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El. knyga: Biothermodynamics, Part B

Edited by Gary K. Ackers (Washington University School of Medicine, St. Louis, Mo, USA), Edited by Jo M. Holt (Washington University Medical Center, St. Louis, MO, USA), Edited by Michael L. Johnson (University of Virginia Health Sciences Center, Charlottesville, USA)

Formatas: EPUB+DRM
Serija: Methods in Enzymology
Išleidimo metai: 11-Nov-2009
Leidėjas: Academic Press Inc
Kalba: eng
ISBN-13: 9780080887814

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Formatas: EPUB+DRM
Serija: Methods in Enzymology
Išleidimo metai: 11-Nov-2009
Leidėjas: Academic Press Inc
Kalba: eng
ISBN-13: 9780080887814

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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. These methods look to answer: What are the sources of energy that drive the function? Which of the pathways are of biological significance? As the base of macromolecular structures continues to expand through powerful techniques of molecular biology, such as X-ray crystal data and spectroscopy methods, the importance of tested and reliable methods for answering these questions will continue to expand as well. 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

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This volume presents robust and modern thermodynamic methods for determining the "functional energetics" of macromolecular structures with their biological functions.

Contributors

xiii

Preface

xix

Volumes in Series

xxi

Using NMR-Detected Backbone Amide 1H Exchange to Assess Macromolecular Crowding Effects on Globular-Protein Stability

(18)

Andrew C. Miklos

Conggang Li

Gary J. Pielak

Introduction

(1)

Globular Protein Stability

(1)

Mechanism and Limits of Amide 1H Exchange

(3)

Requirements for Candidate Systems

(2)

Preliminary Experiments

(6)

A Protocol for Amide 1H Exchange

(1)

Summary and Future Directions

(4)

Acknowledgments

(1)

References

(3)

Fluorescence Spectroscopy in Thermodynamic and Kinetic Analysis of pH-Dependent Membrane Protein Insertion

(24)

Alexey S. Ladokhin

Introduction: Co-Translational Versus Post-Translational Membrane Protein Insertion

(1)

Challenges of Thermodynamic Analysis of Membrane Protein Folding/Insertion

(1)

FCS and Protein---Membrane Interactions

(5)

Thermodynamic Schemes for Analysis of Membrane Partitioning

(4)

Kinetic Analysis of Membrane Protein Insertion

(6)

Perspectives: Annexin B12 as a Model for Thermodynamic and Kinetic Analysis of Membrane Protein Insertion, Folding and Misfolding

(5)

Acknowledgments

(1)

References

(3)

Evaluating the Energy-Dependent ``Binding'' in the Early Stage of Protein Import into Chloroplasts

(22)

Mitsuru Akita

Hitoshi Inoue

Introduction

(1)

The In Vitro Chloroplastic Import Assay Using Recombinant Precursor Proteins

(8)

Limited Proteolysis of Docked Precursor Proteins

(6)

The Behavior of Transit Peptide During the Transition

(3)

Conclusions

(3)

Acknowledgments

(1)

References

(3)

Use of DNA Length Variation to Detect Periodicities in Positively Cooperative, Nonspecific Binding

(18)

Manana Melikishvili

Lance M. Hellman

Michael G. Fried

Introduction

(2)

Protein and DNA Preparations

(1)

Stoichiometry Analyses

(7)

Affinity and Cooperativity as Functions of DNA Length

(8)

Acknowledgments

(1)

References

(5)

The Impact of Ions on Allosteric Functions in Human Liver Pyruvate Kinase

(26)

Aron W. Fenton

Aileen Y. Alontaga

Introduction

(2)

General Strategy to Assess Allosteric Coupling

(2)

PYK Assay

(3)

Buffers

(2)

Divalent Cation

(2)

Monovalent Cation

(5)

Anion

100

(3)

Concluding Remarks

103

(6)

Acknowledgments

105

(1)

References

105

(4)

Conformational Stability of Cytochrome c Probed by Optical Spectroscopy

109

(46)

Reinhard Schweitzer-Stenner

Andrew Hagarman

Daniel Verbaro

Jonathan B. Soffer

Introduction

110

(3)

Basic Theory of Absorption and Circular Dichroism Spectroscopy

113

(4)

Secondary Structure Analysis of Cytochrome c Using Ultra-Violet Circular Dichroism Spectroscopy

117

(4)

Visible CD and Absorption Spectroscopy of Native Cytochrome c

121

(10)

Nonnative States of Ferricytochrome c Probed by Visible CD and Absorption Spectroscopy

131

(17)

Summary and Outlook

148

(7)

References

149

(6)

Examining Ion Channel Properties Using Free-Energy Methods

155

(24)

Carmen Domene

Simone Furini

Introduction

156

(1)

Free-Energy Calculations

157

(2)

Thermodynamic Integration

159

(1)

Free-Energy Perturbation

160

(2)

