Schuck Protein Interactions

Biophysical Approaches for the Study of Complex Reversible Systems
1. Auflage 2007
ISBN: 978-0-387-35966-3
Verlag: Springer-Verlag
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 532 Seiten

When I was invited to edit this volume, I wanted to take the opportunity to assemble reviews of different biophysical methodologies for protein interactions at a level suf?ciently detailed to understand how complex systems can be studied. There are several excellent introductory texts for biophysical methodologies, many with hands-on descriptions or embedded in general introductions to physical b- chemistry. The goal of the present volume was to present state-of-the-art reviews that do not necessarily enable the reader to carry out these techniques, but to gain a deep understanding of the biophysical observables, to stimulate creative thought on how the techniques may be applied to study a particular biological system, and to foster collaboration and multidisciplinary work. Reversible protein interactions involve noncovalent chemical bonds, pro- cing protein complexes with free energies not far from the order of magnitude of the thermal energy kT. As a consequence, they can be highly dynamic and may be controlled, for example, by protein expression levels and changes in the intracel- lar or microenvironment. Reversible protein complexes may have suf?cient stab- ity to be puri?ed for study, but frequently their short lifetime essentially limits their existence to solutions of mixtures of the binding partners in which they remain populated through dissociation and reassociation processes. To understand the function of such protein complexes, it is important to study their structure and dynamics.

Autoren/Hrsg.

