The Resource Dynamics of proteins and nucleic acids, edited by Tatyana Karabencheva-Christova, (electronic resource)

Dynamics of proteins and nucleic acids, edited by Tatyana Karabencheva-Christova, (electronic resource)

Label
Dynamics of proteins and nucleic acids
Title
Dynamics of proteins and nucleic acids
Statement of responsibility
edited by Tatyana Karabencheva-Christova
Contributor
Subject
Genre
Language
  • eng
  • eng
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
Is Subseries of
Cataloging source
MiAaPQ
Dewey number
572.6
Illustrations
  • illustrations
  • charts
Index
index present
Language note
English
LC call number
QD431
LC item number
.D96 2013
Literary form
non fiction
Nature of contents
  • dictionaries
  • bibliography
http://library.link/vocab/relatedWorkOrContributorName
Karabencheva-Christova, Tatyana
Series statement
Advances in protein chemistry and structural biology,
Series volume
v. 92
http://library.link/vocab/subjectName
  • Proteins
  • Nucleic acids
  • Molecular dynamics
Label
Dynamics of proteins and nucleic acids, edited by Tatyana Karabencheva-Christova, (electronic resource)
Instantiates
Publication
Note
Description based upon print version of record
Bibliography note
Includes bibliographical references and indexes
Carrier category
online resource
Carrier category code
cr
Content category
text
Content type code
txt
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
Dimensions
unknown
Edition
1st ed.
Extent
1 online resource (368 p.)
Form of item
online
Isbn
9780124116276
Media category
computer
Media type code
c
Specific material designation
remote
System control number
  • (EBL)1361894
  • (OCoLC)862821083
  • (SSID)ssj0001156744
  • (PQKBManifestationID)11648166
  • (PQKBTitleCode)TC0001156744
  • (PQKBWorkID)11217196
  • (PQKB)11042527
  • (MiAaPQ)EBC1361894
  • (EXLCZ)992550000001110774
Label
Dynamics of proteins and nucleic acids, edited by Tatyana Karabencheva-Christova, (electronic resource)
Publication
Note
Description based upon print version of record
Bibliography note
Includes bibliographical references and indexes
Carrier category
online resource
Carrier category code
cr
Content category
text
Content type code
txt
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
Dimensions
unknown
Edition
1st ed.
Extent
1 online resource (368 p.)
Form of item
online
Isbn
9780124116276
Media category
computer
Media type code
c
Specific material designation
remote
System control number
  • (EBL)1361894
  • (OCoLC)862821083
  • (SSID)ssj0001156744
  • (PQKBManifestationID)11648166
  • (PQKBTitleCode)TC0001156744
  • (PQKBWorkID)11217196
  • (PQKB)11042527
  • (MiAaPQ)EBC1361894
  • (EXLCZ)992550000001110774

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