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Biophysical Tools for Biologists: In Vitro Techniques, Volume 84 [Kietas viršelis]

Edited by John J. Correia (University of Mississippi Medical Center, Jackson, USA), Edited by H. William Detrich III (Professor of Biochemistry and Marine Biology at Northeastern University)

Formatas: Hardback, 1014 pages, aukštis x plotis: 235x191 mm, weight: 1830 g
Serija: Methods in Cell Biology
Išleidimo metai: 14-Dec-2007
Leidėjas: Academic Press Inc
ISBN-10: 0123725208
ISBN-13: 9780123725202

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Biochemistry - (Šiuo metu turimos knygos: 2 prekės)

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Formatas: Hardback, 1014 pages, aukštis x plotis: 235x191 mm, weight: 1830 g
Serija: Methods in Cell Biology
Išleidimo metai: 14-Dec-2007
Leidėjas: Academic Press Inc
ISBN-10: 0123725208
ISBN-13: 9780123725202

Kitos knygos pagal šią temą:

Biochemistry - (Šiuo metu turimos knygos: 2 prekės)

Pastovi nuoroda: https://www.kriso.lt/db/9780123725202.html

Raktažodžiai:

Driven in part by the development of genomics, proteomics, and bioinformatics as new disciplines, there has been a tremendous resurgence of interest in physical methods to investigate macromolecular structure and function in the context of living cells. This volume in Methods in Cell Biology is devoted to biophysical techniques in vitro and their applications to cellular biology. The volume covers methods-oriented chapters on fundamental as well as cutting-edge techniques in molecular and cellular biophysics. This book is directed toward the broad audience of cell biologists, biophysicists, pharmacologists, and molecular biologists who employ classical and modern biophysical technologies or wish to expand their expertise to include such approaches. It will also interest the biomedical and biotechnology communities for biophysical characterization of drug formulations prior to FDA approval.

* Describes techniques in the context of important biological problems
* Delineates critical steps and potential pitfalls for each method
* Includes full color plates to illustrate techniques

Driven in part by the development of genomics, proteomics, and bioinformatics as new disciplines, there has been a tremendous resurgence of interest in physical methods to investigate macromolecular structure and function in the context of living cells. This volume in Methods in Cell Biology is devoted to biophysical techniques in vitro and their applications to cellular biology. The volume covers methods-oriented chapters on fundamental as well as cutting-edge techniques in molecular and cellular biophysics. This book is directed toward the broad audience of cell biologists, biophysicists, pharmacologists, and molecular biologists who employ classical and modern biophysical technologies or wish to expand their expertise to include such approaches. It will also interest the biomedical and biotechnology communities for biophysical characterization of drug formulations prior to FDA approval.

* Describes techniques in the context of important biological problems
* Delineates critical steps and potential pitfalls for each method
* Includes full-color plates to illustrate techniques

Daugiau informacijos

Single-source reference that details state-of-the-art biophysical techniques.

Contributors

Preface

xix

Dedication

xxiii

SECTION 1 Solution Methods

Binding: A Polemic and Rough Guide

Nichola C. Garbett

Jonathan B. Chaires

Introduction

(1)

Binding Constants Provide an Entry into Thermodynamics

(2)

General Properties of Binding Isotherms

(3)

Thermodynamics from Thermal Denaturation Methods

(3)

Completing the Thermodynamic Profile

(1)

Thermodynamics in the Real World: Some Useful Strategies

(2)

Ligand-Receptor Binding in the Absence of an Optical Signal

(2)

Toward High-Throughput Thermodynamics

(2)

Summary

(6)

References

(5)

Linked Equilibria in Regulation of Transcription Initiation

Dorothy Beckett

Introduction

(1)

Multiple Levels of Linkage in Transcription Regulation

(3)

A Road Map for Quantitative Studies of Assembly of Gene Regulatory Complexes

(1)

Measurements of Binding Interactions in Transcription Regulation

(14)

Case Studies of Multiple Linked Equilibria in Transcription Regulatory Systems

(10)

References

(4)

Biosensor-Surface Plasmon Resonance Methods for Quantitative Analysis of Biomolecular Interactions

Farial A. Tanious

Binh Nguyen

W. David Wilson

Introduction

(1)

Rationale: Biomolecular Interactions with SPR Detection

(3)

Materials and Methods

(10)

Results and Data Analysis

(6)

Summary

(6)

References

(5)

