Analytical ultracentrifugation / James L. Cole ; contributors, Belinda M. Abbott [and twelve others].

Format:

Book

Author/Creator:

Cole, James L., author.

Contributor:

Abbott, Belinda M., contributor.

Series:

Methods in enzymology ; Volume 562.

Methods in Enzymology, 0076-6879 ; Volume 562

Language:

English

Subjects (All):

Ultracentrifugation.

Physical Description:

1 online resource (0 p.)

Edition:

First edition.

Place of Publication:

Amsterdam, [Netherlands] : Academic Press, 2015.

Language Note:

English

Summary:

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.

Contents:

Front Cover

Analytical Ultracentrifugation

Copyright

Contents

Contributors

Preface

Chapter One: Next-Generation AUC Adds a Spectral Dimension: Development of Multiwavelength Detectors for the Analytical U...

1. Introduction

2. Development of MWL Absorbance Detectors

2.1. First-Generation MWL

2.2. Second-Generation MWL Developments

2.3. Third-Generation MWA

3. Hardware and Control System of Second-Generation MWL Detectors

3.1. Second-Generation MWL Open AUC Design

3.2. Second-Generation MWL from Nanolytics

3.3. Nanolytics Hardware

3.4. Nanolytics Data Acquisition

3.5. Nanolytics Omega Device

3.6. Nanolytics Acquisition and Control Software

4. MWL Data From AUC

4.1. Open AUC Data Format and Management

4.2. Nanolytics Data Format and Management

5. Data Visualization and Experimental Results

5.1. SNR and Stability

5.2. Radial Resolution

6. Discussion

6.1. Qualitative Visualization of Data without Analysis

6.2. MWL Data Quality

7. Summary and General Discussion of the Impacts of MWL AUC Data in the Field of Biopolymers

Acknowledgments

References

Chapter Two: Next-Generation AUC: Analysis of Multiwavelength Analytical Ultracentrifugation Data

2. Computational Treatment of Multiwavelength Data

2.1. Data Representation

2.2. Data Preprocessing

2.3. Data Analysis

2.4. Analysis of MWLD Containing Species with Known Extinction Profiles

2.5. Parallelization

2.6. Visualization

2.6.1. Experimental Data

2.6.2. Analysis Results

3. Applications

4. Discussion

5. Conclusion

Chapter Three: Sedimentation Velocity: A Classical Perspective

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

Chapter Four: Hydrodynamic Modeling and Its Application in AUC

2. AUC and Hydrodynamics

2.1. Hydrodynamic Bead Modeling

2.2. Boundary Element Modeling

2.3. Electrostatic-Hydrodynamic Analogy

3. The Hydration Issue

4. Segmental Flexibility and Intrinsically Disordered Structures

5. Available Programs for Rigid Body HM

5.1. Modeling in the Absence of Atomic Coordinates

5.2. Modeling Based on Atomic Coordinates

5.2.1. HYDROPRO

5.2.2. BEST (as Implemented Within US-SOMO)

5.2.3. AtoB in US-SOMO

5.2.4. SoMo in US-SOMO

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 UltracentrifugationData

2. General Features of GUSSI

2.1. The svdfr Module

2.2. The cofs Module

2.3. The General dfr Module

3. Utility Functions of GUSSI

3.1. Assembling SV-Based Isotherms

3.2. Sorting SEData

3.3. Determining the Oligomeric State of Glycoproteins and Membrane Proteins

3.3.1. Protein, Solution, and Chemical Information

3.3.2. Glycoproteins

3.3.3. Membrane Proteins

4. Summary

Chapter Six: Sedimentation Equilibrium Analysis of ClpB Self-Association in Diluted and Crowded Solutions

