Mass Spectrometry in Structural Biology and Biophysics Architecture, Dynamics, and Interaction of Biomolecules
, by Kaltashov, Igor A.; Eyles, Stephen J.; Desiderio, Dominic M.; Nibbering, Nico M.- ISBN: 9780470937792 | 0470937793
- Cover: Hardcover
- Copyright: 4/3/2012
IGOR A. KALTASHOV, PHD, is a Professor in the Department of Chemistry at the University of Massachusetts Amherst.
STEPHEN J. EYLES, PHD, is a Senior Lecturer in the Department of Biochemistry and Molecular Biology, and the Director of the Mass Spectrometry Center at the University of Massachusetts Amherst.
Preface to the Second Edition | p. xi |
Preface to the First Edition | p. xiii |
General Overview of Basic Concepts in Molecular Biophysics | p. 1 |
Covalent Structure of Biopolymers | p. 1 |
Noncovalent Interactions and Higher Order Structure | p. 3 |
Electrostatic Interaction | p. 3 |
Hydrogen Bonding | p. 6 |
Steric Clashes and Allowed Conformations of the Peptide Backbone: Secondary Structure | p. 6 |
Solvent--Solute Interactions, Hydrophobic Effect, Side-Chain Packing, and Tertiary Structure | p. 7 |
Intermolecular Interactions and Association: Quaternary Structure | p. 9 |
The Protein Folding Problem | p. 9 |
What Is Protein Folding? | p. 9 |
Why Is Protein Folding So Important? | p. 10 |
What Is the Natively Folded Protein and How Do We Define a Protein Conformation? | p. 11 |
What Are Non-Native Protein Conformations?: Random Coils, Molten Globules, and Folding Intermediates | p. 12 |
Protein Folding Pathways | p. 13 |
Protein Energy Landscapes and the Folding Problem | p. 14 |
Protein Conformational Ensembles and Energy Landscapes: Enthalpic and Entropic Considerations | p. 14 |
Equilibrium and Kinetic Intermediates on the Energy Landscape | p. 16 |
Protein Dynamics and Function | p. 17 |
Limitations of the Structure--Function Paradigm | p. 17 |
Protein Dynamics under Native Conditions | p. 17 |
Is Well-Defined Structure Required for Functional Competence? | p. 18 |
Biomolecular Dynamics and Binding from The Energy Landscape Perspective | p. 19 |
Energy Landscapes Within a Broader Context of Nonlinear Dynamics: Information Flow and Fitness Landscapes | p. 21 |
Protein Higher Order Structure and Dynamics from A Biotechnology Perspective | p. 22 |
References | p. 22 |
Overview of Traditional Experimental Arsenal to Study Biomolecular Structure and Dynamics | p. 26 |
X-Ray Crystallography | p. 26 |
Fundamentals | p. 26 |
Crystal Structures at Atomic and Ultrahigh Resolution | p. 27 |
Crystal Structures of Membrane Proteins | p. 27 |
Protein Dynamics and X-Ray Diffraction | p. 28 |
Solution Scattering Techniques | p. 28 |
Static and Dynamic Light Scattering | p. 28 |
Small-Angle X-Ray Scattering | p. 29 |
Cryo-Electron Microscopy | p. 29 |
Neutron Scattering | p. 30 |
NMR Spectroscopy | p. 30 |
Heteronuclear NMR | p. 32 |
Hydrogen Exchange by NMR | p. 33 |
Other Spectroscopic Techniques | p. 34 |
Cumulative Measurements of Higher Order Structure: Circular Dichroism | p. 34 |
Vibrational Spectroscopy | p. 37 |
Fluorescence: Monitoring Specific Dynamic Events | p. 39 |
Other Biophysical Methods to Study Macromolecular Interactions and Dynamics | p. 41 |
Calorimetric Methods | p. 41 |
Analytical Ultracentrifugation | p. 43 |
Surface Plasmon Resonance | p. 45 |
Size Exclusion Chromatography (Gel Filtration) | p. 46 |
