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Published continuously since 1944, Advances in Protein Chemistry and Structural Biology has been a continuous, essential resource for protein chemists. Covering reviews of method… Read more
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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
TK