Dynamics of Proteins and Nucleic Acids

Introduction to Dynamics of Proteins and Nucleic Acids

References

Chapter One. Drug–DNA Intercalation: From Discovery to the Molecular Mechanism

1 Introduction

2 Structure and Dynamics of Intercalation

3 Molecular Mechanism of Intercalation

4 Conclusion

Acknowledgment

References

Chapter Two. Ligand Docking Simulations by Generalized-Ensemble Algorithms

1 Introduction

2 Methods

3 Results

4 Conclusions

Acknowledgments

References

Chapter Three. Conformational Dynamics of Single Protein Molecules Studied by Direct Mechanical Manipulation

Abbreviations

1 Introduction

2 Mechanical Manipulation of Single Protein Molecules

3 Theoretical Models of Single-Molecule Force Spectroscopy

4 Biological Applications

5 Future Perspectives

Acknowledgments

References

Chapter Four. Generation of Ligand Specificity and Modes of Oligomerization in β-Prism I Fold Lectins

1 Introduction

2 Setting the Stage: Issues Addressed

3 β-Prism I Fold Lectins: The Basics

4 Available Structures and Relationships Among them

5 Protein–Carbohydrate Interactions

6 Plasticity of the Molecule: A Case Study Primarily Involving Jacalin

7 Variability in Quaternary Association

8 Conclusions

Acknowledgments

References

Chapter Five. Conformational Changes of Enzymes and DNA in Molecular Dynamics: Influenced by pH, Temperature, and Ligand

1 Introduction

2 CpHMD Simulations on Insect OBPs

3 Thermal Stabilization of Hyperthermophilic Protein Sso7d and Cren7 Complex with DNA

4 Substrate Selectivity and Major Active-Site Access Channels of Human Cytochrome P4507B1

5 Summary and Conclusion

Acknowledgments

References

Chapter Six. Protein Functional Dynamics in Multiple Timescales as Studied by NMR Spectroscopy

1 Functional Dynamics and NMR

2 Examples of Functional Dynamics

3 Concluding Remarks

Acknowledgments

References

Chapter Seven. Protein–DNA Electrostatics: Toward a New Paradigm for Protein Sliding

1 Introduction: The Search of Target Sequences

2 Protein Diffusion in the Cell

3 Diffusion Along the DNA: What Role for the Sequence?

4 Electrostatics: The DNA–Protein Interaction

5 Theoretical Approach

6 Toward a New Paradigm for the Target Search Process

References

Chapter Eight. Structural and Dynamical Aspects of HIV-1 Protease and Its Role in Drug Resistance

1 Introduction

2 HIV Protease

3 Side Effects and Resistance of Protease Inhibitors

4 Protein Dynamics

5 Computational Simulation Studies

6 HIV-pr Conformation and Dynamics

7 Future Perspectives

8 Conclusion

Acknowledgment

References

Author Index

Subject Index