Biothermodynamics, Part D

1. Auflage 2011
ISBN: 978-0-12-386004-0
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band Volume 492, 369 Seiten, Web PDF

Reihe: Methods in Enzymology

The use of thermodynamics in biological research can be equated to an energy book-keeping system. While the structure and function of a molecule is important, it is equally important to know what drives the energy force.ÿThis volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions. - Elucidates the relationships between structure and energetics and their applications to molecular design, aiding researchers in the design of medically important molecules - Provides a 'must-have' methods volume that keeps MIE buyers and online subscribers up-to-date with the latest research - Offers step-by-step lab instructions, including necessary equipment, from a global research community

Autoren/Hrsg.

Inhaltsverzeichnis

1;Front Cover;1
2;Biothermodynamics,Part D;4
3;Copyright;5
4;Contents;6
5;Contributors;10
6;Preface;14
7;Methods in Enzymology;16
8;Chapter 1: A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands;46
8.1;1. Introduction;47
8.2;2. Materials and Methods;49
8.3;3. Results and Discussion;53
8.4;4. Conclusions;68
8.5;Acknowledgments;69
8.6;References;69
9;Chapter 2: Thermodynamics of Biological Processes;72
9.1;1. Introduction: Thermodynamics is Not Just for Dead Stuff;73
9.2;2. States and Weights from the Boltzmann Rule;74
9.3;3. Binding Reactions and Biological Thermodynamics;78
9.4;4. The Unreasonable Effectiveness of Random-Walk Models;97
9.5;5. Conclusions;100
9.6;Acknowledgments;101
9.7;References;101
10;Chapter 3: Protein Stability in the Presence of Cosolutes;106
10.1;1. Introduction;107
10.2;2. Isothermal Folding/Unfolding of Protein in the Presence of Stabilizing/Denaturing Osmolyte;109
10.3;3. Isothermal Protein (Un)Folding in the Presence of Osmolyte Mixtures;123
10.4;4. Osmolyte-Induced Unfolding at Variable Temperature;131
10.5;5. Thermal Unfolding in the Presence of Osmolytes;137
10.6;6. Where Do the Little Equations Come From?;146
10.7;Acknowledgments;166
10.8;References;166
11;Chapter 4: Small-Angle X-ray Scattering Studies of Peptide-Lipid Interactions Using the Mouse Paneth Cell a-Defensin Cryptdin;172
11.1;1. Introduction;173
11.2;2. X-Rays as Structural Probes of Biological Systems Under Biomimetic Conditions;177
11.3;3. Preparation of Peptide-Lipid Complexes for X-Ray Measurements;182
11.4;4. Summary;190
11.5;Acknowledgments;190
11.6;References;190
12;Chapter 5: Synergy of Molecular Dynamics and Isothermal Titration Calorimetry in Studies of Allostery;196
12.1;1. Allostery;197
12.2;2. Arginine Repressor;199
12.3;3. Preparation for Simulations;202
12.4;4. Sampling of States;204
12.5;5. Equilibration;205
12.6;6. Observing System Motions;208
12.7;7. Correlated Motions;208
12.8;8. Structural Features of Correlated Motions;209
12.9;9. Arg Residues Promote Rotation and Oscillation;212
12.10;10. Structural Correlates of Rotational Oscillation;214
12.11;11. Single-Arginine Simulations;214
12.12;12. Rotational Ensembles;215
12.13;13. Energetic Contributions;218
12.14;14. Reconciliation with Crystallographic Data;222
12.15;15. Complementarity and Synergy of MD and ITC;224
12.16;16. Prospects;229
12.17;Acknowledgments;231
12.18;References;231
13;Chapter 6: Using Tryptophan Fluorescence to Measure the Stability of Membrane Proteins Folded in Liposomes;234
13.1;1. Introduction;235
13.2;2. Issues with Managing Light Scattering from Liposomes;236
13.3;3. Using Tryptophan Spectral Properties to Monitor Membrane Protein Folding into Liposomes;245
13.4;4. Choosing an Appropriate Tryptophan Spectral Property to Measure the Thermodynamic Stabilities of Folded Membrane Proteins..;250
13.5;5. Conclusions;252
13.6;6. Materials and Methods;254
13.7;Acknowledgments;255
13.8;References;255
14;Chapter 7: Non-B Conformations of CAG Repeats Using 2-Aminopurine;258
14.1;1. Introduction;259
14.2;2. Materials and Methods;261
14.3;3. Structure and Thermodynamics of Isolated and Integrated (CAG)8;268
14.4;4. Conclusions;274
14.5;Acknowledgments;274
14.6;References;274
15;Chapter 8: Disulfide Bond-Mediated Passenger Domain Stalling as a Structural Probe of Autotransporter Outer Membrane Secretio;278
15.1;1. Protein Secretion: An Essential Component of Bacterial Virulence;279
15.2;2. The Autotransporter Secretion Pathway;279
15.3;3. Overview of Cys-Loop Stalling;281
15.4;4. Architecture and Processing of AT Passenger Domains;281
15.5;5. Heterologous Passenger Domain Secretion;284
15.6;6. Selecting a Model Autotransporter for Cys-Loop Stalling;285
15.7;7. Disulfide Mediated Passenger Domain Stalling;286
15.8;8. Methods to Measure OM Secretion and Folding of the Stalled AT Passenger;289
15.9;9. Applications: Using Cys-Loop Stalling to Define the Mechanism of AT OM Secretion;293
15.10;References;294
16;Chapter 9: Strategies for the Thermodynamic Characterization of Linked Binding/Local Folding Reactions Within the Native Stat;298
16.1;1. Introduction;299
16.2;2. A Mutation Strategy to Amplify Locally Unfolded States;301
16.3;3. Thermodynamic Properties of Linked Folding and Binding Reactions;305
16.4;4. Strategies for Quantitative Interpretation of Measured Enthalpies for a Linked Folding and Binding System;310
16.5;5. Interplay of Local Mutational Effects, Global Stability, and Binding Affinity;313
16.6;6. Success of the Strategy in Preserving Structure;318
16.7;7. Comparison of Interaction Versus Entropy Based Mutation Strategy;319
16.8;8. How Similar Are Local and Global Unfolding?;321
16.9;9. Summary;324
16.10;References;325
17;Chapter 10: Fluorescence-Detected Sedimentation in Dilute and Highly Concentrated Solutions;328
17.1;1. Overview of AUC;329
17.2;2. Fluorescence Optics for the Ultracentrifuge;330
17.3;3. Advantages of AU-FDS;332
17.4;4. Sample Requirements for Fluorescence Detection;333
17.5;5. Applications of AU-FDS;338
17.6;6. Current Challenges for AU-FDS;343
17.7;7. Conclusion;346
17.8;References;347
18;Author Index;350
19;Subject Index;362
20;Color plate;370