Protein Interactions (eBook)

Dr. Peter Schuck is the acting chief of the Protein Biophysics department in the National Institute of Health’s Division of Bioengineering and Physical Science. His current research work is on protein structure and function, with studies in multi-protein complexes, membrane proteins in detergent solution, self-assembling and filamenting proteins, structural and nonstructural viral proteins, homogeneous and heterogeneous interactions of immunological cell surface receptors; and biophysical methods and instrumentation through analytical ultracentrifugation, optical biosensors, static and dynamic light scattering, calorimetry, and circular dichroism.

Contents 6
Contributors 8
Preface 11
The Characterization of Biomolecular Interactions Using Fluorescence Fluctuation Techniques 13
1.1. INTRODUCTION 13
1.2. ADVANTAGES OF FLUCTUATION SPECTROSCOPY 15
1.3. FLUORESCENCE CORRELATION SPECTROSCOPY, AND MOLECULAR DIFFUSION 17
1.4. CROSS-CORRELATION AND HETEROLOGOUS ASSOCIATIONS 21
1.5. PHOTON STATISTICS 25
1.6. EXAMPLES OF THE USE OF FLUCTUATION SPECTROSCOPY TO STUDY BIOMOLECULAR INTERACTIONS 31
1.7. LIMITATIONS OF FCS 37
1.8. CONCLUSION 44
REFERENCES 44
Characterization of Protein– Protein Interactions Using Atomic Force Microscopy 51
2.1. INTRODUCTION 51
2.2. USE OF AFM 52
2.3. CHARACTERIZATION OF PROTEIN–PROTEIN COMPLEXES 60
2.4. CONCLUDING REMARKS 81
ACKNOWLEDGMENTS 81
REFERENCES 81
Combined Solid-Phase Detection Techniques for Dissecting Multiprotein Interactions on Membranes 90
3.1. INTRODUCTION 90
3.2. LABEL-FREE DETECTION TECHNIQUES 91
3.3. SIMULTANEOUS LABEL-FREE AND FLUORESCENCE DETECTION 93
3.4. CONCLUSIONS 104
REFERENCES 105
Surface Plasmon Resonance Biosensing in the Study of Ternary Systems of Interacting Proteins 108
4.1. INTRODUCTION 108
4.2. SURFACE PLASMON RESONANCE BASICS 110
4.3. LIMITATIONS OF USING SURFACE-IMMOBILIZED SITES TO STUDY PROTEIN– PROTEIN INTERACTIONS 117
4.4. STUDYING INTERACTING SYSTEMS WITH MULTIPLE COMPONENTS, BINDING SITES, OR CONFORMATIONAL STATES 123
4.5. A PRACTICAL APPLICATION TO THE STUDY OF MULTIPROTEIN COMPLEXES 135
4.6. CONCLUSIONS 144
ACKNOWLEDGMENT 145
REFERENCES 145
Mass Spectrometry for Studying Protein Modifications and for Discovery of Protein Interactions 153
5.1. INTRODUCTION 153
5.2. MASS SPECTROMETRY 154
5.3. PROTEIN IDENTIFICATION AND CHARACTERIZATION BY MASS SPECTROMETRY 165
5.4. ANALYSIS OF PROTEIN COMPLEXES BY MASS SPECTROMETRY 169
REFERENCES 175
H/2H Exchange Mass Spectrometry of Protein Complexes 178
6.1. INTRODUCTION 178
6.2. TYPES OF AMIDE EXCHANGE EXPERIMENTS ON PROTEIN COMPLEXES 180
6.3. THE BASIC EXPERIMENTAL METHOD 185
6.4. CONFORMATIONAL CHANGES ON PROTEIN– PROTEIN INTERACTION 191
REFERENCES 194
Elucidation of Protein–Protein and Protein– Ligand Interactions by NMR Spectroscopy 197
7.1. INTRODUCTION 197
7.2. PRINCIPLES OF NMR STRUCTURE DETERMINATION 198
7.3. NMR-BASED METHODS FOR THE STUDY OF PROTEIN– PROTEIN AND PROTEIN– LIGAND INTERACTIONS 207
REFERENCES 228
