Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics

• Presents a wide variety of mass spectrometry methods used to explore structural mechanisms, protein dynamics and interactions between proteins.
• Preliminary chapters cover mass spectrometry methods for examining proteins and are then followed by chapters devoted to presenting very practical, how-to methods in a detailed way.
• Includes footprinting and plistex specifically, setting this book apart from the competition.

Foreword xiii

Contributors xv

1 Overview of Mass Spectrometry Technologies for Examining Protein Structure: Current and Future Directions 1
Shannon M. Swiatkowski and Mark R. Chance

1.1 Introduction 1

1.2 Hydrogen/Deuterium Exchange Mass Spectrometry 3

1.3 Hydroxyl-Radical-Mediated Protein Footprinting 5

1.4 Chemical Cross-linking 8

References 8

2 Hydrogen Exchange Mass Spectrometry: Principles and Capabilities 11
Sébastien Brier and John R. Engen

2.1 The Chemistry of Hydrogen Exchange 11

2.2 HX Mechanisms in Proteins 19

2.3 Deuterium Incorporation into Proteins 23

2.4 Measuring HX with Mass Spectrometry 26

2.5 Capabilities of HX MS in Structural Biology 31

Acknowledgment 36

References 36

3 Covalent Labeling Methods for Examining Protein Structure and Protein Interactions 45
Keiji Takamoto and Janna Kiselar

3.1 Introduction 45

3.2 Chemistry of Hydroxyl Radical Footprinting 46

3.3 Mass Spectrometry Approaches for Quantitative Protein Footprinting 52

3.4 Examples of Various Methods that Generate Hydroxyl Radicals in Solution to Examine Protein Structure 55

3.5 The Future: Hybrid Approaches that Combine Experimental and Computational Data 62

References 63

4 Complementary Methods for Structure Determination: Hydroxyl-Radical-Mediated Footprinting and Deuterium Exchange Mass Spectrometry as Applied to Serpin Structure 69
Xiaojing Zheng and Patrick L. Wintrode

4.1 Introduction 69

4.2 Technical Comparison of Hydroxyl-Radical-Mediated Footprinting and H/D Exchange Methodologies 73

4.3 Structural Mass Spectrometry Data 76

4.4 Solvent Accessibility 79

4.5 Dynamics 84

4.6 Significance for Serpin Structure and Function 87

4.7 Summary 87

Acknowledgment 88

References 88

5 Deuterium Exchange Approaches for Examining Protein Interactions: Case Studies of Complex Formation 91
Elizabeth A. Komives

5.1 Interactions of Regulatory and Catalytic Subunits of Protein Kinase A 91

5.2 Allostery in Protein–Protein Interactions Revealed by H/D Exchange 95

5.3 Interactions of the Inhibitor IκBα with the Transcription Factor NF-κB 97

References 101

6 Hydrogen/Deuterium Exchange Studies of Viruses 105
Sebyung Kang and Peter E. Prevelige Jr.

6.1 Overview of Virus Lifecycles 105

6.2 Structural Investigations of Viral Capsids 105

6.3 Dynamics of Viral Capsids 106

6.4 Hydrogen/Deuterium Exchange Studies of Virus Capsid Structure 107

6.5 Hydrogen/Deuterium Exchange Studies of Viral Protein Dynamics 114

6.6 Technical Aspects of Performing Hydrogen/Deuterium Exchange Experiments on Viruses 118

References 119

7 Use of Enhanced Peptide Amide Hydrogen/Deuterium Exchange-Mass Spectrometry (DXMS) in the Examination of Protein–Protein Interactions 123
Yoshitomo Hamuro, Stephen J. Coales, Lora L. Hamuro, and Virgil L. Woods Jr.

7.1 Introduction 123

7.2 Theory of H/D Exchange 124

7.3 Overview of DXMS Technology for Protein–Protein Interactions 126

7.4 DXMS of Human Growth Hormone and Its Binding Protein 129

7.5 DXMS of PKA Regulatory Subunits 133

7.6 DXMS of PKA R-Subunit D/D Domains and D-AKAP2 AKB Domain 139

7.7 Epitope Mapping by DXMS 146

7.8 Conclusions 148

Abbreviations 149

Acknowledgments 150

References 150

8 Cross-linking as a Tool to Examine Protein Complexes: Examples of Cross-linking Strategies and Computational Modeling 157
Evgeniy V. Petrotchenko and Christoph H. Borchers

8.1 Introduction 157

8.2 Cross-linking Strategies 157

8.3 Cross-linking Methodology 158

8.4 Challenges Associated with Combining Cross-linking with Mass Spectrometry 159

8.5 Advances in Mass Spectrometry Instrumentation and Capabilities 160

8.6 Novel Cross-linking Reagents for Mass Spectrometry Applications 162

8.7 Analytical Software 165

8.8 Using Cross-linking Distance Constraints to Build Experimental Models of Protein Complexes 167

References 167

9 Complex Formation in the Actin Cytoskeleton: Cross-linking Tools to Define Actin Protein Structure and Interactions 169
Sabrina Benchaar and Emil Reisler

