Biothermodynamics, Part D

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ISBN: 9780123860033 | 0123860032
Cover: Hardcover
Copyright: 2/25/2011

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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.#xA0;This 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

Contributors	p. ix
Preface	p. xiii
Volumes in Series	p. xv
A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands	p. 1
Introduction	p. 2
Materials and Methods	p. 4
Results and Discussion	p. 8
Conclusions	p. 23
Acknowledgments	p. 24
References	p. 24
Thermodynamics of Biological Processes	p. 27
Introduction: Thermodynamics is Not Just for Dead Stuff	p. 28
States and Weights from the Boltzmann Rule	p. 29
Binding Reactions and Biological Thermodynamics	p. 33
The Unreasonable Effectiveness of Random-Walk Models	p. 52
Conclusions	p. 55
Acknowledgments	p. 56
References	p. 56
Protein Stability in the Presence of Cosolutes	p. 61
Introduction	p. 62
Isothermal Folding/Unfolding of Protein in the Presence of Stabilizing/Denaturing Osmolyte	p. 64
Isothermal Protein (Un)Folding in the Presence of Osmolyte Mixtures	p. 78
Osmolyte-Induced Unfolding at Variable Temperature	p. 86
Thermal Unfolding in the Presence of Osmolytes	p. 92
Where Do the Little Equations Come From?	p. 101
Acknowledgment	p. 121
References	p. 121
Small-Angle X-ray Scattering Studies of Peptide-Lipid Interactions Using the Mouse Paneth Cell ¿-Defensin Cryptdin-4	p. 127
Introduction	p. 128
X-Rays as Structural Probes of Biological Systems Under Biomimetic Conditions	p. 132
Preparation of Peptide-Lipid Complexes for X-Ray Measurements	p. 137
Summary	p. 145
Acknowledgments	p. 145
References	p. 145
Synergy of Molecular Dynamics and Isothermal Titration Calorimetry in Studies of Allostery	p. 151
Allostery	p. 152
Arginine Repressor	p. 154
Preparation for Simulations	p. 157
Sampling of States	p. 159
Equilibration	p. 160
Observing System Motions	p. 163
Correlated Motions	p. 164
Structural Features of Correlated Motions	p. 164
Arg Residues Promote Rotation and Oscillation	p. 167
Structural Correlates of Rotational Oscillation	p. 169
Single-Arginine Simulations	p. 169
Rotational Ensembles	p. 170
Energetic Contributions	p. 173
Reconciliation with Crystallographic Data	p. 177
Complementarity and Synergy of MD and ITC	p. 179
Prospects	p. 184
Acknowledgement	p. 186
References	p. 186
Using Tryptophan Fluorescence to Measure the Stability of Membrane Proteins Folded in Liposomes	p. 189
Introduction	p. 190
Issues with Managing Light Scattering from Liposomes	p. 191
Using Tryptophan Spectral Properties to Monitor Membrane Protein Folding into Liposomes	p. 200
Choosing an Appropriate Tryptophan Spectral Property to Measure the Thermodynamic Stabilities of Folded Membrane Proteins	p. 205
Conclusions	p. 207
Materials and Methods	p. 209
Acknowledgments	p. 210
References	p. 210
Non-B Conformations of CAG Repeats Using 2-Aminopurine	p. 213
Introduction	p. 214
Materials and Methods	p. 216
Structure and Thermodynamics of Isolated and Integrated (CAG)₈	p. 223
Conclusions	p. 229
Acknowledgments	p. 229
References	p. 229
Disulfide Bond-Mediated Passenger Domain Stalling as a Structural Probe of Autotransporter Outer Membrane Secretion In Vivo	p. 233
Protein Secretion: An Essential Component of Bacterial Virulence	p. 234
The Autotransporter Secretion Pathway	p. 234
Overview of Cys-Loop Stalling	p. 236
Architecture and Processing of AT Passenger Domains	p. 236
Heterologous Passenger Domain Secretion	p. 239
Selecting a Model Autotransporter for Cys-Loop Stalling	p. 240
Disulfide Mediated Passenger Domain Stalling	p. 241
Methods to Measure OM Secretion and Folding of the Stalled AT Passenger	p. 244
Applications: Using Cys-Loop Stalling to Define the Mechanism of AT OM Secretion	p. 248
References	p. 249
Strategies for the Thermodynamic Characterization of Linked Binding/Local Folding Reactions Within the Native State: Application to the LID Domain of Adenylate Kinase from Escherichia coli	p. 253
Introduction	p. 254
A Mutation Strategy to Amplify Locally Unfolded States	p. 256
Thermodynamic Properties of Linked Folding and Binding Reactions	p. 260
Strategies for Quantitative Interpretation of Measured Enthalpies for a Linked Folding and Binding System	p. 265
Interplay of Local Mutational Effects, Global Stability, and Binding Affinity	p. 268
Success of the Strategy in Preserving Structure	p. 273
Comparison of Interaction Versus Entropy Based Mutation Strategy	p. 274
How Similar Are Local and Global Unfolding?	p. 276
Summary	p. 279
References	p. 280
Fluorescence-Detected Sedimentation in Dilute and Highly Concentrated Solutions	p. 283
Overview of AUC	p. 284
Fluorescence Optics for the Ultracentrifuge	p. 285
Advantages of AU-FDS	p. 287
Sample Requirements for Fluorescence Detection	p. 288
Applications of AU-FDS	p. 293
Current Challenges for AU-FDS	p. 298
Conclusion	p. 301
References	p. 302
Author Index	p. 305
Subject Index	p. 317
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