Application of Isothermal Titration Calorimetry in Exploring the Extended Interface 238
8.1. INTRODUCTION 238
8.2. ISOTHERMAL TITRATION CALORIMETRY: GENERAL PRINCIPLES 239
8.3. BINDING AND RELEASE OF SOLVENT IONS 241
8.4. CHANGES IN HEAT CAPACITY REVEAL THE EXTENDED INTERFACE 244
8.5. THERMODYNAMIC EFFECTS OF PROTEIN STRUCTURAL PERTURBATION ON BINDING 249
8.6. SUMMARY 258
REFERENCES 259
Solvent Mediated Protein– Protein Interactions 262
9.1. INTRODUCTION 262
9.2. THERMODYNAMICS BACKGROUND 264
9.3. DESCRIPTION OF THE SOLVATION OF MACROMOLECULES IN TWO- COMPONENT SOLVENT 266
9.4. MACROMOLECULE–MACROMOLECULE INTERACTIONS 271
9.5. LINKAGE BETWEEN PROTEIN–SOLVENT AND PROTEIN– PROTEIN INTERACTIONS 276
9.6. MODELS FOR DESCRIBING SOLVATION AND ITS ORIGINS 276
9.7. EXAMPLES OF PERTUBATION OF MACROMOLECULAR EQUILIBRIUM BY COSOLVENTS 279
9.8. METHODS THAT ALLOW THE CHARACTERIZATION OF THE PROTEIN AS A SOLVATED PARTICLE 284
ACKNOWLEDGMENT 290
REFERENCES 290
Sedimentation Equilibrium Analytical Ultracentrifugation for Multicomponent Protein Interactions 295
10.1. INTRODUCTION 295
10.2. BASIC PRINCIPLES 296
10.3. EXPERIMENTAL 299
10.4. THEORY 300
10.5. DATA ANALYSIS 306
10.6. APPLICATIONS 309
10.7. CONCLUSIONS 317
ACKNOWLEDGMENT 317
REFERENCES 317
Structure Analysis of Macromolecular Complexes by Solution Small- Angle Scattering 323
11.1. INTRODUCTION 323
11.2. MAIN THEORETICAL AND EXPERIMENTAL ASPECTS 324
11.3. RECENT DEVELOPMENTS IN DATA ANALYSIS METHODS 338
11.4. EXAMPLES OF PRACTICAL APPLICATIONS 346
11.5. CONCLUSIONS 363
REFERENCES 365
Fluorescence Detection of Proximity 372
12.1. INTRODUCTION 372
12.2. FRET 373
12.3. APPLICATIONS 383
12.4. CONCLUSION 396
ACKNOWLEDGMENTS 397
REFERENCES 397
Steady-State and Time-Resolved Emission Anisotropy 402
13.1. INTRODUCTION 402
13.2. THEORY OF TIME-RESOLVED EMISSION ANISOTROPY 402
13.3. EXPERIMENTAL 412
13.4. PROSPECTS 418
ACKNOWLEDGEMENTS 418
REFERENCES 419
Analysis of Protein–DNA Equilibria by Native Gel Electrophoresis 422
14.1. INTRODUCTION 422
14.2. CHOICE OF SUBSTRATE 423
14.3. DETECTION AND QUANTITATION OF COMPLEXES AND FREE DNA 425
14.4. STABILITY OF COMPLEXES DURING ELECTROPHORESIS 429
14.5. MEASUREMENT OF STOICHIOMETRY 434
14.6. MEASUREMENT OF BINDING ACTIVITY 438
14.7. MEASUREMENT OF ASSOCIATION CONSTANTS 438
14.8. A LOOK INTO THE FUTURE 445
REFERENCES 446
Electrospray Ionization Mass Spectrometry and the Study of Protein Complexes 452
15.1. INTRODUCTION 452
15.2. HISTORY AND DEVELOPMENT OF MASS SPECTROMETRY AS A TOOL FOR STUDYING PROTEIN COMPLEXES 453
15.3. PRINCIPLES OF ESI MASS SPECTROMETRY OF PROTEIN COMPLEXES 454
15.4. APPLICATIONS OF MASS SPECTROMETRY TO STRUCTURAL BIOLOGY 466
15.5. SUMMARY 471
REFERENCES 471
Sedimentation Velocity in the Study of Reversible Multiprotein Complexes 474
16.1. INTRODUCTION 474
16.2. EXPERIMENTAL SET-UP 476
16.3. BASIC PRINCIPLES OF SEDIMENTATION VELOCITY ANALYSIS 481
16.4. ASSESSING CONFORMATION OF PROTEINS AND PROTEIN COMPLEXES 492
16.5. SEDIMENTATION OF INTERACTING SYSTEMS 495
16.6. CONCLUSIONS 516
ACKNOWLEDGMENT 517
REFERENCES 517
Index 524