| Contributors |
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ix | |
| Preface |
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xiii | |
| Volumes in Series |
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xv | |
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1 A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands |
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1 | (26) |
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2 | (2) |
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4 | (4) |
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8 | (15) |
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23 | (1) |
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24 | (1) |
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24 | (3) |
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2 Thermodynamics of Biological Processes |
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27 | (34) |
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1 Introduction: Thermodynamics is Not Just for Dead Stuff |
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28 | (1) |
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2 States and Weights from the Boltzmann Rule |
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29 | (4) |
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3 Binding Reactions and Biological Thermodynamics |
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33 | (19) |
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4 The Unreasonable Effectiveness of Random-Walk Models |
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52 | (3) |
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55 | (1) |
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56 | (1) |
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56 | (5) |
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3 Protein Stability in the Presence of Cosolutes |
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61 | (66) |
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Luis Marcelo F. Holthauzen |
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62 | (2) |
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2 Isothermal Folding/Unfolding of Protein in the Presence of Stabilizing/Denaturing Osmolyte |
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64 | (14) |
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3 Isothermal Protein (Un)Folding in the Presence of Osmolyte Mixtures |
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78 | (8) |
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4 Osmolyte-Induced Unfolding at Variable Temperature |
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86 | (6) |
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5 Thermal Unfolding in the Presence of Osmolytes |
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92 | (9) |
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6 Where Do the Little Equations Come From? |
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101 | (20) |
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121 | (1) |
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121 | (6) |
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4 Small-Angle X-ray Scattering Studies of Peptide-Lipid Interactions Using the Mouse Paneth Cell α-Defensin Cryptdin-4 |
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127 | (24) |
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128 | (4) |
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2 X-Rays as Structural Probes of Biological Systems Under Biomimetic Conditions |
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132 | (5) |
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3 Preparation of Peptide-Lipid Complexes for X-Ray Measurements |
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137 | (8) |
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145 | (1) |
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145 | (1) |
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145 | (6) |
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5 Synergy of Molecular Dynamics and Isothermal Titration Calorimetry in Studies of Allostery |
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151 | (38) |
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152 | (2) |
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154 | (3) |
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3 Preparation for Simulations |
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157 | (2) |
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159 | (1) |
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160 | (3) |
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6 Observing System Motions |
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163 | (1) |
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163 | (1) |
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8 Structural Features of Correlated Motions |
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164 | (3) |
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9 Arg Residues Promote Rotation and Oscillation |
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167 | (2) |
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10 Structural Correlates of Rotational Oscillation |
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169 | (1) |
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11 Single-Arginine Simulations |
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169 | (1) |
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170 | (3) |
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13 Energetic Contributions |
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173 | (4) |
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14 Reconciliation with Crystallographic Data |
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177 | (2) |
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15 Complementarity and Synergy of MD and ITC |
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179 | (5) |
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184 | (2) |
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186 | (1) |
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186 | (3) |
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6 Using Tryptophan Fluorescence to Measure the Stability of Membrane Proteins Folded in Liposomes |
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189 | (24) |
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190 | (1) |
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2 Issues with Managing Light Scattering from Liposomes |
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191 | (9) |
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3 Using Tryptophan Spectral Properties to Monitor Membrane Protein Folding into Liposomes |
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200 | (5) |
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4 Choosing an Appropriate Tryptophan Spectral Property to Measure the Thermodynamic Stabilities of Folded Membrane Proteins |
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205 | (2) |
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207 | (2) |
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209 | (1) |
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210 | (1) |
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210 | (3) |
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7 Non-B Conformations of CAG Repeats Using 2-Aminopurine |
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213 | (20) |
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214 | (2) |
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216 | (7) |
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3 Structure and Thermodynamics of Isolated and Integrated (CAG)8 |
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223 | (6) |
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229 | (1) |
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229 | (1) |
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229 | (4) |
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8 Disulfide Bond-Mediated Passenger Domain Stalling as a Structural Probe of Autotransporter Outer Membrane Secretion In Vivo |
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233 | (20) |
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1 Protein Secretion: An Essential Component of Bacterial Virulence |
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234 | (1) |
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2 The Autotransporter Secretion Pathway |
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234 | (2) |
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3 Overview of Cys-Loop Stalling |
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236 | (1) |
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4 Architecture and Processing of AT Passenger Domains |
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236 | (3) |
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5 Heterologous Passenger Domain Secretion |
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239 | (1) |
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6 Selecting a Model Autotransporter for Cys-Loop Stalling |
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240 | (1) |
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7 Disulfide Mediated Passenger Domain Stalling |
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241 | (3) |
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8 Methods to Measure OM Secretion and Folding of the Stalled AT Passenger |
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244 | (4) |
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9 Applications: Using Cys-Loop Stalling to Define the Mechanism of AT OM Secretion |
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248 | (1) |
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249 | (4) |
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9 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 |
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253 | (30) |
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254 | (2) |
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2 A Mutation Strategy to Amplify Locally Unfolded States |
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256 | (4) |
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3 Thermodynamic Properties of Linked Folding and Binding Reactions |
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260 | (5) |
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4 Strategies for Quantitative Interpretation of Measured Enthalpies for a Linked Folding and Binding System |
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265 | (3) |
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5 Interplay of Local Mutational Effects, Global Stability, and Binding Affinity |
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268 | (5) |
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6 Success of the Strategy in Preserving Structure |
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273 | (1) |
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7 Comparison of Interaction Versus Entropy Based Mutation Strategy |
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274 | (2) |
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8 How Similar Are Local and Global Unfolding? |
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276 | (3) |
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279 | (1) |
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280 | (3) |
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10 Fluorescence-Detected Sedimentation in Dilute and Highly Concentrated Solutions |
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283 | (22) |
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284 | (1) |
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2 Fluorescence Optics for the Ultracentrifuge |
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285 | (2) |
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287 | (1) |
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4 Sample Requirements for Fluorescence Detection |
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288 | (5) |
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293 | (5) |
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6 Current Challenges for AU-FDS |
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298 | (3) |
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301 | (1) |
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302 | (3) |
| Author Index |
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305 | (12) |
| Subject Index |
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317 | |
