Dynamics of Proteins and Nucleic Acids - 1st Edition - ISBN: 9780124116368, 9780124116276

Dynamics of Proteins and Nucleic Acids, Volume 92

1st Edition

Serial Volume Editors: Tatyana Karabencheva-Christova
eBook ISBN: 9780124116276
Hardcover ISBN: 9780124116368
Imprint: Academic Press
Published Date: 1st September 2013
Page Count: 368
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Table of Contents

Introduction to Dynamics of Proteins and Nucleic Acids


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



Chapter Two. Ligand Docking Simulations by Generalized-Ensemble Algorithms

1 Introduction

2 Methods

3 Results

4 Conclusions



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


1 Introduction

2 Mechanical Manipulation of Single Protein Molecules

3 Theoretical Models of Single-Molecule Force Spectroscopy

4 Biological Applications

5 Future Perspectives



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



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



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



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


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



Author Index

Subject Index


Published continuously since 1944, Advances in Protein Chemistry and Structural Biology has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics.

Key Features

  • Covers reviews of methodology and research in all aspects of protein chemistry
  • Brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics


Biochemists, biophysicists, cell biologists, protein chemists, structural geneticists, and structural biologists


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© Academic Press 2013
Academic Press
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"The authority, originality, and editing of the reviews are first class." -- NATURE

Ratings and Reviews

About the Serial Volume Editors

Tatyana Karabencheva-Christova Serial Volume Editor

Dr. Tatyana Karabencheva-Christova works at the Department of Applied Sciences, University of Northumbria, UK.

Affiliations and Expertise

Northumbria University, UK