1.1. ClpB Assembly and Function

1.2. Biological Compartments Are Crowded.

2. Experimental Approaches and Analysis

2.1. Sedimentation Velocity

2.1.1. SV Assays and Analysis

2.2. Sedimentation Equilibrium

2.2.1. SE Assays and Analysis

2.3. Composition-Gradient Static Light Scattering

2.3.1. CG-SLS Assays

2.3.2. Scattering Analysis of ClpB

2.4. Studying ClpB Self-Association in Crowded Solutions

2.4.1. Estimation of Crowding Effects on ClpB Self-Association

2.4.2. Nonideal Tracer SE

2.4.3. NITSE Assays

2.4.4. NITSE Analysis

3. Summary of Experimental Results

3.1. Environmental Factors That Modulate the Association Equilibrium of ClpB: Ionic Strength

3.2. The M Domain Stabilizes ClpB Hexamers

3.3. Nucleotides Modulate the Stability and Hydrodynamic Behavior of ClpB Hexamers

3.4. Crowding Shifts the Association Equilibrium Toward the Hexameric Species

4. ClpB Association Equilibrium and Disaggregase Activity

5. Concluding Remarks

Chapter Seven: Analysis of Linked Equilibria

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 Veloc ...

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

Chapter Nine: Quaternary Structure Analyses of an Essential Oligomeric Enzyme

2. Catalytic Function of DHDPS

3. Structure of DHDPS

3.1. Subunit Structure

3.2. Active Site

3.3. Canonical Bacterial Tetramer

3.4. Dimeric Structure of S. aureus DHDPS

3.5. Canonical Structure of Plant DHDPS

4. Conclusions

Chapter Ten: Characterization of Intrinsically Disordered Proteins by Analytical Ultracentrifugation

2. Ultracentrifugal Procedures

2.1. Sedimentation Equilibrium

2.2. Sedimentation Velocity

2.3. Sucrose Density Gradient Centrifugation

3. Extent of Structural Information Obtained

3.1. Stokes Radius and the Frictional Ratio

3.2. Analysis of Boundary Spreading: Theoretical Aspects

3.3. Analysis of Boundary Spreading: Practical Applications

4. Concluding Remarks

Chapter Eleven: Sedimentation Velocity Analysis of the Size Distribution of Amyloid Oligomers and Fibrils

2. Preparative Ultracentrifugation

2.1. Separation of Fibrils that Differ in Morphology

2.2. Separation of Linear and Closed-Loop Fibrils

2.3. Isolation of Huntingtin Oligomers and Aggregates

3. Analytical Ultracentrifugation

3.1. Sedimentation Velocity Theory

3.2. Sedimentation Velocity Procedures

4. Heterogeneous Systems

4.1. Effects of αB-Crystallin on Mature ApoC-II Amyloid Fibrils

4.2. The Use of Fluorescence Detection

5. Summary

Chapter Twelve: AUC and Small-Angle Scattering for Membrane Proteins

2. Membrane Proteins in AUC

2.1. On the General Principles of AUC and Analysis for Membrane Proteins

2.2. Expression of the Buoyant Molar Mass for Membrane Proteins.

2.3. Sedimentation Equilibrium Is Difficult and Restricted to Favorable Cases

2.4. SV-General Considerations

2.5. SV in a Given Buffer Condition

2.6. Complementarity with Size-Exclusion Chromatography Coupled to Light Scattering (SEC/MALS)

2.7. SV in Two Buffers, One Containing Isotopically Labeled Water

2.8. Following Complex Formation in Cellular Extracts Using the Fluorescence Detection

2.9. Preliminary Investigation of Lipid Vesicles Sedimentation Using Fluorescent Detection

3. Membrane Proteins in SAXS and SANS

3.1. General Information on SAS Devices and Analysis

3.2. Contrast and Forward Intensity in SAS

3.3. Review on Recent Strategies to Investigate Membrane Proteins

Chapter Thirteen: Hydrodynamic Models of G-Quadruplex Structures

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 StructureFiles

7. Extending the Static Hydrodynamic Bead Model By Analyzing Molecular Dynamics Trajectories

8. Accelerated Molecular Dynamics Can Explore More ConformationalSpace

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

2. Nonspecific Interaction Model

2.1. Nonspecific Binding of Proteins to Linear Nucleic Acids (Non-Cooperative Versus Cooperative)

2.2. MvH Model.

2.3. Specific and Nonspecific Competitive Binding of Proteins to Linear Nucleic Acids.

Notes:

Description based upon print version of record.

Includes bibliographical references at the end of each chapters and indexes.

Description based on online resource; title from PDF title page (ebrary, viewed December 1, 2015).

Description based on publisher supplied metadata and other sources.

ISBN:

9780128029091

0128029099

9780128029084

0128029080

OCLC:

932328933