Isothermal Titration Calorimetry: Experimental Design, Data Analysis, and Probing Macromolecule/Ligand Binding and Kinetic Interactions

Matthew W. Freyer

Edwin A. Lewis

Introduction

(2)

Calorimetry Theory and Operation

(3)

Thermodynamic ITC Experiments

(15)

Kinetic ITC Experiments

100

(10)

Conclusions

110

(6)

References

111

(5)

Differential Scanning Calorimetry

Charles H. Spink

Introduction

116

(1)

DSC Instrumentation

117

(2)

Experimental Protocols and Preliminary Data Treatment

119

(7)

Modeling DNA Unfolding

126

(13)

Summary

139

(5)

References

140

(4)

Analytical Ultracentrifugation: Sedimentation Velocity and Sedimentation Equilibrium

James L. Cole

Jeffrey W. Lary

Thomas P. Moody

Thomas M. Laue

Introduction

144

(2)

Basic Theory

146

(1)

Dilute Solution Measurements

147

(2)

Concentrated and Complex Solutions

149

(1)

Instrumentation and Optical Systems

150

(8)

Sample Requirements

158

(2)

Sample Preparation

160

(1)

Sedimentation Velocity

161

(7)

Sedimentation Equilibrium

168

(6)

Discussion and Summary

174

(8)

References

176

(6)

Determination of Membrane Protein Molecular Weights and Association Equilibrium Constants Using Sedimentation Equilibrium and Sedimentation Velocity

Nancy K. Burgess

Ann Marie Stanley

Karen G. Fleming

Introduction

182

(1)

Rationale

183

(7)

Materials and Methods

190

(5)

Results

195

(11)

Discussion

206

(2)

Summary

208

(6)

References

209

(5)

Basic Aspects of Absorption and Fluorescence Spectroscopy and Resonance Energy Transfer Methods

Natasha Shanker

Susan L. Bane

Introduction

214

(1)

Absorption Spectroscopy

214

(9)

Fluorescence Spectroscopy

223

(16)

Summary

239

(5)

References

239

(5)

Applications of Fluorescence Anisotropy to the Study of Protein---DNA Interactions

Vince J. LiCata

Andy J. Wowor

Introduction and General Background

244

(3)

Advantages and Disadvantages of Anisotropy in Monitoring DNA Binding

247

(1)

Equipment

248

(3)

Experimental Design and Performance

251

(9)

Other Applications of Fluorescence Anisotropy to the Study of Protein---DNA Interactions

260

(4)

References

260

(4)

Circular Dichroism and Its Application to the Study of Biomolecules

Stephen R. Martin

Maria J. Schilstra

Introduction

264

(2)

Instrumentation and Sample Preparation

266

(3)

Data Collection

269

(2)

Data Processing and Spectral Characteristics

271

(5)

Applications

276

(14)

Summary

290

(6)

References

290

(6)

Protein Folding and Stability Using Denaturants

Timothy O. Street

Naomi Courtemanche

Dong Barrick

Introduction

296

(1)

Rationale

297

(1)

Methods

298

(12)

Materials

310

(3)

Discussion

313

(9)

Summary

322

(6)

References

323

(5)

Hydrodynamic Modeling: The Solution Conformation of Macromolecules and Their Complexes

Olwyn Byron

Introduction

328

(1)

Background to HBM

329

(3)

Model Construction

332

(16)

Model Visualization

348

(1)

Hydration

349

(4)

Hydrodynamic Calculations

353

(13)

Advanced Hydrodynamic Calculations

366

(4)

Concluding Comments

370

(6)

References

370

(6)

X-Ray and Neutron Scattering Data and Their Constrained Molecular Modeling

Stephen J. Perkins

Azubuike I. Okemefuna

Anira N. Fernando

Alexandra Bonner

Hannah E. Gilbert

Patricia B. Furtado

Introduction

376

(4)

Rationale

380

(2)

X-Ray and Neutron Facilities

382

(8)

Experimental Methods

390

(10)

Constrained Scattering Modeling

400

(7)

Examples

407

(9)

Discussion

416

(10)

References

420

(6)

Structural Investigations into Microtubule-MAP Complexes

Andreas Hoenger

Heinz Gross

Introduction

426

(2)

Rationale

428

(2)

Methods

430

(9)

Discussion

439

(7)

References

441

(5)

Rapid Kinetic Techniques

John F. Eccleston

Stephen R. Martin

Maria J. Schilstra

Introduction

446

(2)

