Mass Spectrometry in Biophysics : Conformation and Dynamics of Biomolecules

481 Pages·2005·20.343 MB·English

by  Igor A. Kaltashov, Stephen J. Eyles

MASS SPECTROMETRY
IN BIOPHYSICS
Conformation and Dynamics
of Biomolecules
Igor A. Kaltashov
Stephen J. Eyles
University of Massachusetts at Amherst
A JOHN WILEY & SONS, INC., PUBLICATION

MASS SPECTROMETRY
IN BIOPHYSICS
WILEY-INTERSCIENCE SERIES IN MASS SPECTROMETRY
Series Editors:
Dominic M. Desiderio
Departments ofNeurology and Biochemistry
University of TennesseeHealth ScienceCenter
Nico M. M. Nibbering
Vrije Universiteit Amsterdam, The Netherlands
John R. de Laeter ž Applications of Inorganic Mass Spectrometry
MichaelKinterandNicholasE.ShermanžProteinSequencingandIdentification
Using Tandem Mass Spectrometry
Chhabil Dass, Principles and Practice ofBiological Mass Spectrometry
Mike S. Lee ž LC/MSApplications inDrug Development
Jerzy Silberring and Rolf Eckman ž Mass Spectrometry and Hyphenated Tech-
niques in NeuropeptideResearch
J. Wayne Rabalais ž PrinciplesandApplicationsofIonScatteringSpectrometry:
Surface Chemicaland Structural Analysis
Mahmoud Hamdan and Pier Giorgio Righetti ž Proteomics Today: Protein
AssessmentandBiomarkersUsingMassSpectrometry,2DElectrophoresis,and
Microarray Technology
Igor A. Kaltashov and Stephen J. Eyles ž Mass Spectrometry in Biophysics:
Conformation andDynamicsof Biomolecules
MASS SPECTROMETRY
IN BIOPHYSICS
Conformation and Dynamics
of Biomolecules
Igor A. Kaltashov
Stephen J. Eyles
University of Massachusetts at Amherst
A JOHN WILEY & SONS, INC., PUBLICATION
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LibraryofCongressCataloging-in-PublicationData:
Kaltashov,IgorA.
Massspectrometryinbiophysics:conformationanddynamicsof
biomolecules/IgorA.Kaltashov,StephenJ.Eyles.
p.cm.
Includesbibliographicalreferencesandindex.
ISBN0-471-45602-0(Cloth)
1. Massspectrometry.2. Biophysics.3. Biomolecules—Spectra.I. Eyles,
StephenJ.II. Title.
QP519.9.M3K352005
572(cid:1).33—dc22 2004012532
PrintedintheUnitedStatesofAmerica.
10987654321
CONTENTS
Preface xiii
1 General Overview of Basic Concepts in Molecular Biophysics 1
1.1. Covalent Structure of Biopolymers, 1
1.2. Noncovalent Interactions and Higher-order Structure, 10
1.2.1. Electrostatic Interaction, 10
1.2.2. Hydrogen Bonding, 11
1.2.3. Steric Clashes and Allowed Conformations of the Peptide
Backbone: Secondary Structure, 11
1.2.4. Solvent–Solute Interactions, Hydrophobic Effect, Side
Chain Packing, and Tertiary Structure, 14
1.2.5. Intermolecular Interactions and Association: Quaternary
Structure, 18
1.3. The Protein Folding Problem, 18
1.3.1. What Is Protein Folding? 18
1.3.2. Why Is Protein Folding So Important, 19
1.3.3. What Is the Natively Folded Protein and How Do We
Define a Protein Conformation? 21
1.3.4. What Are Non-native Protein Conformations? Random
Coils, Molten Globules, and Folding Intermediates, 22
1.3.5. Protein Folding Pathways, 24
1.4. Protein Energy Landscapes and the Folding Problem, 25
1.4.1. Protein Conformational Ensembles and Energy
Landscapes: Enthalpic and Entropic Considerations, 25
v
vi CONTENTS
1.4.2. Equilibrium and Kinetic Intermediates on the Energy
Landscape, 28
1.5. Protein Dynamics and Function, 30
1.5.1. Limitations of the Structure–Function Paradigm, 30
1.5.2. Protein Dynamics Under Native Conditions, 31