Electrophoresis | p. 47 |
Affinity Chromatography | p. 48 |
References | p. 48 |
Overview of Biological Mass Spectrometry | p. 52 |
Basic Principles of Mass Spectrometry | p. 52 |
Stable Isotopes and Isotopic Distributions | p. 53 |
Macromolecular Mass: Terms and Definitions | p. 57 |
Methods of Producing Biomolecular Ions | p. 57 |
Macromolecular Ion Desorption Techniques: General Considerations | p. 57 |
Electrospray Ionization | p. 58 |
Matrix Assisted Laser Desorption Ionization (MALDI) | p. 60 |
Mass Analysis | p. 63 |
General Considerations: m/z Range and Mass Discrimination, Mass Resolution, Duty Cycle, and Data Acquisition Rate | p. 63 |
Mass Spectrometry Combined with Separation Methods | p. 64 |
Tandem Mass Spectrometry | p. 65 |
Basic Principles of Tandem Mass Spectrometry | p. 65 |
Collision-Induced Dissociation: Collision Energy, Ion Activation Rate, and Dissociation of Large Biomolecular Ions | p. 66 |
Surface- and Photoradiation-Induced Dissociation | p. 68 |
Electron-Based Ion Fragmentation Techniques: Electron Capture Dissociation and Electron Transfer Dissociation | p. 71 |
Ion-Molecule Reactions in the Gas Phase: Internal Rearrangement and Charge Transfer | p. 71 |
Brief Overview of Common Mass Analyzers | p. 72 |
Mass Analyzer As an Ion Dispersion Device: Magnetic Sector Mass Spectrometry | p. 72 |
Temporal Ion Dispersion: Time-of-Flight Mass Spectrometer | p. 73 |
Mass Analyzer As an Ion Filter | p. 75 |
Mass Analyzer As an Ion-Storing Device: The Quadrupole (Paul) Ion Trap and Linear Ion Trap | p. 76 |
Mass Analyzer As an Ion Storing Device: FT ICR MS | p. 78 |
Mass Analyzer as An Ion Storing Device: Orbitrap MS | p. 80 |
Ion Mobility Analyzers | p. 81 |
Hybrid Mass Spectrometers | p. 82 |
References | p. 82 |
Mass Spectrometry Based Approaches to Study Biomolecular Higher Order Structure | p. 89 |
Direct Methods of Structure Characterization: Native Electrospray Ionization Mass Spectrometry | p. 89 |
Preservation of Noncovalent Complexes in the Gas Phase: Stoichiometry of Biomolecular Assemblies | p. 89 |
Utilization of Ion Chemistry in the Gas Phase to Aid Interpretation of ESI MS Data | p. 91 |
Dissociation of Noncovalent Complexes in the Gas Phase: Can It Lead to Wrong Conclusions? | p. 93 |
Evaluation of Macromolecular Shape in Solution: The Extent of Multiple Charging in ESI MS | p. 94 |
Macromolecular Shape in the Gas Phase: Ion Mobility--Mass Spectrometry | p. 97 |
How Relevant Are Native ESI MS Measurements? Restrictions on Solvent Composition in ESI | p. 98 |
Noncovalent Complexes by MALDI MS | p. 98 |
Chemical Cross-Linking for Characterization of Biomolecular Topography | p. 99 |
Mono- and Bifunctional Cross-Linking Reagents | p. 99 |
Chemical Cross-Linkers with Fixed Arm-Length: Molecular Rulers or Tape Measures? | p. 100 |
Mass Spectrometry Analysis of Chemical Cross-Linking Reaction Products | p. 102 |
Intrinsic Cross-Linkers: Methods to Determine Disulfide Connectivity Patterns in Proteins | p. 108 |
Other Intrinsic Cross-Linkers: Oxidative Cross-Linking of Tyrosine Side Chains | p. 109 |
Mapping Solvent-Accessible Areas with Chemical Labeling and Footprinting Methods | p. 110 |
Selective Chemical Labeling | p. 110 |
Nonspecific Chemical Labeling | p. 115 |
Hydrogen Exchange | p. 116 |