Schuck, Peter

Inhaltsverzeichnis

1;Contents;6
2;Contributors;8
3;Preface;11
4;The Characterization of Biomolecular Interactions Using Fluorescence Fluctuation Techniques;13
4.1;1.1. INTRODUCTION;13
4.2;1.2. ADVANTAGES OF FLUCTUATION SPECTROSCOPY;15
4.3;1.3. FLUORESCENCE CORRELATION SPECTROSCOPY, AND MOLECULAR DIFFUSION;17
4.4;1.4. CROSS-CORRELATION AND HETEROLOGOUS ASSOCIATIONS;21
4.5;1.5. PHOTON STATISTICS;25
4.6;1.6. EXAMPLES OF THE USE OF FLUCTUATION SPECTROSCOPY TO STUDY BIOMOLECULAR INTERACTIONS;31
4.7;1.7. LIMITATIONS OF FCS;37
4.8;1.8. CONCLUSION;44
4.9;REFERENCES;44
5;Characterization of Protein– Protein Interactions Using Atomic Force Microscopy;51
5.1;2.1. INTRODUCTION;51
5.2;2.2. USE OF AFM;52
5.3;2.3. CHARACTERIZATION OF PROTEIN–PROTEIN COMPLEXES;60
5.4;2.4. CONCLUDING REMARKS;81
5.5;ACKNOWLEDGMENTS;81
5.6;REFERENCES;81
6;Combined Solid-Phase Detection Techniques for Dissecting Multiprotein Interactions on Membranes;90
6.1;3.1. INTRODUCTION;90
6.2;3.2. LABEL-FREE DETECTION TECHNIQUES;91
6.3;3.3. SIMULTANEOUS LABEL-FREE AND FLUORESCENCE DETECTION;93
6.4;3.4. CONCLUSIONS;104
6.5;REFERENCES;105
7;Surface Plasmon Resonance Biosensing in the Study of Ternary Systems of Interacting Proteins;108
7.1;4.1. INTRODUCTION;108
7.2;4.2. SURFACE PLASMON RESONANCE BASICS;110
7.3;4.3. LIMITATIONS OF USING SURFACE-IMMOBILIZED SITES TO STUDY PROTEIN– PROTEIN INTERACTIONS;117
7.4;4.4. STUDYING INTERACTING SYSTEMS WITH MULTIPLE COMPONENTS, BINDING SITES, OR CONFORMATIONAL STATES;123
7.5;4.5. A PRACTICAL APPLICATION TO THE STUDY OF MULTIPROTEIN COMPLEXES;135
7.6;4.6. CONCLUSIONS;144
7.7;ACKNOWLEDGMENT;145
7.8;REFERENCES;145
8;Mass Spectrometry for Studying Protein Modifications and for Discovery of Protein Interactions;153
8.1;5.1. INTRODUCTION;153
8.2;5.2. MASS SPECTROMETRY;154
8.3;5.3. PROTEIN IDENTIFICATION AND CHARACTERIZATION BY MASS SPECTROMETRY;165
8.4;5.4. ANALYSIS OF PROTEIN COMPLEXES BY MASS SPECTROMETRY;169
8.5;REFERENCES;175
9;H/2H Exchange Mass Spectrometry of Protein Complexes;178
9.1;6.1. INTRODUCTION;178
9.2;6.2. TYPES OF AMIDE EXCHANGE EXPERIMENTS ON PROTEIN COMPLEXES;180
9.3;6.3. THE BASIC EXPERIMENTAL METHOD;185
9.4;6.4. CONFORMATIONAL CHANGES ON PROTEIN– PROTEIN INTERACTION;191
9.5;REFERENCES;194
10;Elucidation of Protein–Protein and Protein– Ligand Interactions by NMR Spectroscopy;197
10.1;7.1. INTRODUCTION;197
10.2;7.2. PRINCIPLES OF NMR STRUCTURE DETERMINATION;198
10.3;7.3. NMR-BASED METHODS FOR THE STUDY OF PROTEIN– PROTEIN AND PROTEIN– LIGAND INTERACTIONS;207
10.4;REFERENCES;228
11;Application of Isothermal Titration Calorimetry in Exploring the Extended Interface;238
11.1;8.1. INTRODUCTION;238
11.2;8.2. ISOTHERMAL TITRATION CALORIMETRY: GENERAL PRINCIPLES;239
11.3;8.3. BINDING AND RELEASE OF SOLVENT IONS;241
11.4;8.4. CHANGES IN HEAT CAPACITY REVEAL THE EXTENDED INTERFACE;244
11.5;8.5. THERMODYNAMIC EFFECTS OF PROTEIN STRUCTURAL PERTURBATION ON BINDING;249
11.6;8.6. SUMMARY;258
11.7;REFERENCES;259
12;Solvent Mediated Protein– Protein Interactions;262
12.1;9.1. INTRODUCTION;262
12.2;9.2. THERMODYNAMICS BACKGROUND;264
12.3;9.3. DESCRIPTION OF THE SOLVATION OF MACROMOLECULES IN TWO- COMPONENT SOLVENT;266
12.4;9.4. MACROMOLECULE–MACROMOLECULE INTERACTIONS;271
12.5;9.5. LINKAGE BETWEEN PROTEIN–SOLVENT AND PROTEIN– PROTEIN INTERACTIONS;276
12.6;9.6. MODELS FOR DESCRIBING SOLVATION AND ITS ORIGINS;276
12.7;9.7. EXAMPLES OF PERTUBATION OF MACROMOLECULAR EQUILIBRIUM BY COSOLVENTS;279
12.8;9.8. METHODS THAT ALLOW THE CHARACTERIZATION OF THE PROTEIN AS A SOLVATED PARTICLE;284
12.9;ACKNOWLEDGMENT;290
12.10;REFERENCES;290
13;Sedimentation Equilibrium Analytical Ultracentrifugation for Multicomponent Protein Interactions;295
13.1;10.1. INTRODUCTION;295
13.2;10.2. BASIC PRINCIPLES;296
13.3;10.3. EXPERIMENTAL;299
13.4;10.4. THEORY;300
13.5;10.5. DATA ANALYSIS;306
13.6;10.6. APPLICATIONS;309
13.7;10.7. CONCLUSIONS;317
13.8;ACKNOWLEDGMENT;317
13.9;REFERENCES;317
14;Structure Analysis of Macromolecular Complexes by Solution Small- Angle Scattering;323
14.1;11.1. INTRODUCTION;323
14.2;11.2. MAIN THEORETICAL AND EXPERIMENTAL ASPECTS;324
14.3;11.3. RECENT DEVELOPMENTS IN DATA ANALYSIS METHODS;338
14.4;11.4. EXAMPLES OF PRACTICAL APPLICATIONS;346
14.5;11.5. CONCLUSIONS;363
14.6;REFERENCES;365
15;Fluorescence Detection of Proximity;372
15.1;12.1. INTRODUCTION;372
15.2;12.2. FRET;373
15.3;12.3. APPLICATIONS;383
15.4;12.4. CONCLUSION;396
15.5;ACKNOWLEDGMENTS;397
15.6;REFERENCES;397
16;Steady-State and Time-Resolved Emission Anisotropy;402
16.1;13.1. INTRODUCTION;402
16.2;13.2. THEORY OF TIME-RESOLVED EMISSION ANISOTROPY;402
16.3;13.3. EXPERIMENTAL;412
16.4;13.4. PROSPECTS;418
16.5;ACKNOWLEDGEMENTS;418
16.6;REFERENCES;419
17;Analysis of Protein–DNA Equilibria by Native Gel Electrophoresis;422
17.1;14.1. INTRODUCTION;422
17.2;14.2. CHOICE OF SUBSTRATE;423
17.3;14.3. DETECTION AND QUANTITATION OF COMPLEXES AND FREE DNA;425
17.4;14.4. STABILITY OF COMPLEXES DURING ELECTROPHORESIS;429
17.5;14.5. MEASUREMENT OF STOICHIOMETRY;434
17.6;14.6. MEASUREMENT OF BINDING ACTIVITY;438
17.7;14.7. MEASUREMENT OF ASSOCIATION CONSTANTS;438
17.8;14.8. A LOOK INTO THE FUTURE;445
17.9;REFERENCES;446
18;Electrospray Ionization Mass Spectrometry and the Study of Protein Complexes;452
18.1;15.1. INTRODUCTION;452
18.2;15.2. HISTORY AND DEVELOPMENT OF MASS SPECTROMETRY AS A TOOL FOR STUDYING PROTEIN COMPLEXES;453
18.3;15.3. PRINCIPLES OF ESI MASS SPECTROMETRY OF PROTEIN COMPLEXES;454
18.4;15.4. APPLICATIONS OF MASS SPECTROMETRY TO STRUCTURAL BIOLOGY;466
18.5;15.5. SUMMARY;471
18.6;REFERENCES;471
19;Sedimentation Velocity in the Study of Reversible Multiprotein Complexes;474
19.1;16.1. INTRODUCTION;474
19.2;16.2. EXPERIMENTAL SET-UP;476
19.3;16.3. BASIC PRINCIPLES OF SEDIMENTATION VELOCITY ANALYSIS;481
19.4;16.4. ASSESSING CONFORMATION OF PROTEINS AND PROTEIN COMPLEXES;492
19.5;16.5. SEDIMENTATION OF INTERACTING SYSTEMS;495
19.6;16.6. CONCLUSIONS;516
19.7;ACKNOWLEDGMENT;517
19.8;REFERENCES;517
20;Index;524