Computer Methods, Part C

Preface

Measurement and Analysis of Equilibrium Binding Titrations

1. Material Requirements for Binding Measurements

2. Monitoring a Binding Reaction

3. The Binding Equation and Its Relationship to Binding Measurements

4. Plotting and Analysis of Binding Data

5. Protein Concentration Is Important: Equilibrium Versus Stoichiometric Conditions

6. When Are Total and Free Ligand Concentrations Equal?

7. Deviations from Simple Binding

Macromolecular Competition Titration Method

1. Introduction

2. A Single Titration Curve: Some Simple Considerations of Possible Pitfalls

3. Quantitative Equilibrium Spectroscopic Titrations: Thermodynamic Bases

4. Nucleotide Binding to the RepA Protein of Plasmid RSF1010

5. Applying the Statistical Thermodynamic Model for the Nucleotide Binding to the RSF1010 RepA Protein Hexamer

6. Empirical Function Approach

7. MCT Method: General Considerations

8. Application of the MCT Method to the Base Specificity Problem in ASFV Pol X–ssDNA System

9. Application of MCT Method to Protein–ssDNA Lattice Binding Systems

10. Quantitative Analysis of the Binding of the E. coli DnaB Helicase to Unmodified Nucleic Acids Using the MCT Method

11. Direct Analysis of the Experimental Isotherm of Protein Ligand Binding to Two Competing Nucleic Acid Lattices

12. Using a Single Concentration of a Nonfluorescent Unmodified Nucleic Acid

13. Using Short Fluorescent Oligonucleotides in Competition with the Polymer Nucleic Acid

14. Conclusions

Acknowledgments

Analysis of PKR–RNA Interactions by Sedimentation Velocity

1. Introduction

2. Reagents and Cells

3. Experimental Design

4. Examples

5. Conclusions

Acknowledgments

Structural and Thermodynamic Analysis of PDZ–Ligand Interactions

Abbreviations

1. Introduction

2. Structural Studies of the Tiam1 PDZ Domain

3. Fluorescence Anisotropy Methods for Measuring the Energetics of PDZ–Ligand Interactions

4. Double-Mutant Cycle Analysis of PDZ-Binding Pockets

5. Peptide Evolution as a Tool for Probing PDZ Specificity

6. Conclusions

Acknowledgments

Thermodynamic Analysis of Metal Ion-Induced Protein Assembly

1. Introduction

2. Linked Equilibria—General Concepts

3. Experimental Approaches—Analytical Ultracentrifugation

4. Summary

Acknowledgments

Thermodynamic Dissection of Colicin Interactions

1. Introduction

2. DNase Domain–Immunity Protein Interactions

3. Receptor Binding

4. Mapping Binding Epitopes and Signaling Networks

5. Discussion

Energetics of Src Homology Domain Interactions in Receptor Tyrosine Kinase-Mediated Signaling

1. Introduction

2. Interactions of Src Homology 2 Domains

3. Recognition by the “Two-Pinned Plug”

4. Recognition by the β-Turn Motif

5. Selectivity Versus Specificity for SH2 Domain Interactions

6. Proline Sequence-Recognition Domains

7. Interactions of SH3 Domains

8. What Constitutes Specificity in SH3 Domain Interactions?

9. Selectivity in SH3 Domain Interactions

10. Interactions Through Multiple Domains

11. Conclusions

Structural and Functional Energetic Linkages in Allosteric Regulation of Muscle Pyruvate Kinase

1. Introduction

2. General Principles of Linked Multiequilibria Reactions

3. Functional Energetic Linkages in Allosteric Regulation of Rabbit Muscle Pyruvate Kinase

4. Functional Linkage Through Steady-State Kinetics

5. Structural Perturbations by Ligands

6. Functional Linkage Scheme of Allostery for RMPK

7. Functional Linkage Through Ligand Binding Measurements

8. Protein Structural Dynamics—Amide Hydrogen Exchange Monitored by FT-IR (HX-FT-IR)

9. Probing Interfacial Interactions

10. Summary Statement

Acknowledgments

Analysis of Free Energy Versus Temperature Curves in Protein Folding and Macromolecular Interactions

1. Stability Curves=Gibbs–Helmholtz Curves=ΔG Versus Temperature

2. Analysis of ΔG Versus Temperature in Protein Folding

3. Using Stability Curves to Compare Mesophilic and Thermophilic Protein Pairs

4. Temperature Dependence of Folding Enthalpies and Entropies

5. Analysis of ΔG Versus Temperature Data in Macromolecular Interactions

6. Fitting ΔH and ΔG Versus Temperature for a ΔΔCp

7. Examples of Potential Consequences of a Small ΔΔCp

Application of the Sequential n-Step Kinetic Mechanism to Polypeptide Translocases

1. Introduction

2. Single-Turnover Fluorescence Stopped-Flow Method to Monitor Polypeptide Translocation

3. Application of the Sequential n-Step Mechanism

4. Concluding Remarks

Acknowledgments

A Coupled Equilibrium Approach to Study Nucleosome Thermodynamics

1. Introduction

2. Salt-Mediated Nucleosome (Dis)Assembly

3. A Chaperone-Mediated Coupled Approach to Nucleosome Thermodynamics

4. Experimental Setup and Considerations

5. Data Analysis and Theory

6. Summary and Implications

Quantitative Methods for Measuring DNA Flexibility In Vitro and In Vivo

1. Introduction

2. DNA Polymer Theory

3. Ligase-Catalyzed DNA Cyclization Kinetics In Vitro

4. In Vivo Analysis of E. coli lac Repression Loops

Acknowledgments

Appendix A. R Code for j-Factor Experiments

Appendix B. R Code for lac Looping Experiments

Appendix C. Required Files for R scripts