved in complex formation between cyt f and PC and serve to minimize distance between electron donor and acceptor. Thus, by removing these residues, the Cu- Fe distance in cyt f -PC complex increases, slowing electron transfer rates. In previous NMR studies(21) it was shown that PC from cyanobacteria interacts with cyt f differently than the comparable proteins in higher plants and algae. The PC-cyt f complex in the cyanobacterium Phormidium laminosum(21) involves a ‘head on’ contact between the hydrophobic (‘northern’) patch of PC with a hydrophobic surface surrounding the cyt f heme, with an average Cu-Fe separation of 15Å. Moreover, Prochlorothrix hollandica PC has a structurally distinct docking surface among other cyanobacteria(23) that likely makes these interactions somewhat different with additional interaction of PC with a flexible loop of cyt f forming a ‘pocket-like’ region in the iii vicinity of cyt f residues 99-104. There are two aromatic amino acids Tyr and Phe among them that face toward the PC and are possibly involved in protein-protein contacts. A parallel study was initiated to study the interactions of mutated cyanobacterial PC with Photosystem I (PSI) and some non-physiological electron-transfer partners (Lysine 2+ peptide and tris (2,2’-bipyridine)ruthenium (II) Ru(bpy)3 ). Additionally, negatively charged P.hollandica PC mutants, mimicking the higher plant protein, should explain better the necessity of electrostatic interactions in the PC/cyt f complex in chloroplast systems. iv ACKNOWLEDGMENTS I would like to thank my husband, Radiy Islangulov who came with this crazy idea to do a PhD so far away from home and family. There is no regret now and I am happy that we made this decision five years ago. Thank you for your enthusiasm, patience and strength. Also, thanks to my parents for letting me to do it, for their unlimited support and love during these long years. I will not make it without you! I am deeply indebted to my advisor Dr George S. Bullerjahn, who encourages my independence and gave freedom in work. Thank you George for your advice, help and comfortable atmosphere in the lab. I would like to acknowledge my committee members: Dr. Michael Y. Ogawa, Dr Neocles Leontis and Dr J. Devin McAuley for you suggestion, corrections and advices. I thank Dr Haoming Zang and Lucy Waskell (University of Michigan, Ann Arbor) for collaboration and stopped-flow equipment, Dr Venkatesha Basrur for MALDI-TOF analysis, Dr Marcellus Ubbink for HSQC NMR studies, Dr Eugene Danilov for help and advice and Dr Vintonenko for initial introduction to this scientific area. I thank Center for Photochemical Sciences for giving me an opportunity to study in Bowling Green State University and Department of Biological Sciences for financial support during last years. I wish to thank my host family – Diane and Scott Regan for being my American parents, for their care, love and support. Special thanks to my friends Natalia, Sergey Rybas and Irina, Armen Ilikchan for keeping me sane. v Dedicated to my father, Vladimir Konstantinovich Baranov, who always teach me to do my best or not to do it at all. I think I did my best! And to my mother Olga Vladimirovna Baranova who use to tell me that the problem must be stated in order to be solved. Thank you mom! vi TABLE OF CONTENTS Page CHAPTER I. INTRODUCTION.......................................................................................... 1 CHAPTER II. CYTOCHROME F FROM THE CYANOBACTERIUM PROCHLOROTHRIX HOLLANDICA. EXPRESSION IN ESCHERICHIA COLI AND PHYSICAL CHARACTERIZATION................................................................................... 13 Introduction ........................................................................................................... 13 Materials and Methods .............................................................................................. 20 Results and Discussion ............................................................................................. 25 CHAPTER III. PROTEIN-PROTEIN INTERACTIONS AND ELECTRON TRANSFER BETWEEN PROCHLOROTHRIX CYTOCHROME F AND PLASTOCYANIN – MUTAGENESIS OF A CYT F LOOP REGION............................... 38 Introduction ............................................................................................................ 38 Materials and Methods .............................................................................................. 47 Results and Discussion ............................................................................................. 52 Concluding Remarks.................................................................................................. 66 CHAPTER IV. STUDIES OF MUTANT P. HOLLANDICA PLASTOCYANIN INTERACTIONS WITH PHYSIOLOGICAL AND NON-PHYSIOLOGICAL PARTNERS. (TRIALS AND FUTURE PERSPECTIVES)................................................. 67 Introduction ............................................................................................................ 67 Materials and Methods .............................................................................................. 73 Results and Discussion ............................................................................................. 78 FUTURE PERSPECTIVES ................................................................................................ 86 REFERENCES ........................................................................................................... 87 vii LIST OF FIGURES Figure Page 1. Photosynthetic electron transport chain ..................................................................... 2 2. Schematic representation of transient complex formation, illustrating the three-step mechanism, where long-range electrostatic interactions preoriented partners to optimal configuration by surface diffusion. Once the specific complex is formed, electron transfer occurs and the products dissociate .................................................................................................................. 7 3. Structure of the C-type heme ..................................................................................... 14 4. Hexacoordination of the cyt f heme........................................................................... 14 5. Ribbon diagram of the soluble domain turnip cyt f …….. ........................................ 15 6. Model of the topography of cytochrome f in the thylakoid membrane .................... 15 7. Expression vectors ..................................................................................................... 21 8. Amino acids sequences alignment of mature cytochrome f. The sequences were all taken from the NCBI protein data base. N-terminal peptide leader and C- terminal polypeptides were truncated. Conservative amino acids highlighted in red. Yellow patch represent the heme binding site and green patch shows the loop region involved in protein interactions. Higher plants are in blue: Br- Brassica rapa; Sa-Spinacia aleracea; Pa- Poplar alba. Cyanobacteria are in green: Syn – Synechocystis PCC 6803; Nos – Nostoc PCC 7906; Pl – Phormidium laminosum; Ph – Prochlorothrix hollandica. Green alga Chlamydomonas reinhardtii – Cr is black ……………………………………………………………………………...... 26 viii 9. SDS-PAGE of purified cytochrome f ……..…... ...................................................... 30 10. Mass Spectrum indicating molecular mass of cytochrome f as 27.3 kDa…………. 31 11. Visible absorption spectrum of reduced cyt f in 10mM phosphate buffer, 1mM sodium ascorbate, pH 6.0; Black line, cytochrome f from P.hollandica; Red line, Cytochrome f from P.laminosum; Green line, cytochrome f from turnip. B, Enlargement of absorption spectrum of α- and β-peaks............................................ 32 12. Absorption spectra of oxidized (dashed line) and reduced (solid line) P.hollandica cytochrome f from 610nm to 350nm. Eleven micromolar cytochrome f in 10mM sodium phosphate buffer pH 7.5 with 1mM sodium ascorbate (reduced) and 5 mM potassium ferricyanide (oxidized)...................................................................... 32 13. Reduced minus oxidized absorption spectrum (green line) of the pyridine hemochrome produced from treatment of P.hollandica cytochrome f. Oxidized cytochrome f spectrum (black line), Reduced
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