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Aktas Ou 0169D 10042.Pdf (4.261Mb) UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE SITE-DIRECTED MUTAGENESIS AS A PROBE OF NAD +-BINDING SITE IN MALIC ENZYME A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements of the Degree of DOCTOR OF PHILOSOPHY By DENIZ FULYA AKTAS Norman, Oklahoma 2008 SITE-DIRECTED MUTAGENESIS AS A PROBE OF NAD +-BINDING SITE IN MALIC ENZYME A DISSERTATION APPROVED FOR THE DEPARTMENT OF CHEMISTRY AND BIOCHEMISTRY BY Dr. Paul F. Cook, Chair Dr. Ann H. West Dr. Phillip E. Klebba Dr. Kenneth M. Nicholas Dr. Roger G. Harrison © Copyright by DENIZ FULYA AKTAS 2008 All Rights Reserved. ACKNOWLEDGEMENT I would like to express my deepest gratitude for my academic advisor Dr. Paul F. Cook. I want to thank him for encouraging and challenging me throughout my graduate studies. He has been more than an advisor to me. Besides being a great mentor, he has an amazing personality, and he is always nice, kind and humorous. I will always miss the days I have spent in his lab. I also would like to thank my advisory committee, Dr. Ann H. West, Dr. Philip E. Klebba, Dr. Kenneth M. Nicholas and Dr. Roger G. Harrison who have generously given their time and expertise to better my work. Their comments and suggestions which positively guided this work were invaluable. There are many who have contributed to this work in various ways. Among those, I want to express my deepest appreciation to Dr. William Karsten. He was always helpful whenever I needed his expertise from the very beginning. He not only taught me almost all the techniques I needed, but also helped me to interpret my data. I also want to acknowledge all my lab mates who supported and helped me throughout my Ph.D, especially Dr. Babak Andi, Dr. Lei Li, Dr. Ying Lin, Dr. Hengyu ‘Carina’ Xu and Dr. Lillian Chooback. I want to thank my lab mate and very good friend Devi Kosala Ekanayake whose friendship and hospitality have supported and entertained me over the many years of our friendship. I want to thank as well Jean Keil, Arlene Crawford and Carol Jones for helping me with all the paperwork. This dissertation could not have been written without the support and love of my parents, Tulay and Kenan Bolukbasi, my grandparents Serife and Ramazan Acarturk and my sister Begum Bolukbasi. They always have been an inspiration and support to me. I iv also want to thank my parents-in-law, Vefa and Gultekin Aktas, my brother-in-law Mert Can Aktas, my uncle-in-law Reha Aktas and his family for loving and supporting me all those years. And finally, I want to thank and dedicate this dissertation to my husband Levent Aktas, who has always been there for me, who gave me strength to go on, who always made me feel that I could achieve anything I wanted! Thanks for loving and trusting me. v TABLE OF CONTENTS ACKNOWLEDGEMENT ............................................................................................................... IV TABLE OF CONTENTS ................................................................................................................. VI LIST OF TABLES .......................................................................................................................... IX LIST OF FIGURES ......................................................................................................................... X ABSTRACT ................................................................................................................................. XII CHAPTER 1: ................................................................................................................................. 1 INTRODUCTION .......................................................................................................................... 1 1.1. PYRIDINE -NUCLEOTIDE DEPENDENT OXIDATIVE DECARBOXYLASES .................................................. 1 1.2. BACKGROUND AND SIGNIFICANCE ........................................................................................... 3 1.3. REACTIONS OF MALIC ENZYMES .............................................................................................. 5 1.4. MALIC ENZYME FROM ASCARIS SUUM ..................................................................................... 5 1.5. PURIFICATION , CLONING AND EXPRESSION OF ASCARIS SUUM ME ................................................ 7 1.6. THE STRUCTURE OF THE MALIC ENZYME ................................................................................... 9 1.6.1. Metal-ion binding site ............................................................................................. 12 1.6.2. Tartronate binding site ............................................................................................ 14 1.6.3. NAD binding site ...................................................................................................... 16 1.7. KINETIC MECHANISM OF THE ASCARIS SUUM MALIC ENZYME ...................................................... 16 1.8. CHEMICAL MECHANISM OF ASCARIS SUUM MALIC ENZYME ........................................................ 19 1.8.1. Stepwise chemical mechanism of NAD-malic enzyme ............................................ 19 1.8.2. General acid/general base mechanism of A. suum ME ........................................... 22 1.9. REGULATION OF MALIC ENZYME ........................................................................................... 25 1.10. SCOPE OF THIS STUDY ........................................................................................................ 27 CHAPTER 2: ............................................................................................................................... 29 vi 2.1. INTRODUCTION ................................................................................................................. 29 2.2. MATERIALS AND METHODS ................................................................................................. 31 2.2.1. Chemicals and Enzymes. .......................................................................................... 31 2.2.2. Malate-2-d. ............................................................................................................. 32 2.2.3. Enzyme assays. ........................................................................................................ 33 13 2.2.4. C kinetic isotope effects. ....................................................................................... 33 2.2.5. Data analysis. .......................................................................................................... 34 2.2.6. Calculation of intrinsic isotope effects and commitment factors. ........................... 36 2.3. RESULTS . ......................................................................................................................... 39 2.3.1. Initial velocity studies. ............................................................................................. 39 2.3.2. Isotope effect studies. ............................................................................................. 43 2.4. DISCUSSION . .................................................................................................................... 45 2.4.1. Kinetic parameters of N479Q, S mutant enzymes. .................................................. 45 2.4.2. Isotope effects. ........................................................................................................ 46 2.4.3. Kinetic parameters for S433 and N434 mutant enzymes. ....................................... 50 2.4.4. Isotope effects. ........................................................................................................ 51 2.4.5. Conclusion. .............................................................................................................. 53 CHAPTER 3: ............................................................................................................................... 54 3.1. INTRODUCTION ................................................................................................................. 54 3.2. MATERIALS AND METHODS . ................................................................................................ 57 3.2.1. Chemicals and enzymes. .......................................................................................... 57 3.2.2. Enzyme assays. ........................................................................................................ 57 3.2.3. Fluorescence titration. ............................................................................................. 58 13 3.2.4. C Kinetic isotope effects. ....................................................................................... 58 3.2.5. Data analysis. .......................................................................................................... 59 3.3. RESULTS . ......................................................................................................................... 61 vii 3.3.1. Aspartate-361 mutant enzymes. ............................................................................. 61 3.3.2. Arginine-370 mutant enzymes. ............................................................................... 63 3.3.3. Histidine-377 mutant enzymes. ............................................................................... 63 3.3.4. Isotope effects. ........................................................................................................ 63 3.4. DISCUSSION . ...................................................................................................................
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