Dynamics of Proteins and Nucleic Acids

Dynamics of Proteins and Nucleic Acids

1st Edition - August 14, 2013

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  • Editor: Tatyana Karabencheva-Christova
  • Hardcover ISBN: 9780124116368
  • eBook ISBN: 9780124116276

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Description

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

Readership

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

Table of Contents

  • 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

Product details

  • No. of pages: 368
  • Language: English
  • Copyright: © Academic Press 2013
  • Published: August 14, 2013
  • Imprint: Academic Press
  • Hardcover ISBN: 9780124116368
  • eBook ISBN: 9780124116276

About the Serial Volume Editor

Tatyana Karabencheva-Christova

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

Affiliations and Expertise

Department of Chemistry, Michigan Technological University, Houghton, MI, USA

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