9.1 Introduction 169

9.2 Mapping Cross-linking with Methods Other than Mass Spectrometry 171

9.3 Actin-Actin Cross-linking 171

9.4 Intrastrand Cross-linked Actin between GLN41 and CYS374 174

9.5 Regulation of Cytoskeleton by ABPs and Mapping their Interfaces with Actin by Cross-linking 175

9.6 Cross-linking of Actin and Muscle Proteins—Examples of Experimental Approaches 181

9.7 Concluding Remarks 182

Acknowledgment 183

References 183

10 Computational Approaches to Examining Protein–Protein Interactions: Combining Experimental and Computational Data in the Era of Structural Genomics 189
J.K. Amisha Kamal

10.1 Interactome in Structural Genomics 189

10.2 Importance of Computational Methods in Structural Genomics 190

10.3 Combining Computational Method with Experimental Data in Modeling the Structure of Protein Binary Complex 190

10.4 Method Summary 208

10.5 Experimental Methods 210

Acknowledgment 212

References 213

11 Studies of Intact Proteins and Protein Complexes: ESI MS Approaches 217
Igor A. Kaltashov, Rinat R. Abzalimov, Agya K. Frimpong, and Stephen J. Eyles

11.1 Introduction 217

11.2 Tertiary Structure Integrity and Conformational Heterogeneity (Charge State Distributions) 220

11.3 Quaternary Structure Integrity and Composition of Non-Covalent Complexes 224

11.4 Functional Competence 226

11.5 Flexibility Maps and Binding Interfaces 229

11.6 Gas Phase Ion Chemistry and Its Influence on the Measurement of Protein Properties in Solution 231

11.7 Challenges and Future Outlook 234

Acknowledgments 237

References 237

12 Two Approaches to Mass Spectrometric Protein Footprinting: PLIMSTEX and FPOP 243
Michael L. Gross, Mei M. Zhu, and David M. Hambly

12.1 Introduction: Protein–Ligand Interactions by Mass Spectrometry, Titration, and Hydrogen/Deuterium Amide Exchange and Fast Photochemical Oxidation of Proteins 243

12.2 Protein–Ligand Interactions by Mass Spectrometry, Titration, and H/D Amide Exchange (PLIMSTEX) 245

12.3 Applications of PLIMSTEX 247

12.4 Self-Association of Insulin: A Protein/Protein Interaction 253

12.5 Features of PLIMSTEX 254

12.6 Fast Photochemical Oxidation of Proteins: An Example of Fast Protein Footprinting 256

12.7 Features of FPOP 263

12.8 Future 264

Abbreviations 265

Acknowledgments 265

References 265

Index 271

Mark Chance, PhD, is the Director of the Case Center for Proteomics and Professor of Physiology and Biophysics at Case Western Reserve University. He also directs the Case Center for Synchrotron Biosciences, located at the National Synchrotron Light Source at Brookhaven National Laboratory, New York. Dr. Chance received his bachelor's degree in biology from Wesleyan University and his PhD in biophysics from the University of Pennsylvania. He furthered his training as a postdoctoral research associate at AT&T Bell Laboratories, then went on to become assistant professor in the department of chemistry at Georgetown University. He moved to Albert Einstein College of Medicine in the Bronx, New York, in 1992, and was soon promoted to associate professor of the departments of physiology & biophysics and biochemistry, and full professor in 1998. While at AECOM, he was the Joseph and Anne Wunsch fellow in biophysical engineering and recipient of the Irma Hirschl Career Scientist Award. In 2005, he moved to Case Western Reserve University as the founding director of the Center for Proteomics. His research primarily concerns development of structural and cellular proteomics technologies to understand protein structure-function.

A how-to guide that helps you take advantage of the latest mass spectrometry methods

This book brings together and examines the latest mass spectrometry methods used to investigate proteins, including structural mechanisms, protein dynamics, and interactions among proteins. Written by a team of experts with many years of hands-on experience developing and working with mass spectrometry methods, the book offers a wealth of practical advice and tips to help readers fully exploit the capabilities of a mass spectrometer.

The book begins with an overview of mass spectrometry technologies, including an expert forecast of future directions. Next, the authors offer step-by-step guidance for such topics as:

• Complementary methods for structure determination: hydroxyl radical-mediated footprinting and deuterium exchange mass spectrometry as applied to serpin structure

• Covalent labeling methods for examining protein structure and protein interactions

• Computational approaches to examine protein-protein interactions: combining experimental and computational data in the era of structural genomics

• Two approaches to mass spectrometric protein footprinting: PLIMSTEX and FPOP

• Hydrogen/deuterium exchange studies of viruses

Carefully edited, the book presents a uniform standard of high quality and thoroughness throughout all the chapters. References to the literature enable readers to explore each individual topic in greater depth.

Any researcher seeking to advance his or her own protein research will benefit from this book's insights and how-to guidance. The spectrometry methods can be applied to support investigations in such fields as biomedicine, biotechnology, and pharmaceutical research.