Analytical Ultracentrifugation - 1st Edition - ISBN: 9780128029084, 9780128029091

Analytical Ultracentrifugation, Volume 562

1st Edition

Serial Volume Editors: James Cole
eBook ISBN: 9780128029091
Hardcover ISBN: 9780128029084
Imprint: Academic Press
Published Date: 24th September 2015
Page Count: 588
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Table of Contents

  • Preface
  • Chapter One: Next-Generation AUC Adds a Spectral Dimension: Development of Multiwavelength Detectors for the Analytical Ultracentrifuge
    • Abstract
    • 1 Introduction
    • 2 Development of MWL Absorbance Detectors
    • 3 Hardware and Control System of Second-Generation MWL Detectors
    • 4 MWL Data From AUC
    • 5 Data Visualization and Experimental Results
    • 6 Discussion
    • 7 Summary and General Discussion of the Impacts of MWL AUC Data in the Field of Biopolymers
    • Acknowledgments
    • Supplemental Information
  • Chapter Two: Next-Generation AUC: Analysis of Multiwavelength Analytical Ultracentrifugation Data
    • Abstract
    • 1 Introduction
    • 2 Computational Treatment of Multiwavelength Data
    • 3 Applications
    • 4 Discussion
    • 5 Conclusion
    • Acknowledgments
  • Chapter Three: Sedimentation Velocity: A Classical Perspective
    • Abstract
    • 1 Early History
    • 2 Irreversible Thermodynamics
    • 3 Sedimentation Velocity
    • 4 Balanced Forces in Diffusion
    • 5 Balanced Forces in Sedimentation
    • 6 Derivation of the Lamm Equation
    • 7 Heterogeneous Paucidisperse Systems
    • 8 Nonideal Systems
    • 9 Interacting Systems
    • 10 Solutions of the Lamm Equation
    • 11 Equipment and Optical Systems
    • 12 Sedimentation Velocity Experimental Design
    • Acknowledgments
  • Chapter Four: Hydrodynamic Modeling and Its Application in AUC
    • Abstract
    • 1 Introduction
    • 2 AUC and Hydrodynamics
    • 3 The Hydration Issue
    • 4 Segmental Flexibility and Intrinsically Disordered Structures
    • 5 Available Programs for Rigid Body HM
    • 6 Comparing the Performance of Various Methods
    • 7 A Step-by-Step Guide to Performing Correct HM Using Atomic Coordinates
    • 8 Selected Literature Examples
    • 9 Concluding Remarks
  • Chapter Five: Calculations and Publication-Quality Illustrations for Analytical Ultracentrifugation Data
    • Abstract
    • 1 Introduction
    • 2 General Features of GUSSI
    • 3 Utility Functions of GUSSI
    • 4 Summary
    • Acknowledgments
  • Chapter Six: Sedimentation Equilibrium Analysis of ClpB Self-Association in Diluted and Crowded Solutions
    • Abstract
    • 1 Introduction
    • 2 Experimental Approaches and Analysis
    • 3 Summary of Experimental Results
    • 4 ClpB Association Equilibrium and Disaggregase Activity
    • 5 Concluding Remarks
    • Acknowledgments
  • Chapter Seven: Analysis of Linked Equilibria
    • Abstract
    • 1 Introduction
    • 2 Determination of Ln,0 for an Assembling System
    • 3 Global Fitting of Sedimentation Velocity Data as a Function of Protein Concentration Kinetic Considerations
    • 4 Global Analysis Using the 1-2-4-6 Model with Rapid Dissociating Oligomers
    • 5 Global Analysis Using the 1-2-4-6 Model with Slow Dissociation of Oligomers
    • 6 Global Analysis with Rate Constants in the Detectable Range
    • 7 Conclusions
  • Chapter Eight: Elucidating Complicated Assembling Systems in Biology Using Size-and-Shape Analysis of Sedimentation Velocity Data
    • Abstract
    • 1 Techniques for Studying Macromolecular Mixtures
    • 2 An Overview of the Standard Sedimentation Coefficient Distribution Approach
    • 3 Two-Dimensional Size-and-Shape Analysis
    • 4 Case Study: Cyclic GMP-AMP Synthase Oligomerization
    • 5 Case Study: IRF-3 Phosphorylation by TBK-1
    • 6 Conclusions
    • Acknowledgments
  • Chapter Nine: Quaternary Structure Analyses of an Essential Oligomeric Enzyme
    • Abstract
    • 1 Introduction
    • 2 Catalytic Function of DHDPS
    • 3 Structure of DHDPS
    • 4 Conclusions
  • Chapter Ten: Characterization of Intrinsically Disordered Proteins by Analytical Ultracentrifugation
    • Abstract
    • 1 Introduction
    • 2 Ultracentrifugal Procedures
    • 3 Extent of Structural Information Obtained
    • 4 Concluding Remarks
  • Chapter Eleven: Sedimentation Velocity Analysis of the Size Distribution of Amyloid Oligomers and Fibrils
    • Abstract
    • 1 Introduction