Umbrella Sampling

162

(2)

Adaptive Biasing Force

164

(3)

Matadynamics

167

(2)

Applications of Free-Energy Methods to Study Ion Channel Properties

169

(5)

Conclusions and Future Outlook

174

(5)

Acknowledgments

175

(1)

References

175

(4)

Examining Cooperative Gating Phenomena in Voltage-Dependent Potassium Channels: Taking the Energetic Approach

179

(32)

Ofer Yifrach

Nitzan Zandany

Tzilhav Shem-Ad

Introduction

180

(1)

High-Order Thermodynamic Mutant Cycle Coupling Analysis

181

(7)

The Voltage-Activated Potassium Channel Allosteric Model System

188

(5)

Deriving a Hill Coefficient for Assessing Cooperativity in Voltage-Dependent Ion Channels

193

(3)

Direct Analysis of Cooperativity in Multisubunit Allosteric Proteins

196

(6)

Long-Range Energetic Coupling Mediated Through Allosteric Communication Trajectories

202

(5)

Concluding Remarks

207

(4)

Acknowledgments

207

(1)

References

207

(4)

Thermal Stability of Collagen Triple Helix

211

(22)

Yujia Xu

Introduction

212

(2)

Methods

214

(19)

References

231

(2)

Electrostatic Contributions to the Stabilities of Native Proteins and Amyloid Complexes

233

(26)

Sarah R. Sheftic

Robyn L. Croke

Jonathan R. LaRochelle

Andrei T. Alexandrescu

Introduction

234

(2)

Practical Aspects of pKa Measurements by NMR

236

(4)

Interpreting pKa Values in Terms of Stability

240

(1)

Importance of the Reference (Unfolded) State

240

(1)

Results from Globular Proteins

240

(1)

Results from Coiled Coils

241

(1)

Comparison of NMR and Crystallographic Results

242

(1)

Comparison of NMR and Mutagenesis: Nonadditivity of Ion Pairs

243

(1)

Improving Structure-Based Modeling of pKa Values

244

(1)

Results with Micelle-Bound Proteins

245

(4)

Results from Fibrillization Kinetics

249

(4)

Conclusion

253

(6)

Acknowledgments

254

(1)

References

254

(5)

Kinetics of Allosteric Activation

259

(14)

Enrico Di Cera

Linkage

259

(2)

Allosteric Activation at Steady State

261

(5)

Different Types of Activation (Type la, Type Ib, and Type II)

266

(3)

Concluding Remarks

269

(4)

Acknowledgment

270

(1)

References

270

(3)

Thermodynamics of the Protein Translocation

273

(20)

Alexej Kedrov

Tanneke den Blaauwen

Arnold J. M. Driessen

Introduction

274

(4)

Example 1: SecA Nucleotide Binding

278

(5)

Example 2: Probing SecB: Substrate Interactions

283

(5)

Concluding Remarks

288

(5)

References

289

(4)

Thermodynamic Analysis of the Structure---Function Relationship in the Total DNA-Binding Site of Enzyme---DNA Complexes

293

(32)

Wlodzimierz Bujalowski

Maria J. Jezewska

Introduction

294

(2)

Thermodynamic Bases of Quantitative Equilibrium Spectroscopic Titrations

296

(6)

Anatomy of the Total DNA-Binding Site in the PriA Helicase-ssDNA Complex

302

(15)

Structure-Function Relationship in the Total ssDNA-Binding Site of the DNA Repair Pol X From ASFV

317

(8)

Acknowledgments

322

(1)

References

322

(3)

Equilibrium and Kinetic Approaches for Studying Oligomeric Protein Folding

325

(34)

Lisa M. Gloss

Introduction

326

(1)

Methods to Monitor Folding and Association

327

(9)

Equilibrium Studies

336

(7)

Kinetic Studies

343

(16)

Acknowledgments

354

(1)

References

354

(5)

Methods for Quantifying T cell Receptor Biding Affinities and Thermodynamics

359

(24)

Kurt H. Piepenbrink

Brian E. Gloor

Kathryn M. Armstrong

Brian M. Baker

Introduction

360

(2)

Isothermal Titration Calorimetry of TCR---Peptide/MHC Interactions

362

(5)

Surface Plasmon Resonance Studies of TCR---Peptide/MHC Interactions

367

(6)

Fluorescence Anisotropy as a Tool for Characterizing TCR---Peptide/MHC Interactions

373

(5)

Concluding Remarks

378

(5)

Acknowledgments

378

(1)

References

378

(5)

Thermodynamic and Kinetic Analysis of Bromodomain---Histone Interactions

383

(26)

Martin Thompson

Introduction

384

(1)

Fluorescence Anisotropy Theory and Concepts

384

(2)

Developing Binding Models for the Analysis of Fluorescence Anisotropy Data

386

(4)

Experimental Considerations in Designing Fluorescence Anisotropy Assays

390

(1)

