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Lombricine Kinase Structure and Substrate Specificity: a Paradigm for Elucidation of Substrate Specificity in Phosphagen Kinases D

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Lombricine Kinase Structure and Substrate Specificity: a Paradigm for Elucidation of Substrate Specificity in Phosphagen Kinases D Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2007 Lombricine Kinase Structure and Substrate Specificity: A Paradigm for Elucidation of Substrate Specificity in Phosphagen Kinases D. Jeffrey. Bush Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES LOMBRICINE KINASE STRUCTURE AND SUBSTRATE SPECIFICITY: A PARADIGM FOR ELUCIDATION OF SUBSTRATE SPECIFICITY IN PHOSPHAGEN KINASES By D. JEFFREY BUSH A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy Degree Awarded: Spring Semester, 2007 The members of the Committee approve the Dissertation of D. Jeffrey Bush defended on February 20, 2007. Michael S. Chapman Professor Co-Directing Dissertation John Dorsey Professor Co-Directing Dissertation W. Ross Ellington Outside Committee Member Michael Blaber Committee Member Approved: ____________________________________________ Joseph Schlenoff, Department Chair, Department of Chemistry & Biochemistry ____________________________________________ Joseph Travis, Dean, College of Arts & Sciences The Office of Graduate Studies has verified and approved the above named committee members. ii To the late Clifford M. Bush, who with statements such as “A heterogeneous compound of two or more substances whose ray through certain limits is confined to a specific area…” fostered a strong interest of the author in science at a very young age, if only just to know more about what he spoke. iii ACKNOWLEDGEMENTS I wish to first convey my sincere gratitude to my parents, Donald and Roberta for raising me in the nurture and admonition of the Almighty God. With loving support and encouragement, all have fostered a strong belief that religion and science are by no means mutually exclusive, contrary to popular myth. I certainly would not have been able to achieve the accomplishments that I have without the discipline, perseverance, support and encouragement instilled at an early age. My mentor, Dr. Michael Chapman has also been a tremendous source of inspiration, advice and encouragement. I am forever grateful for his support, depth of knowledge in so many areas, and for his continued patience and kind demeanor, while directing and focusing this research. I would also like to thank my supervisory committee, particularly, collaborating Professor Dr. W. Ross Ellington, whose helpful advice, suggestions and encouragement were crucial to the success of the work described herein. Many laboratory colleagues were also instrumental in the success of this research. Among those providing much helpful advice were Dr. Shawn Clark, Dr. Qing Xie, Dr. Arezki Azzi, Dr. James Gattis, Ms. Eliza Ruben, Mr. Omar Davulcu, Dr. Pamela Pruett, Dr. Mohammad Yousef, Dr. Andrei Korostelev, Dr. Felcy Gabriel Ms. Nancy Meyer, Dr. Gregg Hoffman, Ms. Deanne Compaan, Ms. Irina Carbone, Dr. Wei Yang, Ms. Sarah Murray, Dr. Michael Zawrotny, and Mr. Travis Smith. Two important influences who fostered my interest in science at an early age and to whom I am also grateful are my high school chemistry teacher, Mary Solarczyk, and Mr. Patrick Weaver, who urged me to take Ms. Solarczyk’s AP chemistry class, which I found remarkably fascinating. iv My sister, Laura, also encouraged me and motivated me to put tremendous effort toward my studies from sheer amicable sibling rivalry if not simply out of spite to try to outperform her own considerable academic proclivities. Last but certainly not least, I would like to thank the director of the FSU X-ray Facility, Dr. Thayumanasamy Somasundaram. Without the support and expert advice of ‘Soma’ in areas from crystal mounting, cryoprotection, data collection and processing, synchrotron data collection procedures, as well as his familiarity with unix-based crystallographic software packages, this work would certainly not have been possible. Substrate-free dimeric (sf-d) x-ray data for lombricine kinase was collected at the Cornell High Energy Synchrotron Source (CHESS) which is supported by the National Science Foundation and the National Institutes of Health/National Institute of General Medical Sciences under award DMR-0225180. Substrate-free monomeric (sf-m) x-ray data was collected at the Advanced Photon Source which was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract No. W-31-109-ENG- 38. Funding of this research by the National Institutes of Health (NIH) grant R01 GM55837 to Michael S. Chapman, the American Heart Association (AHA) grant 0315101B to D. Jeffrey Bush, and in part by the National Science Foundation (NSF) research training grant to Florida State University’s Institute of Molecular Biophysics is gratefully acknowledged. v TABLE OF CONTENTS List of Tables .................................................................................... Page viii List of Figures .................................................................................... Page ix Abbreviations ........................................................................................ Page x Abstract .......................................................................................... Page xi 1. Introduction .................................................................................... Page 1 Phosphagen (guanidino) kinase structure and function .................. Page 1 Properties of the phosphagen substrates ....................................... Page 2 Clinical significance of phosphagen kinases .................................. Page 4 Enzyme mechanism ....................................................................... Page 4 Preorganization, substrate-substrate alignment and proximity ....... Page 7 Substrate specificity ....................................................................... Page 10 2. Materials and Methods ..................................................................... Page 14 Biochemical reagents and instrumentation ..................................... Page 14 RNA isolation and cDNA construction ............................................ Page 14 PCR amplification, cloning and sequencing ................................... Page 14 Expression and purification of lombricine kinase ............................ Page 15 Multiple sequence alignments ........................................................ Page 21 Crystallization and cryoprotection .................................................. Page 21 X-ray data collection, processing and reciprocal-space refinement Page 24 Calculation of structure factors and R-free test set generation ....... Page 29 Homology modeling ........................................................................ Page 29 Molecular replacement ................................................................... Page 30 Determination of the non-crystallographic symmetry operator ....... Page 31 Structural refinement ...................................................................... Page 33 Model building and real-space refinement ...................................... Page 36 Comparative structural alignment of phosphagen kinases ............. Page 37 Targeted molecular dynamics simulation of active-site closure ...... Page 38 3. Results and Discussion .................................................................... ….. Page 40 Expression and purification of lombricine kinase ............................ Page 40 Multiple sequence alignment of phosphagen kinases .................... Page 41 Substrate Specificity ....................................................................... Page 44 Crystallization and cryoprotection optimization .............................. Page 51 Structural validation ........................................................................ Page 52 Evaluation of the reliability of predicted transition-state models of LK Page 53 vi Structural rationalization of potential specificity determinants ........ Page 56 5. Conclusions .................................................................................... Page 63 APPENDICES .................................................................................... Page 64 A Commercially-available potential enzyme inhibitors .................. Page 64 B Protocol for real-space refinement in “O” .................................. Page 69 C Biological buffers and solutions……………. .............................. Page 74 REFERENCES .................................................................................... Page 75 BIOGRAPHICAL SKETCH .................................................................... Page 84 vii LIST OF TABLES Table 1: Comparative space group, unit cell and crystallization conditions Page 27 Table 2: Refinement strategy and R-factor statistics for sf-m data Page 33 Table 3: Refinement strategy and R-factor statistics for sf-d data Page 34 Table 4: Kinetic parameters of Annelid phosphagen kinases Page 46 viii LIST OF FIGURES Figure 1: Structures of the phosphagen kinase substrates Page 3 Figure 2: The enzymatic mechanistic pathways of phosphoryl transfer Page 5 Figure 3: Presumed schematic kinetic mechanism of LK Page 6 Figure 4: The transition-state structure of phosphagen kinases Page 8 Figure 5: Lombricine kinase ADP-agarose chromatogram Page 17 Figure 6: Typical SDS PAGE gel after ADP chromatography Page 18 Figure 7: Purity verification by superdex-200HR chromatography
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