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1.7 Hydrogen/Deuterium Exchange Mass Spectrometry UC San Diego UC San Diego Electronic Theses and Dissertations Title Facilitation of protein 3-D structure determination using enhanced peptide amide deuterium exchange mass spectrometry (DXMS) Permalink https://escholarship.org/uc/item/05h1b0jv Author Pantazatos, Dennis Peter Publication Date 2006 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO FACILITATION OF PROTEIN 3-D STRUCTURE DETERMINATION USING ENHANCED PEPTIDE AMIDE DEUTERIUM EXCHANGE MASS SPECTROMETRY (DXMS) A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Dennis Peter Pantazatos Committee in charge: Professor Virgil L. Woods Jr., Chair Professor Philip Bourne Professor Jeff Esko Professor Mortin Printz Professor Fransisco Villareal 2006 ii Copyright Dennis Peter Pantazatos, 2006 All rights reserved. ii iii The dissertation of Dennis Peter Pantazatos is approved, and is acceptable in quality and form for publication on microfilm: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2006 iii iv DEDICATION This dissertation is dedicated in loving memory of my father whose early inspiration led me along my life's path, my brother, and for my loving mother whose strength and courage have taught me how to endure. iv v EPIGRAPH "It's not the accomplishments in life that help you grow but the experience of the journey.” Dennis Peter Pantazatos v vi TABLE OF CONTENTS DEDICATION ............................................................................................................IV EPIGRAPH.................................................................................................................. V TABLE OF CONTENTS...........................................................................................VI LIST OF FIGURES AND TABLES .........................................................................XI ACKNOWLEDGEMENTS..................................................................................... XV CURRICULUM VITA.......................................................................................... XVII ABSTRACT OF THE DISSERTATION ..............................................................XIX CHAPTER 1……………………………………………………………………………1 HYDROGEN/DEUTERIUM EXCHANGE MASS SPECTROMETRY FOR INVESTIGATING PROTEIN-LIGAND INTERACTIONS 1.1 ABSTRACT............................................................................................................ 1 1.2 INTRODUCTION................................................................................................... 2 1.3 STANDARD APPROACHES FOR HIGH-RESOLUTION PROTEIN STRUCTURE ANALYSIS........................................................................................... 3 1.4 THEORY OF HYDROGEN EXCHANGE ............................................................ 4 1.5 AMIDE HYDROGEN/DEUTERIUM EXCHANGE STUDIES ........................... 5 1.6 EX1 AND EX2 KINETICS FOR HYDROGEN/DEUTERIUM EXCHANGE .... 8 1.7 HYDROGEN/DEUTERIUM EXCHANGE MASS SPECTROMETRY .............. 9 1.8 INSTRUMENTATION AND DATA ANALYSIS.............................................. 10 vi vii 1.9 THROMBIN-LEPIRUDIN COMPLEX: MODEL STUDIES USING HYDROGEN/DEUTERIUM EXCHANGE MASS SPECTROMETRY .................. 11 1.10 MAPPING LEPIRUDIN BINDING SITES ON THROMBIN .......................... 12 1.11 ALLOSTERIC CHANGES IN THROMBIN STRUCTURE INDUCED BY LEPIRUDIN BINDING.............................................................................................. 13 1.12 RESOLVING CONFORMATIONAL CHANGES AND LIGAND BINDING 15 1.13 HYDROGEN/DEUTERIUM EXCHANGE TO CHARACTERIZE DRUG- PROTEIN INTERACTIONS...................................................................................... 17 1.14 CONCLUSION................................................................................................... 18 1.15 ACKNOWLEDGEMENTS ................................................................................ 19 1.16 REFERENCES.................................................................................................... 27 CHAPTER 2…………………………………………………………………………..32 HIGH RESOLUTION DEFINITION OF THE STABILITY LANDSCAPE OF CHICKEN BRAIN α-SPECTRIN (R1617) WITH ENHANCED HYDROGEN/DEUTERIUM EXCHANGE MASS SPECTROMETRY (DXMS): IMPLICATIONS FOR THE BASIS OF SPECTRIN ELASTICITY 2.1 ABSTRACT.......................................................................................................... 32 2.2 INTRODUCTION................................................................................................. 34 2.3 METHODS ........................................................................................................... 38 2.4 RESULTS ............................................................................................................. 42 2.5 DISCUSSION ....................................................................................................... 54 2.6 ACKNOWLEDGEMENTS .................................................................................. 60 2.7 SUPPLEMENTAL MATERIAL.......................................................................... 62 vii viii 2.8 REFERENCES...................................................................................................... 74 CHAPTER 3…………………………………………………………………………...78 MOLECULAR INTERACTIONS BETWEEN MATRILYSIN AND THE MATRIX METALLOPROTEINASE INHIBITOR DOXYCYCLINE INVESTIGATED BY DEUTERIUM EXCHANGE MASS SPECTROMETRY 3.1 ABSTRACT.......................................................................................................... 78 3.2 INTRODUCTION................................................................................................. 79 3.3 METHODS .......................................................................................................... 83 3.4 RESULTS ............................................................................................................. 89 3.5 DISCUSSION ..................................................................................................... 105 3.6 ACKNOWLEDGEMENTS. ............................................................................... 110 3.7 REFERENCES.................................................................................................... 111 CHAPTER 4………………………………………………………………………….115 RAPID REFINEMENT OF CRYSTALLOGRAPHIC PROTEIN CONSTRUCT DEFINITION EMPLOYING ENHANCED HYDROGEN/ DEUTERIUM EXCHANGE MASS SPECTROMETRY (DXMS) 4.1 ABSTRACT........................................................................................................ 115 4.2 INTRODUCTION............................................................................................... 116 4.3 METHODS ......................................................................................................... 120 4.4 RESULTS ........................................................................................................... 123 4.5 DISCUSSION ..................................................................................................... 128 4.6 ACKNOWLEDGMENTS................................................................................... 129 4.7 SUPPLEMENTAL MATERIALS...................................................................... 137 viii ix 4.8 REFERENCES.................................................................................................... 144 CHAPTER 5………………………………………………………………………….147 ON THE USE OF DXMS TO PRODUCE MORE CRYSTALLIZABLE PROTEINS – STRUCTURES OF THE THERMOTOGA PROTEINS TM0160 AND TM1171 5.1 ABSTRACT........................................................................................................ 147 5.2 INTRODUCTION............................................................................................... 148 5.3 METHODS..........................................................................................................150 5.4 RESULTS ............................................................................................................159 5.5 DISCUSSION ..................................................................................................... 169 5.6 ACKNOWLEDGEMENTS ................................................................................ 171 5.7 REFERENCES.................................................................................................... 189 CHAPTER 6………………………………………………………………… ...…….193 METHODS FOR THE DETERMINATION OF PROTEIN THREE- DIMENSIONAL STRUCTURE EMPLOYING HYDROGEN EXCHANGE ANALYSIS TO REFINE COMPUTATIONAL STRUCTURE PREDICTION 6.1 ABSTRACT........................................................................................................ 193 6.2 INTRODUCTION............................................................................................... 196 6.3 RESULTS ........................................................................................................... 208 6.4 ACKNOWLEDGMENTS................................................................................... 221 6.5 REFERENCES...................................................................................................
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