    • 2 Preparative Ultracentrifugation
    • 3 Analytical Ultracentrifugation
    • 4 Heterogeneous Systems
    • 5 Summary
    • Acknowledgments
  • Chapter Twelve: AUC and Small-Angle Scattering for Membrane Proteins
    • Abstract
    • 1 Introduction
    • 2 Membrane Proteins in AUC
    • 3 Membrane Proteins in SAXS and SANS
    • Acknowledgments
  • Chapter Thirteen: Hydrodynamic Models of G-Quadruplex Structures
    • Abstract
    • 1 Introduction
    • 2 Correlating Molecular Structure with Experimental Solution Hydrodynamic Measurements—General Comments
    • 3 HYDROPRO Software
    • 4 Getting Structure Files and Building Models
    • 5 Software for Model Building
    • 6 Protocol for Running HYDROPRO on Quadruplex Nucleic Acid Structure Files
    • 7 Extending the Static Hydrodynamic Bead Model By Analyzing Molecular Dynamics Trajectories
    • 8 Accelerated Molecular Dynamics Can Explore More Conformational Space
    • 9 Examining Higher Order Quadruplexes from the Human Telomere Sequence
    • 10 Experimental Determination by Analytical Ultracentrifugation
    • 11 The Partial Specific Volume Problem
    • 12 Correlation of Calculated and Measured Hydrodynamic Properties
  • Chapter Fourteen: Analytical Ultracentrifugation as a Tool to Study Nonspecific Protein–DNA Interactions
    • Abstract
    • 1 Introduction
    • 2 Nonspecific Interaction Model
    • 3 Case Studies
    • 4 Summary
    • Acknowledgments
  • Chapter Fifteen: Characterization of Homogeneous, Cooperative Protein–DNA Clusters by Sedimentation Equilibrium Analytical Ultracentrifugation and Atomic Force Microscopy
    • Abstract
    • 1 Introduction
    • 2 Measurement of DNA Binding
    • 3 AFM Tests of the HBC Model
    • Acknowledgments
  • Chapter Sixteen: Sedimentation Velocity Analysis of Large Oligomeric Chromatin Complexes Using Interference Detection
    • Abstract
    • 1 Introduction
    • 2 Theory
    • 3 Equipments
    • 4 Setting Up the Interferometer Laser: Laser Delay and Duration
    • 5 Radial Calibration of Interference Detector
    • 6 Final Considerations for Interference Sedimentation Velocity Run
    • 7 Experimental
    • 8 Data Analysis
    • 9 Discussion
  • Chapter Seventeen: Dissecting Steroid Receptor Function by Analytical Ultracentrifugation
    • Abstract
    • 1 Introduction
    • 2 AUC Analysis of Steroid Receptor Self-Assembly
    • 3 Integrating AUC Results into Understanding Receptor–Promoter Interactions
    • 4 Implications for Receptor-Mediated Transcriptional Regulation
    • 5 Conclusions and Future Directions
    • Acknowledgments
  • Chapter Eighteen: Ultracentrifuge Methods for the Analysis of Polysaccharides, Glycoconjugates, and Lignins
    • Abstract
    • 1 Introduction
    • 2 Polysaccharides
    • 3 Glycoconjugates
    • 4 Lignins
    • 5 Relevant Recent Advances in AUC and Related Procedures
    • 6 Examples of Applications to Specific Carbohydrate Systems
    • 7 Analytical Ultracentrifuge Analysis of Interactions Involving Carbohydrate Polymers
    • 8 Conclusions
  • Chapter Nineteen: Analytical Ultracentrifugation and Its Role in Development and Research of Therapeutical Proteins
    • Abstract
    • 1 The Development of Analytical Ultracentrifugation and Its Role in Biology and Biotechnology
    • 2 Analysis of Aggregates by AUC
    • 3 Early Studies of the Use of AUC in Determining Molecular Weight and Size Distribution of Protein Drugs
    • 4 AUC and Formulation Development
    • 5 Using AUC to Characterize Immune Complexes
    • 6 Assessment of Dosing of Anti-IgE by AUC Competitive Binding Experiments
    • 7 Using the Competitive Binding AUC Method to Critically Evaluate SPR Measurements
    • 8 Investigation of Protein–Protein Interactions and Impact on Viscosity
    • 9 Summary and Conclusions
  • Chapter Twenty: Guidance to Achieve Accurate Aggregate Quantitation in Biopharmaceuticals by SV-AUC
    • Abstract
    • 1 Introduction
    • 2 Applications of SV-AUC
    • 3 Optimizing SV-AUC Method Parameters and Applying Real-Time Controls
    • 4 Method Lifecycle Maintenance: Monitoring and Controlling SV-AUC Method Performance Over Time
    • 5 Conclusions
  • Chapter Twenty-One: Protein Assembly in Serum and the Differences from Assembly in Buffer
    • Abstract
    • 1 Introduction
    • 2 Materials and Methods
    • 3 Results
    • 4 Conclusions
    • Acknowledgments
  • Author Index
  • Subject Index

