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Development of Tools for Phosphosite-Specific Kinase Identification and Discovery of Phosphatase Substrates

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Development of Tools for Phosphosite-Specific Kinase Identification and Discovery of Phosphatase Substrates Wayne State University Wayne State University Dissertations 1-1-2017 Development Of Tools For Phosphosite-Specific Kinase Identification And Discovery Of Phosphatase Substrates Pavithra Maheshani Dedigama Arachchige Wayne State University, Follow this and additional works at: https://digitalcommons.wayne.edu/oa_dissertations Part of the Biochemistry Commons Recommended Citation Dedigama Arachchige, Pavithra Maheshani, "Development Of Tools For Phosphosite-Specific Kinase Identification And Discovery Of Phosphatase Substrates" (2017). Wayne State University Dissertations. 1693. https://digitalcommons.wayne.edu/oa_dissertations/1693 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. DEVELOPMENT OF TOOLS FOR PHOSPHOSITE-SPECIFIC KINASE IDENTIFICATION AND DISCOVERY OF PHOSPHATASE SUBSTRATES by PAVITHRA DEDIGAMA ARACHCHIGE 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 2017 MAJOR: CHEMISTRY (Biochemistry) Approved By: ____________________________________ Advisor Date ____________________________________ ____________________________________ ____________________________________ DEDICATION To all those who seek the truth AND To all those who shine the light where it is dark ii ACKNOWLEDGEMENTS The past few years were a very important period in my life. I learnt so much and achieved a lot as a person. Looking back at myself, I see a happy change that will stay with me for the rest of my life and will continue to improve. I owe my happiness to a lot of you. Thank you so much for creating a conducive environment where I could grow. I wish you all the happiness in the world. Although I don’t have space to acknowledge all of you, I would like to mention a few names. First of all, I would like to thank my wonderful supervisor Prof. Mary Kay Pflum. Thank you so much for being an amazing mentor! You have no idea how much of a positive impact you have had on my life. It is not an exaggeration to say that you are one of the best individuals I have met in my whole life. Thank you so much for giving me both the freedom and the support to grow, not just as a scientist but also as a person. I wish you all the happiness in the world. Secondly, I would like to thank my lab members for their help and support. I am especially grateful to Anita Chalasani and Todd Faner for their very kind guidance during my early years in the lab. In addition, my special thanks also goes to my fantastic undergraduate student, Monika Franco for her valuable help in research work. Other members of the Pflum lab, Chamara Senevirathne, Satish Garre, Geetha Padige, Magdalene Wambua, Alexander Stark, Thilani Anthony, Maheeka Embogama, Ahmed Fouda, Dhanusha Nalawansha, Ahmed Negmeldin, Inosha Gomes, Cyprein Nanah, Ben James, Nuwan Chinthaka, Vindya Rathnayake and Aparni Gamage, thank you all so much for the fun memories and support. You all made my time in the Pflum lab highly enjoyable and exciting. iii Next, I should offer my gratitude to the staff of proteomics core at Institute of Environmental Health Sciences, Wayne State University for the help in proteomics analysis. I am especially thankful to Dr. Paul Stemmer, Dr. Joseph Caruso, Dr.Nicholas Carruthers and Namhee Shin for both performing the proteomics experiments and also for offering helpful advice on data analysis. My special thanks also go to my wonderful collaborators, Prof.Jing Liu at Northwestern University and Prof. Zhengping Yi and Dr. Xiangmin Zhang at College of Pharmacy and Health Sciences. Thank you so much for the exciting research opportunity and your valuable input on data interpretation. In addition, I would also like to convey my gratitude to my committee for their constructive comments and useful suggestions on the research work. Thank you so much for your flexibility and support. I would also like to express my thanks to the kind, helpful staff of the Wayne State Chemistry Department. I am especially grateful to Greg Kish, Elizabeth Ries, Bonnie Cetlinski, Jason Parizon, Emil Lozanov, Melissa Barton, Yuriy Danylyuk, Olena Danylyuk, Kellie Lauder and Jacqueline Baldyga for their help in various ways. In addition, I would like to express my heartfelt gratitude to all the students and faculty of the Wayne State Chemistry Department. Even though I don’t have the chance to mention you all by your names, I am very grateful to all of you in the Department for your kind help on numerous situations. I am thankful to all my Sri Lankan friends in USA for your help throughout these years. Thank you so much for your friendship and kind help. iv I am forever indebted to my parents and family for their love and support. Thanks for giving birth to me, allowing me a chance to discover the true purpose of life. My dear sisters and brother, thank you for your sweet love and company. Last but not least, my gratitude goes to my best friend and husband, Thilina. Words can’t do justice for what you have given me. Thanks for being who you are and being there with me and showing me the way. v TABLE OF CONTENTS DEDICATION .................................................................................................................. ii ACKNOWLEDGEMENTS .............................................................................................. iii LIST OF TABLES .......................................................................................................... xi LIST OF FIGURES........................................................................................................ xii LIST OF ABBREVIATIONS .......................................................................................... xv CHAPTER 1 INTRODUCTION ....................................................................................... 1 1.1 Protein phosphorylation ......................................................................................... 1 1.2 Phosphorylation and signal transduction ................................................................ 2 1.3 Phosphorylation and diseases................................................................................ 4 1.4 Protein kinase classification, structure, mechanism and consensus sequence ...... 4 1.5 Challenges associated with studying phosphorylation ........................................... 9 1.6 γ-modified ATP analogs ........................................................................................ 9 1.6.1 ATP-γS ............................................................................................................. 10 1.6.2 Other γ-modified ATP analogs used to study phosphorylation ......................... 12 1.6.3 γ-modified ATP analogs used by Pflum and colleagues ................................... 14 1.6.3.1 ATP-biotin ...................................................................................................... 14 1.6.3.2 ATP-dansyl .................................................................................................... 17 1.6.3.3 γ-modified ATP analogs with photocrosslinkers ............................................. 18 1.7 Thesis Project ...................................................................................................... 21 CHAPTER 2 K-CLASP (KINASE CATALYZED CROSS-LINKING AND STREPTAVIDIN PURIFICATION.................................................................................. 23 2.1 Current methods available for phosphosite specific kinase identification ............ 24 vi 2.1.1 In silico kinase prediction ................................................................................. 24 2.1.2 Mechanism based crosslinking ......................................................................... 25 2.2 K-CLASP strategy ............................................................................................... 27 2.3 K-CLASP using Protein Kinase A (PKA) and kemptide ....................................... 29 2.3.1 In vitro crosslinking reactions with recombinant PKA and kemptide ................. 30 2.3.2 In vitro crosslinking with recombinant CK2 and CK2 peptide ........................... 33 2.3.3 In vitro crosslinking with lysates and kemptide ................................................. 33 2.3.4 K-CLASP with kemptide and lysates ................................................................ 36 2.4 K-CLASP to uncover the kinase/s that phosphorylate Miz1 protein .................... 41 2.4.1 Miz1 protein ...................................................................................................... 41 2.4.2 K-CLASP with Miz1 protein .............................................................................. 42 2.5 Conclusions and Future Directions ...................................................................... 49 2.6 Experimental Methods ......................................................................................... 51 2.6.1 Synthesis of ATP-ArN3 ..................................................................................... 51 2.6.2 Peptide Synthesis and Purification ................................................................... 51 2.6.3 In vitro crosslinking reaction with recombinant PKA ......................................... 54 2.6.4 SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) ........ 55 2.6.5 Protein transfer
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