Advances in protein chemistry and structural biology. Volume ninety two, Dynamics of proteins and nucleic acids / edited by Tatyana Karabencheva-Christova, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.

Format:

Book

Contributor:

Karabencheva-Christova, Tatyana, editor.

Series:

Advances in protein chemistry and structural biology ; v. 92.

Advances in protein chemistry and structural biology, 1876-1623 ; v. 92

Advances in protein chemistry and structural biology ; volume ninety two

Gale eBooks

Language:

English

Subjects (All):

Proteins.

Nucleic acids.

Physical Description:

1 online resource (x, 357 pages) : illustrations (some color).

Edition:

1st ed.

Place of Publication:

Oxford : Academic Press, 2013.

Language Note:

English

Summary:

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.Covers reviews of methodology and research in all aspects

Contents:

Front Cover; Dynamics of Proteins and Nucleic Acids; Copyright; Contents; Introduction to Dynamics of Proteins and Nucleic Acids; References; Chapter One: Drug-DNA Intercalation: From Discovery to the Molecular Mechanism; 1. Introduction; 1.1. History of intercalators; 1.2. Biological significance of intercalation process; 1.2.1. Clinical use of intercalators; 1.2.1.1. Anticancer compounds; 1.2.1.2. Antiparasitic compounds; 1.2.1.3. Antimicrobial agents; 1.2.2. Biological consequence; 1.2.2.1. Inhibition of DNA-dependent enzymes; 1.2.2.2. Frame-shift mutations; 1.2.2.3. DNA damage

1.3. Classification2. Structure and Dynamics of Intercalation; 2.1. Structural characterization; 2.1.1. Viscosity enhancement; 2.1.2. Sedimentation coefficient; 2.1.3. Autocardiograph; 2.1.4. Dynamic light scattering; 2.1.5. Increase in melting temperature; 2.1.6. X-ray technique; 2.1.7. Photophysical study; 2.2. Thermodynamic characterization; 2.2.1. Methods; 2.2.1.1. Equilibrium dialysis; 2.2.1.2. Spectroscopic (absorbance and fluorescence) titration analysis; 2.2.1.3. Surface plasmon resonance; 2.2.2. Isothermal titration calorimetry; 2.2.3. Outcome; 2.3. Kinetic characterization

2.3.1. Methods2.3.1.1. Temperature jump technique; 2.3.1.2. Pressure jump technique; 2.3.1.3. Stopped-flow technique; 2.3.1.4. Dissociation using sodium dodecyl sulphate micelle; 2.3.2. Outcome; 2.4. Theoretical and computational evidences; 2.4.1. Molecular mechanical studies; 2.4.2. Quantum chemical calculation; 3. Molecular Mechanism of Intercalation; 3.1. Methods used; 3.1.1. Umbrella sampling; 3.1.2. Metadynamics; 3.1.3. Well-tempered metadynamics; 3.2. Description of the CVs; 3.3. Simulation protocol; 3.4. Mechanism of intercalation; 4. Conclusion; Acknowledgment; References

Chapter Two: Ligand Docking Simulations by Generalized-Ensemble Algorithms1. Introduction; 2. Methods; 2.1. Replica-exchange method; 2.2. Multidimensional REM; 2.3. Principal component analysis; 3. Results; 4. Conclusions; Acknowledgments; References; Chapter Three: Conformational Dynamics of Single Protein Molecules Studied by Direct Mechanical Manipulation; 1. Introduction; 2. Mechanical Manipulation of Single Protein Molecules; 2.1. Optical tweezers; 2.1.1. Alternative, novel, and hybrid optical tweezers instruments; 2.1.2. Sample preparation; 2.2. Atomic force microscopy

3. Theoretical Models of Single-Molecule Force Spectroscopy3.1. Effect of force on the thermodynamics of a single-molecule reaction; 3.2. Effect of force on the kinetics of a single-molecule reaction; 3.3. Extracting kinetic parameters from force distributions; 3.4. Extracting thermodynamic parameters from nonequilibrium measurements; 3.5. Extracting kinetics and thermodynamic parameters from equilibrium fluctuations; 4. Biological Applications; 4.1. Mechanical processes in the cell; 4.2. Protein folding; 4.2.1. Folding pathways and the energy landscape

4.2.2. Molecular response to force, secondary structure, and topology

Notes:

Includes bibliographical references and indexes.

"ISSN: 1876-1623."

ISBN:

9780124116276

0124116272

OCLC:

881385079