Hydrogen Exchange in Peptides and Proteins: General Considerations | p. 116 |
Probing Exchange Patterns with HDX MS at the Local Level | p. 116 |
References | p. 119 |
Mass Spectrometry Based Approaches to Study Biomolecular Dynamics: Equilibrium Intermediates | p. 127 |
Direct Methods of Monitoring Equilibrium Intermediates: Protein Ion Charge-State Distributions in ESI MS | p. 127 |
Protein Conformation as a Determinant of the Extent of Multiple Charging in ESI MS | p. 127 |
Detection and Characterization of Large-Scale Conformational Transitions by Monitoring Protein Ion Charge-State Distributions in ESI MS | p. 128 |
Detection of Small-Scale Conformational Transitions by Monitoring Protein Ion Charge-State Distributions | p. 130 |
Pitfalls and Limitations of Protein Ion Charge-State Distribution Analysis | p. 133 |
Chemical Labeling and Trapping Equilibrium States in Unfolding Experiments | p. 135 |
Characterization of the Solvent-Exposed Surfaces with Chemical Labeling | p. 135 |
Exploiting Intrinsic Protein Reactivity: Disulfide Scrambling and Protein Misfolding | p. 136 |
Structure and Dynamics of Intermediate Equilibrium States by Hydrogen Exchange | p. 137 |
Protein Dynamics and Hydrogen Exchange | p. 137 |
Global Exchange Kinetics in the Presence of Non-Native States: EX1, EX2, and EXX Exchange Regimes in a Simplified Two-State Model System | p. 138 |
A More Realistic Two-State Model System: Effect of Local Fluctuations on the Global Exchange Pattern Under EX2 Conditions | p. 141 |
Effects of Local Fluctuations on the Global Exchange Pattern Under EX1 and Mixed (EXX) Conditions | p. 143 |
Exchange in Multistate Protein Systems: Superposition of EX1 and EX2 Processes and Mixed-Exchange Kinetics | p. 144 |
Measurements of Local Patterns of Hydrogen Exchange in the Presence of Non-Native States | p. 146 |
Bottom-Up Approaches to Probing the Local Structure of Intermediate States | p. 146 |
Top-Down Approaches to Probing the Local Structure of Intermediate States | p. 150 |
Further Modifications and Improvements of HDX MS in Conformationally Heterogeneous Systems | p. 153 |
References | p. 153 |
Kinetic Studies By Mass Spectrometry | p. 160 |
Kinetics of Protein Folding | p. 160 |
Stopped-Flow Measurement of Kinetics | p. 160 |
Kinetic Measurements with Hydrogen Exchange | p. 162 |
Kinetics by Mass Spectrometry | p. 163 |
Pulse Labeling Mass Spectrometry | p. 163 |
Continuous-Flow Mass Spectrometry | p. 168 |
Stopped-Flow Mass Spectrometry | p. 169 |
Kinetics of Disulfide Formation During Folding | p. 171 |
Irreversible Covalent Labeling As a Probe of Protein Kinetics | p. 172 |
Kinetics of Protein Assembly | p. 174 |
Kinetics of Enzyme Catalysis | p. 178 |
References | p. 181 |
Protein Interactions: A Closer Look at the Structure--Dynamics--Function Triad | p. 186 |
Direct Methods of Monitoring Protein Interactions with Their Physiological Partners in Solution by ESI MS: From Small Ligands to Other Biopolymers | p. 186 |
Assessment of Binding Affinity with Direct ESI MS Approaches | p. 189 |
Indirect Characterization of Non-covalent Interactions Under Physiological and Near-Physiological Conditions | p. 190 |
Assessment of Ligand Binding by Monitoring Dynamics of âÇ£NativeâÇ Proteins with Hydrogen--Deuterium Exchange (HDX MS) | p. 190 |
