| Contributors |
| Preface |
| Volumes in Series |
| A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands / Hui-Ting Lee ; Caroline Carr ; Hollie Siebler ; Lela Waters ; Irine Khutsishvili ; Fany Iseka ; Brian Domack ; Chris M. Olsen ; Luis A. Marky1： |
| Introduction |
| Materials and Methods / 2： |
| Results and Discussion / 3： |
| Conclusions / 4： |
| Acknowledgments |
| References |
| Thermodynamics of Biological Processes / Hernan G. Garcia ; Jane Kondev ; Nigel Orme ; Julie A. Theriot ; Rob Phillips |
| Introduction: Thermodynamics is Not Just for Dead Stuff |
| States and Weights from the Boltzmann Rule |
| Binding Reactions and Biological Thermodynamics |
| The Unreasonable Effectiveness of Random-Walk Models |
| Protein Stability in the Presence of Cosolutes / Luis Marcelo F. Holthauzen ; Matthew Auton ; Mikhail Sinev ; Jörg Rösgen5： |
| Isothermal Folding/Unfolding of Protein in the Presence of Stabilizing/Denaturing Osmolyte |
| Isothermal Protein (Un)Folding in the Presence of Osmolyte Mixtures |
| Osmolyte-Induced Unfolding at Variable Temperature |
| Thermal Unfolding in the Presence of Osmolytes |
| Where Do the Little Equations Come From? / 6： |
| Acknowledgment |
| Small-Angle X-ray Scattering Studies of Peptide-Lipid Interactions Using the Mouse Paneth Cell ?-Defensin Cryptdin-4 / Abhijit Mishra ; Kenneth P. Tai ; Nathan W. Schmidt ; André J. Ouellette ; Gerard C. L. Wong |
| X-Rays as Structural Probes of Biological Systems Under Biomimetic Conditions |
| Preparation of Peptide-Lipid Complexes for X-Ray Measurements |
| Summary |
| Synergy of Molecular Dynamics and Isothermal Titration Calorimetry in Studies of Allostery / Rebecca Strawn ; Thomas Stockner ; Milan Melichercik ; Lihua Jin ; Wei-Feng Xue ; Jannette Carey ; Rüdiger Ettrich |
| Allostery |
| Arginine Repressor |
| Preparation for Simulations |
| Sampling of States |
| Equilibration |
| Observing System Motions |
| Correlated Motions / 7： |
| Structural Features of Correlated Motions / 8： |
| Arg Residues Promote Rotation and Oscillation / 9： |
| Structural Correlates of Rotational Oscillation / 10： |
| Single-Arginine Simulations / 11： |
| Rotational Ensembles / 12： |
| Energetic Contributions / 13： |
| Reconciliation with Crystallographic Data / 14： |
| Complementarity and Synergy of MD and ITC / 15： |
| Prospects / 16： |
| Acknowledgement |
| Using Tryptophan Fluorescence to Measure the Stability of Membrane Proteins Folded in Liposomes / C. Preston Moon ; Karen G. Fleming |
| Issues with Managing Light Scattering from Liposomes |
| Using Tryptophan Spectral Properties to Monitor Membrane Protein Folding into Liposomes |
| Choosing an Appropriate Tryptophan Spectral Property to Measure the Thermodynamic Stabilities of Folded Membrane Proteins |
| Non-B Conformations of CAG Repeats Using 2-Aminopurine / Natalya N. Degtyareva ; Jeffrey T. Petty |
| Disulfide Bond-Mediated Passenger Domain Stalling as a Structural Probe of Autotransporter Outer Membrane Secretion In Vivo / Jonathan P. Renn ; Patricia L. Clark |
| Protein Secretion: An Essential Component of Bacterial Virulence |
| The Autotransporter Secretion Pathway |
| Overview of Cys-Loop Stalling |
| Architecture and Processing of AT Passenger Domains |
| Heterologous Passenger Domain Secretion |
| Selecting a Model Autotransporter for Cys-Loop Stalling |
| Disulfide Mediated Passenger Domain Stalling |
| Methods to Measure OM Secretion and Folding of the Stalled AT Passenger |
| Applications: Using Cys-Loop Stalling to Define the Mechanism of AT OM Secretion |
| 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 / Travis P. Schrank ; W. Austin Elam ; Jing Li ; Vincent J. Hilser |
| A Mutation Strategy to Amplify Locally Unfolded States |
| Thermodynamic Properties of Linked Folding and Binding Reactions |
| Strategies for Quantitative Interpretation of Measured Enthalpies for a Linked Folding and Binding System |
| Interplay of Local Mutational Effects, Global Stability, and Binding Affinity |
| Success of the Strategy in Preserving Structure |
| Comparison of Interaction Versus Entropy Based Mutation Strategy |
| How Similar Are Local and Global Unfolding? |
| Fluorescence-Detected Sedimentation in Dilute and Highly Concentrated Solutions / Jonathan S. Kingsbury ; Thomas M. Laue |
| Overview of AUC |
| Fluorescence Optics for the Ultracentrifuge |
| Advantages of AU-FDS |
| Sample Requirements for Fluorescence Detection |
| Applications of AU-FDS |
| Current Challenges for AU-FDS |
| Conclusion |
| Author Index |
| Subject Index |