Preparation of Histone and Bromodomain Samples

391

(1)

Fluorescence Anisotropy Measurements

392

(3)

Kinetic Analysis

395

(4)

Determination of Thermodynamic Parameters

399

(1)

Thermodynamic Measurements

400

(3)

Developing a Binding Model

403

(2)

Concluding Remarks

405

(4)

Acknowledgments

405

(1)

References

405

(4)

Thermodynamics of 2-Cys Peroxiredoxin Assembly Determined by Isothermal Titration Calorimetry

409

(22)

Sergio Barranco-Medina

Karl-Josef Dietz

Introduction

410

(2)

Dimer-Decamer Equilibrium

412

(3)

Isothermal Titration Calorimetry---General Concepts

415

(1)

ITC Dilution Experiments

416

(2)

Material and Instruments

418

(1)

Experimental Procedure

418

(5)

Results, Data Analysis, and Discussion

423

(5)

Conclusions

428

(3)

Acknowledgments

428

(1)

References

428

(3)

Protein---Lipid Interactions: Role of Membrane Plasticity and Lipid Specificity on Peripheral Protein Interactions

431

(24)

Jesse Murphy

Kristofer Knutson

Anne Hinderliter

Introduction

432

(1)

Defining Protein---Lipid Interactions

433

(1)

Selective Partitioning and Lipid Activities

434

(1)

Protein---Protein Interactions at the Membrane Surface

435

(2)

Measuring Protein---Lipid Interactions

437

(2)

Modeling of Protein---Lipid Interactions

439

(9)

Synopsis

448

(7)

Acknowledgments

450

(1)

References

451

(4)

Predicting pKa Values with Continuous Constant pH Molecular Dynamics

455

(22)

Jason A. Wallace

Jana K. Shen

Introduction

456

(1)

Theoretical Methods for pKa Predictions

457

(8)

Predicting Protein pKas with REX---CPHMD Simulations

465

(5)

Conclusions

470

(7)

Acknowledgment

471

(1)

References

471

(6)

Unfolding Thermodynamics of DNA Intramolecular Complexes Involving Joined Triple- and Double-Hellcal Motifs

477

(26)

Irine Khutsishvili

Sarah Johnson

Hui-Ting Lee

Luis A. Marky

Introduction

478

(3)

Materials and Methods

481

(4)

Results and Discussion

485

(14)

Conclusions

499

(4)

Acknowledgments

499

(1)

References

500

(3)

Thermodynamics and Conformational Change Governing Domain---Domain Interactions of Calmodulin

503

(24)

Susan E. O'Donnell

Rhonda A. Newman

Travis J. Witt

Rainbo Hultman

John R. Froehlig

Adam P. Christensen

Madeline A. Shea

Introduction

504

(3)

Overexpression and Purification of rCaM Fragments

507

(1)

Calcium-Binding Properties of N-Domain CaM Fragments

507

(5)

Tertiary Constraints of N-Domain CaM Fragments

512

(4)

Tertiary Conformation of N-Domain CaM Fragments

516

(3)

High-Resolution Studies of N-Domain CaM Fragments

519

(3)

Conclusions

522

(5)

Acknowledgments

524

(1)

References

525

(2)

Use of Pressure Perturbation Calorimetry to Characterize the Volumetric Properties of Proteins

527

(22)

Katrina L. Schweiker

George I. Makhatadze

Introduction

528

(3)

Determination of the Coefficient of Thermal Expansion (αpr) Using PPC

531

(2)

Sample Preparation

533

(2)

Derivation of a Two-State Model for Analysis of PPC Data

535

(4)

Practical Considerations

539

(6)

Implications of Two-State Model for Future PPC Experiments

545

(4)

References

545

(4)

Solvent Denaturation of Proteins and Interpretations of the m Value

549

(18)

J. Martin Scholtz

Gerald R. Grimsley

C. Nick Pace

Introduction

549

(1)

Protein Unfolding or Denaturation

550

(5)

Linear Extrapolation Method

555

(1)

ΔG(H2O): Conformational Stability

556

(2)

The m Value

558

(4)

Concluding Remarks

562

(5)

Acknowledgments

563

(1)

References

563

(4)

Measuring Cotranslational Folding of Nascent Polypeptide Chains on Ribosomes

567

(24)

Patricia L. Clark

Krastyu G. Ugrinov

Introduction

568

(2)

Translation and the Ribosome: Nascent Chain (RNC) Complex

570

(2)

General Approaches for Generating Stalled RNC Complexes

572

(5)

Methods for Preparing RNC Complexes

577

(2)

Biophysical Studies with RNC Complexes

579

(4)

Measuring Nascent Chain Cotranslational Folding and Rigidity by Limited Protease Digestion

583

(1)

Future Directions

584

(7)

References

585

(6)

Author Index

591

(12)

Subject Index

603

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