PLIMSTEX and Related Techniques: Binding Assessment by Monitoring Conformational Changes with HDX MS in Titration Experiments | p. 192 |
Binding Revealed by Changes in Ligand Mobility | p. 194 |
Indirect Characterization of Noncovalent Interactions Under Partially Denaturing Conditions | p. 194 |
Ligand-Induced Protein Stabilization Under Mildly Denaturing Conditions: Effect of Ligand Binding on Charge-State Distributions of Protein Ions | p. 195 |
SUPREX: Utilizing HDX Under Denaturing Conditions to Discern Protein--Ligand Binding Parameters | p. 196 |
Understanding Protein Action: Mechanistic Insights from the Analysis of Structure and Dynamics under Native Conditions | p. 198 |
Dynamics at the Catalytic Site and Beyond: Understanding Enzyme Mechanism | p. 198 |
Allosteric Effects Probed by HDX MS | p. 201 |
Going Full Circle with MS: Native ESI MS Reveals Structural Changes Predicted by HDX MS Measurements | p. 201 |
Understanding Protein Action: Mechanistic Insights from the Analysis of Structure and Dynamics under Non-Native (Partially Denaturing) Conditions | p. 203 |
References | p. 206 |
Other Biopolymers and Synthetic Polymers of Biological Interest | p. 212 |
Nucleic Acids | p. 212 |
Characterization of the Covalent Structure of Nucleic Acids | p. 212 |
DNA Higher Order Structure and Interactions with Physiological Partners and Therapeutics | p. 215 |
Higher Order Structure and Dynamics of RNA | p. 219 |
Oligosaccharides | p. 223 |
Covalent Structure of Oligosaccharides | p. 225 |
Higher Order Structure of Oligosaccharides and Interactions with their Physiological Partners | p. 226 |
Synthetic Polymers and their Conjugates with Biomolecules | p. 226 |
Covalent Structure of Polymers and Polymer--Protein Conjugates | p. 229 |
Higher Order Structure of Polymers and Polymer--Protein Conjugates | p. 232 |
References | p. 233 |
Mass Spectrometry on the Frontiers of Molecular Biophysics and Structural Biology: Perspectives and Challenges | p. 239 |
Mass Spectrometry and the Unique Challenges of Membrane Proteins | p. 239 |
Analysis of Membrane Proteins in Organic Solvents | p. 240 |
Analysis of Membrane Proteins Using Detergents | p. 241 |
Analysis of Membrane Proteins Utilizing Other Membrane Mimics | p. 244 |
Analysis of Membrane Proteins in Their Native Environment | p. 249 |
The Protein Aggregation Problem | p. 249 |
The Importance and Challenges of Protein Aggregation | p. 249 |
Direct Monitoring of Protein Aggregation and Amyloidosis with Mass Spectrometry | p. 250 |
Structure of Protein Aggregates, Amyloids, and Pre-Amyloid States | p. 253 |
The Many Faces of Complexity: Mass Spectrometry and the Problem of Structural Heterogeneity | p. 258 |
How Large Is âÇ£Too LargeâÇ ? Mass Spectrometry in Characterization of Ordered Macromolecular Assemblies | p. 263 |
Proteasomes | p. 264 |
Ribosomes | p. 264 |
Molecular Chaperones | p. 267 |
Complexity of Macromolecular Interactions In Vivo and Emerging Mass Spectrometry Based Methods to Probe Structure and Dynamics of Biomolecules in Their Native Environment | p. 269 |
Macromolecular Crowding Effect | p. 269 |
Macromolecular Properties In Vitro and In Vivo | p. 270 |
âÇ£LiveâÇ Macromolecules: Equilibrium Systems or Dissipative Structures? | p. 271 |
References | p. 272 |
Appendix: Physics of Electrospray | p. 279 |
Index | p. 285 |
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