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Molecular Details of the Mitochondrial Iron Sulfur Cluster Assembly Pathway

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Molecular Details of the Mitochondrial Iron Sulfur Cluster Assembly Pathway Wayne State University Wayne State University Dissertations 1-1-2011 Molecular Details Of The itM ochondrial Iron Sulfur Cluster Assembly Pathway Swati Rawat Wayne State University Follow this and additional works at: http://digitalcommons.wayne.edu/oa_dissertations Part of the Biochemistry Commons, and the Molecular Biology Commons Recommended Citation Rawat, Swati, "Molecular Details Of The itM ochondrial Iron Sulfur Cluster Assembly Pathway" (2011). Wayne State University Dissertations. Paper 204. This Open Access Dissertation is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Dissertations by an authorized administrator of DigitalCommons@WayneState. MOLECULAR DETAILS OF THE MITOCHONDRIAL IRON SULFUR CLUSTER ASSEMBLY PATHWAY by SWATI RAWAT DISSERTATION Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY 2011 MAJOR: BIOCHEMISTRY AND MOLECULAR BIOLOGY Approved by: _____________________________________ Advisor Date _____________________________________ _____________________________________ _____________________________________ _____________________________________ © COPYRIGHT BY SWATI RAWAT 2011 All Rights Reserved DEDICATION This work is dedicated to my husband Manish Khandelwal and my parents Ganesh and Urmila Rawat. Their endless love, support, and faith in me make anything possible. ii ACKNOWLEDGMENTS This dissertation would not have been possible without the help of so many people in so many ways. First and foremost, I would like to express my profound sense of appreciation to my mentor Dr. Timothy Stemmler for his guidance throughout my graduate research as well as his continuous attention and supervision in the completion of this dissertation. His words of encouragement, quiet urgings and careful reading of all of my writing will never be forgotten. I would also like to thank him for providing the opportunity to attend several conferences and instilling in me the qualities of being a good scientist. I think he is one of the rare mentors that students always dream to find. I am truly thankful to him for all the accomplishments I have today, it would not have been possible without his support. I would also like to express my gratitude to my dissertation committee, which includes Dr. David Evans, Dr. Brian Edwards, and Dr. Andrew Gelasco. I thank you all for your persistent suggestions, critiques, and support throughout my studies. I am also thankful to Dr. Andrew Dancis for providing valuable direction to my project either by sending cell lines/ plasmid constructs. His suggestions regarding my AHA proposal and review article are invaluable. In addition, I had the opportunity to collaborate with some of the best scientists in the country; I would like to extend my gratitude especially to Dr. Amy Rosenzweig, Dr. Barry Rosen, and Dr. Paul Lindahl . I have had the great opportunity to work with many fantastic lab members. I especially learned a lot from Dr. Krisztina Bencze, Dr. Kalyan Kondapalli and Dr. Jeremy Cook. Thank you all for helping me get acquainted with the lab and research techniques and for your friendship. All the other Ph.D. students in the Stemmler lab have also had a positive impact on my experience, especially Poorna Subramanian iii who became more as a friend. I also thank the students who have worked in the lab and have helped me with my work. I give thanks to the Department of Biochemistry and Molecular Biology. During my time in this department I have had the great pleasure to interact with many superb faculty members. I give thanks to all my fellow graduate students and postdocs in the Department of Biochemistry and Molecular Biology as well. I would like to thank my friends Asmita, Victoria, Song and Leo for their help during all these years. I would also like to thank Rose Cooper, Yanna Marsh, Judy Thomas and Joe Fiore for all the administrative help. I give thanks to my family, whom I love dearly. To my grandma, Tulsibai Rawat, who nurtured me with love and care during my childhood. I want to thank my mom, Urmila Rawat, she has been always there to help me and provided me with positive energy even under worst conditions. My dad, Ganesh Rawat, thank you for your endless encouragement and guidance. I thank my brothers, Tapan Rawat and Amit Khandelwal and my sisters, Rashmi, Rupali and Rakhi Rawat for helping and pampering me all this time. They have been role model since I was a teenager and have always been my best counselors. I deeply appreciate the faith and support from my in-laws especially my sister-in-law, Seema Khandelwal, for always encouraging me in every aspect of life. I love you and thank all for your constant encouragement and companionship throughout my life. Last but not least, I thank my husband, Manish Khandelwal, who stood by me and supported me as my best friend. I am grateful to Manish as he gave me the strength to keep working until completion. None of this would have been possible without his love and patience. I thank you for always encouraging me and spending all the sleepless nights to accompany me during my tough times. I don’t have iv enough words to thank you. I couldn’t have asked for anything better. Finally, I thank God for his blessings and giving me this wonderful life. v TABLE OF CONTENTS Dedication …….