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Comparison of Activation Enthalpies for Aminoglycoside Modification Reactions

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Comparison of Activation Enthalpies for Aminoglycoside Modification Reactions University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Masters Theses Graduate School 8-2015 Comparison of Activation Enthalpies for Aminoglycoside Modification Reactions Brittany Sterling Soto University of Tennessee - Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_gradthes Part of the Biochemistry Commons, and the Chemistry Commons Recommended Citation Soto, Brittany Sterling, "Comparison of Activation Enthalpies for Aminoglycoside Modification Reactions. " Master's Thesis, University of Tennessee, 2015. https://trace.tennessee.edu/utk_gradthes/3453 This Thesis is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Masters Theses by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a thesis written by Brittany Sterling Soto entitled "Comparison of Activation Enthalpies for Aminoglycoside Modification Reactions." I have examined the final electronic copy of this thesis for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Master of Science, with a major in Biochemistry and Cellular and Molecular Biology. Engin H. Serpersu, Major Professor We have read this thesis and recommend its acceptance: Elizabeth E. Howell, Francisco Barrera Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Comparison of Activation Enthalpies for Aminoglycoside Modification Reactions A Thesis Presented for the Master of Science Degree The University of Tennessee, Knoxville Brittany Sterling Soto August 2015 DEDICATION This Thesis is dedicated to my parents, Andrea-Lee Friedman and Ron Soto, who have provided a wealth of love and support throughout my academic career. Along with my parents, this Thesis is dedicated to George Ashison, my former childhood soccer coach, and Janet Bayes, a family friend. These two individuals have had a profound impact on my personal development and have been long standing role models throughout my life. “An investment of Knowledge pays the best interest” -Aristole ii ACKNOWLEDGEMENTS I would like to first and foremost express my greatest gratitude to my advisor, Dr. Engin H. Serpersu, my Thesis Committee, Dr. Elizabeth E. Howell, Dr. Alexandre Gladys, and Dr. Francisco Barrera, and Dr. Cynthia Peterson for their guidance and support throughout the entirety of my studies at The University of Tennessee, Knoxville. These professors have continually encouraged me to strive for excellence, push through the most difficult times when my research appeared to reach a dead end, and have taught me to view and analyze information in a different light. I would also like to thank the University of Tennessee, Knoxville for the opportunity to advance my education and Program of Excellence and Equity in Research (PEER) for funding my education for the first two years. In addition, I would like to thank Dr. Ed Wright, Jessica M. Gullett, and my lab members, Xiaomin Jing, Sharin Raval, Katelyn Rosendal, and Prashasti Kumar, for their advice, criticism, and motivation. iii ABSTRACT At highly elevated temperatures, many biological reactions can proceed spontaneously from the ground state to the transition state. However, due to the long half-life of these reactions, catalysts are required to catalyze these reactions at modern day temperatures by lowering the activation energy. Wolfenden et al. has previously shown that catalysts enhance the rate of the reaction by reducing the enthalpy of activation. Therefore, the activation energies have been determined for three aminoglycoside modifying enzymes, APH(3’)-IIIa, AAC(3)-IIIb, and AAC(3)-VIa, to determine whether these three enzymes distinguish between the two classes of aminoglycoside antibiotics by reducing the enthalpy of activation during catalysis. Aminoglycosides are broad-spectrum antibiotics active against Gram-positive and Gram- negative organisms. These antibiotics contain a 2-deoxystreptamine ring and are classified into two classes: the 4,6-di-substituted kanamycin-like aminoglycosides and the 4,5-di- substituted neomycin-like aminoglycosides. Since their discovery in the 1940s, bacteria have shown a high level of resistance to these antimicrobial agents mainly due to the emergence of aminoglycoside modifying enzymes (AGMEs). AGMEs are classified into three main families based on the type of modification reaction: (a) O-Nucleotidyltransferases (ANT) catalyze the adenylation reaction of hydroxyl groups in the presence of ATP; (b) O- Phosphotransferases (APH) phosphorylate hydroxyl groups in the presence of ATP; (c) and N-Acetyltransferases (AAC) which acetylate an amino group on the 2-deoxystreptamine ring or aminohexose sugar rings in the presence of acetyl coenzyme A as the acetyl donor. APH(3’)-IIIa and AAC(3)-IIIb are two very promiscuous AGMEs while AAC(3)-VIa has a limited substrate profile. In general, there were no observed trends in the activation energies that distinguished between the two classes of aminoglycoside antibiotics for APH(3’)-IIIa and AAC(3)-IIIb. When studying the activation energies for a more hydrophobic aminoglycoside, gentamicin C1 [C1] and C2 [C2], AAC(3)-IIIb appeared to favor the more methylated gentamicin component, gentamicin C1 [C1], whereas AAC(3)-VIa was shown to have a lower activation energy for gentamicin C2 [C2]. iv TABLE OF CONTENTS CHAPTER I: Introduction ......................................................................................................... 1 A. Temperature-Dependent Rate Enhancements Produced by a Catalyst .............................. 1 I. Chemical Reaction Pathway .............................................................................................. 1 II. Rate Enhancements produced by Catalysts ...................................................................... 2 B. Aminoglycoside Antibiotics ............................................................................................... 4 I. Discovery of Aminoglycosides and Chemical Structure .................................................... 4 II. Mode of Action .................................................................................................................. 5 C. Aminoglycoside Modifying Enzymes ................................................................................ 6 I. Nomenclature and Mechanism of Modification ................................................................. 6 D. Introduction to Aminoglycoside -3’-Phosphotransferase-IIIa ........................................... 7 I. Structure of APH(3’)-IIIa ................................................................................................... 7 II. Protein Dynamics in Solution ........................................................................................... 9 III. Theorell-Chance Kinetic Mechanism ............................................................................ 11 IV. Kinetic and Thermodynamic Properties ........................................................................ 12 E. Introduction to Aminoglycoside -3-N-Acetyltransferase-IIIb .......................................... 14 I. Protein Dynamics in Solution .......................................................................................... 14 II. Kinetic and Thermodynamic Properties ......................................................................... 15 III. Proposed Orientation for Aminoglycosides in the Active Site ...................................... 17 F. Introduction to Aminoglycoside -3-N-Acetyltransferase-VIa .......................................... 18 G. Enzyme Characteristics for APH(3’)-IIIa, AAC(3)-IIIb, and AAC(3)-VIa .................... 18 CHAPTER II: Gentamicin C Complex .................................................................................... 21 A. Background ...................................................................................................................... 21 I. Origin and Structure ........................................................................................................ 21 II. CHSQC-TOSCY Experiments ......................................................................................... 21 B. Experimental Procedure ................................................................................................... 22 I. Separation of Gentamicin C Complex by Thin Layer Chromatography ......................... 22 II. Separation of Gentamicin C Components, C1, C2, C1a ................................................... 23 v III. NMR Verification of Purified Gentamicin C Components by 1H 1D NMR, Total Correlation Spectroscopy (TOCSY), and Carbon Heteronuclear Single Quantum Coherence (CHSQC) ......................................................................................................... 23 C. Results and Discussion ..................................................................................................... 24 I. Gentamicin C Complex Separation by Thin Layer Chromatography .............................. 24 II. Separation of Gentamicin Components by Ion Exchange Chromatography .................. 25 1 III. Verification of Purified Gentamicin C1 and C2 Components by H 1D NMR, TOCSY, and CHSQC 2D NMR Experiments ..................................................................................
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