1.5.3. Biomolecular Dynamics and Binding from the Energy
Landscape Perspective, 34
1.5.4. Energy Landscapes Within a Broader Context of Nonlinear
Dynamics: Information Flow and Fitness Landscapes, 37
References, 38
2 Overview of “Traditional” Experimental Arsenal to Study
Biomolecular Structure and Dynamics 45
2.1. X-Ray Crystallography, 45
2.1.1. Fundamentals, 45
2.1.2. Crystal Structures at Atomic and Ultrahigh Resolution, 47
2.1.3. Crystal Structures of Membrane Proteins, 48
2.1.4. Protein Dynamics and X-Ray Diffraction, 48
2.2. Solution Scattering Techniques, 49
2.2.1. Static and Dynamic Light Scattering, 49
2.2.2. Small-Angle X-Ray Scattering, 50
2.2.3. Cryo-Electron Microscopy, 51
2.2.4. Neutron Scattering, 53
2.3. NMR Spectroscopy, 53
2.3.1. Heteronuclear NMR, 56
2.3.2. Hydrogen Exchange by NMR, 56
2.4. Other Spectroscopic Techniques, 59
2.4.1. Cumulative Measurements of Higher Order Structure:
Circular Dichroism, 59
2.4.2. Vibrational Spectroscopy, 64
2.4.3. Fluorescence: Monitoring Specific Dynamic Events, 68
2.5. Other Biophysical Methods to Study Macromolecular Interactions
and Dynamics, 71
2.5.1. Calorimetric Methods, 71
2.5.2. Analytical Ultracentrifugation, 74
2.5.3. Surface Plasmon Resonance, 79
2.5.4. Gel Filtration, 80
2.5.5. Gel Electrophoresis, 80
References, 81
3 Overview of Biological Mass Spectrometry 87
3.1. Basic Principles of Mass Spectrometry, 87
3.1.1. Stable Isotopes and Isotopic Distributions, 89
3.1.2. Macromolecular Mass: Terms and Definitions, 96
CONTENTS vii
3.2. Methods of Producing Biomolecular Ions, 97
3.2.1. Macromolecular Ion Desorption Techniques: General
Considerations, 97
3.2.2. Electrospray Ionization, 97
3.2.3. Matrix Assisted Laser Desorption/Ionization, 102
3.3. Mass Analysis, 107
3.3.1. General Considerations: m/z Range and Mass
Discrimination, Mass Resolution, Duty Cycle, Data
Acquisition Rate, 107
3.3.2. Mass Spectrometry Combined with Separation
Methods, 109
3.4. Tandem Mass Spectrometry, 111
3.4.1. Basic Principles of Tandem Mass Spectrometry, 113
3.4.2. Collision-Induced Dissociation: Collision Energy, Ion
Activation Rate, Dissociation of Large Biomolecular
Ions, 114
3.4.3. Other Fragmentation Techniques: Electron-Capture
Dissociation, Photoradiation-Induced Dissociation,
Surface-Induced Dissociation, 116
3.4.4. Ion–Molecule Reactions in the Gas Phase: Internal
Rearrangement, Charge Transfer, 118
3.5. Brief Overview of Common Mass Analyzers, 118
3.5.1. Mass Analyzer as an Ion Dispersion Device: Magnetic
Sector MS, 119
3.5.2. Temporal Ion Dispersion: Time-of-Flight MS, 122
3.5.3. Mass Analyzer as an Ion Filter, 124
3.5.4. Mass Analyzer as an Ion Storing Device: Quadrupole
(Paul) Ion Trap, 127
3.5.5. Mass Analyzer as an Ion Storing Device: FT ICR MS, 130
3.5.6. Hybrid Mass Spectrometers, 133
References, 134
4 Mass Spectrometry-Based Approaches to Study Biomolecular
Higher-Order Structure 143
4.1. Biomolecular Topography: Contact and Proximity Maps via
Chemical Cross-Linking, 144
4.2. Mapping Solvent-Exposed Regions: Footprinting Methods, 157
4.2.1. Selective Chemical Labeling, 157
4.2.2. Nonspecific Chemical Labeling, 161
4.2.3. Hydrogen/Deuterium Exchange, 163
4.3. Emerging Low-Resolution Methods: Zero-Interference
Approaches, 167
4.3.1. Stoichiometry of Protein Assemblies and Topology of the
Interface Regions: Controlled Dissociation of Noncovalent
Complexes, 167