……………………….......................................................................... ii Acknowledgements …….…….....................................................................................iii List of Tables ….….…………...…..…...........................................................................x List of Figures …….……………..................................................................................xi CHAPTER 1 – INTRODUCTION AND BACKGROUND………………........................1 1.0 Prelude .............................................................................................1 1.1 Summary of Dissertation...................................................................3 1.2 Background Material..........................................................................6 1.2.1 Abstract ..........................................................................................6 1.2.2 Introduction.....................................................................................7 1.2.3 Mitochondrial Fe-S Cluster Assembly Pathway..............................9 1.2.3a Isu1 Scaffold Protein…………………………………………....….12 1.2.3b The Nfs1 Cysteine Desulfurase Enzyme……………………..…..16 1.2.3c The Isd11 Accessory Protein…………………………………...….17 1.2.3d The Yfh1 Frataxin Protein……………………………………..…...18 1.3 Interaction Between Assembly Protein Partners………………..…..21 1.4 Summary and Outlook…………………………………………..……..24 1.5 Acknowledgements……………………………………………..………25 1.6 References……………………………………………………….……...25 CHAPTER 2 – BACKBONE ATOM CHEMICAL SHIFT ASSIGNMENTS FOR MATURE DROSOPHILA FRATAXIN HOMOLOG (DFH)..................38 2.0 Prelude ...........................................................................................38 2.1 Biological Context……….................................................................38 2.2 Methods and Experiments...............................................................41 vi 2.2.1 Labeling, Expression and Purification of Drosophila Frataxin......41 2.2.2 Nuclear Magnetic Resonance Spectroscopy................................42 2.2.3 Assignments and Data Deposition……………..............................43 2.3 Acknowledgements……………………………………………..………47 2.4 References……………………………………………………….……...47 CHAPTER 3 – MOLECULAR CHARACTERISTICS OF THE DROSOPHILA FRATAXIN-ISU INTERACTION DURING FE-S CLUSTER ASSEMBLY……………………………………………………………….51 3.0 Prelude ...........................................................................................51 3.1 Introduction……...……….................................................................51 3.2 Material and Methods......................................................................56 3.2.1 Protein Expression and Purification……………………………......56 3.2.2 Binding Assays by Isothermal Titration Calorimetry.....................58 3.2.3 X-ray Absorption Spectroscopy (XAS) Studies ……….................59 3.2.4 Fluorescence Spectroscopy………….……………………..………60 3.3 Results……………………………………………………….……….....61 3.3.1 Isothermal Titration Calorimetry (ITC) Binding Studies……….......61 3.3.2 X-ray Absorption Spectroscopy (XAS) Studies ……….................65 3.3.3 Fluorescence Spectroscopy………….……………………..………72 3.4 Discussion…………………………………………..............................74 3.5 Acknowledgements……………………………………………..………78 3.6 References……………………………………………………….……...79 CHAPTER 4 – MOLECULAR DETAILS OF THE YEAST FRATAXIN-ISU1 INTERACTION DURING MITOCHONDRIAL FE-S CLUSTER ASSEMBLY……………………………………………………………….85 4.0 Prelude ...........................................................................................85 4.1 Introduction……...……….................................................................85 vii 4.2 Material and Methods......................................................................88 4.2.1 Protein Expression and Purification……………………………......88 4.2.2 Binding Assays by Isothermal Titration Calorimetry.....................89 4.2.3 Isu1 Binding Surface on Yfh1 by Nuclear Magnetic Resonance Spectroscopy………………………………………………………….90 4.2.4 X-ray Absorption Spectroscopy Sample Preparation and Analysis………………………………………………………………..91 4.2.5 Molten Globule Nature of Isu1 with and
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