Description

Analytical Ultracentrifugation, the latest volume in Methods in Enzymology, focuses on analytical ultracentrifugation. The scope of this technique has greatly expanded in recent years due to advances in instrumentation, algorithms and software.

This volume describes the latest innovations in the field and in the applications of analytical ultracentrifugation in the analysis of macromolecules, macromolecular assemblies, and biopharmaceuticals.

Key Features

  • Timely contribution that describes a rapidly changing field
  • Leading researchers in the field
  • Broad coverage: instrumentation, basic theory, data analysis, and applications

Readership

The intended audience includes: biophysicists interested in macromolecular interactions, thermodynamics and hydrodynamics, biochemists and molecular biologists who wish to use analytical ultracentrifugation, and researchers in the biotechnology industry who are interested in the applications of analytical ultracentrifugation in characterization of biopharmaceuticals.


Details

No. of pages:
588
Language:
English
Copyright:
© Academic Press 2015
Published:
Imprint:
Academic Press
eBook ISBN:
9780128029091
Hardcover ISBN:
9780128029084

Reviews

Praise for the Series:
"Should be on the shelves of all libraries in the world as a whole collection." --Chemistry in Industry
"The work most often consulted in the lab." --Enzymologia
"The Methods in Enzymology series represents the gold-standard." --Neuroscience


About the Serial Volume Editors

James Cole Serial Volume Editor

Dr. Cole received a Sc.B. in Biochemistry from Brown University. He obtained his Ph.D. in Biophysical Chemistry at UC Berkeley where he investigated the mechanism of photosynthetic oxygen evolution. He carried out postdoctoral research at Stanford University on the structure and function of metalloenzymes that interact with oxygen. In 1991, he took a position at Merck Research Laboratories in antiviral drug discovery. Dr. Cole applied analytical ultracentrifugation and related biophysical techniques to probe macromolecular interactions that regulate replication of HIV, Influenza and Hepatitis C virus. In 2001, he to return to academia and moved to the Department of Molecular and Cell Biology at the University of Connecticut, where he is professor of structural biology, biophysics and biochemistry. His research group uses biophysical approaches to characterize macromolecular interactions that regulate important biological processes. A major focus is the innate immunity pathway for defense against viral infection. In an NIH-supported research program, his group has defined the mechanism for activation of protein kinase R by RNA. He directs the National Analytical Ultracentrifugation Facility and holds a joint appointment in the department of Chemistry at the University of Connecticut. He is a member of the editorial board of Biophysical Journal. He is the author of 84 publications and reviews.

Affiliations and Expertise

University of Connecticut