Basic Theory

448

(4)

Techniques

452

(4)

Instrumentation

456

(3)

Probes

459

(4)

Experimental Design and Data Analysis

463

(7)

Complex Reactions

470

(4)

Data Analysis in Practice

474

(6)

References

476

(4)

Mutagenic Analysis of Membrane Protein Functional Mechanisms: Bacteriorhodopsin as a Model Example

George J. Turner

Introduction

480

(1)

Rationale

481

(5)

Materials and Methods

486

(5)

Results

491

(18)

Conclusions

509

(9)

References

511

(7)

Quantifying DNA---Protein Interactions by Single Molecule Stretching

Mark C. Williams

Ioulia Rouzina

Richard L. Karpel

Introduction

518

(1)

Stretching Single DNA Molecules with Optical Tweezers

519

(2)

Force-Induced Melting of Single DNA Molecules

521

(1)

T4 gp32 Interactions with DNA

522

(9)

Model for Salt-Dependent Regulation of T4 Gene 32 Binding to DNA

531

(6)

Conclusions

537

(5)

References

538

(4)

Isotopomer-Based Metabolomic Analysis by NMR and Mass Spectrometry

Andrew N. Lane

Teresa W.-M. Fan

Richard M. Higashi

Introduction

542

(1)

Rationale

543

(1)

Materials

544

(3)

Methods

547

(30)

Discussion

577

(13)

References

581

(9)

Following Molecular Transitions with Single Residue Spatial and Millisecond Time Resolution

Inna Shcherbakova

Somdeb Mitra

Robert H. Beer

Michael Brenowitz

Introduction

590

(5)

Acquisition of •OH Footprinting Time-Progress Curves

595

(7)

Data Reduction and Production of Time-Progress Curves

602

(3)

Interpretation of Individual Nucleotide Time-Progress Curves

605

(13)

References

611

(7)

Methods and Applications of Site-Directed Spin Labeling EPR Spectroscopy

Candier S. Klug

Jimmy B. Feix

Background and Methods

618

(18)

Examples

636

(17)

Conclusion

653

(7)

References

653

(7)

Fluorescence Correlation Spectroscopy and Its Application to the Characterization of Molecular Properties and Interactions

Hacene Boukari

Dan L. Sackett

Introduction

660

(3)

Fluorescence Correlation Spectroscopy

663

(3)

FCS Experimental Setups

666

(2)

Sample Preparation and Some Practical Considerations

668

(3)

Fluorescence Cross-Correlation Spectroscopy

671

(1)

Illustrative Examples of FCS Applications

672

(4)

Conclusions

676

(4)

References

677

(3)

A Practical Guide on How Osmolytes Modulate Macromolecular Properties

Daniel Harries

Jorg Rosgen

Introduction

680

(3)

Experimental Systems

683

(15)

Experimental Methods

698

(16)

Solvation Information

714

(10)

Prospects

724

(16)

References

726

(14)

SECTION 2 Computational Methods

Stupid Statistics!

Joel Tellinghuisen

Introduction

740

(2)

Statistics of Data: The 10-Min Review

742

(7)

Linear Least Squares---Theory

749

(8)

Linear Least Squares---Monte Carlo Illustrations

757

(6)

Nonlinear Least Squares

763

(3)

Applications and Illustrations

766

(12)

Summary

778

(3)

References

779

(2)

Nonlinear Least-Squares Fitting Methods

Michael L. Johnson

Introduction

781

(4)

Formulate a Hypothesis-Based Mathematical Model

785

(2)

Determining the Optimal Parameters of the Model

787

(4)

Distinguishing Between Multiple Mathematical Models

791

(5)

Estimate the Precision of the Model Parameters

796

(4)

Cross-Correlation of the Estimated Parameters

800

(3)

Uniqueness of the Parameters

803

(1)

Conclusions

804

(4)

References

805

(3)

Methods for Simulating the Dynamics of Complex Biological Processes

Maria J. Schilstra

Stephen R. Martin

Sarah M. Keating

Introduction

808

(1)

Rationale

809

(1)

Modeling

810

(13)

Simulation

823

(12)

Modeling and Simulation in Practice

835

(5)

Concluding Remarks

840

(4)

References

840

(4)

Computational Methods for Biomolecular Electrostatics

Feng Dong

Brett Olsen

Nathan A. Baker

Introduction

844

(1)

Electrostatics in Cellular Systems

844

(3)

Models for Biomolecular Solvation and Electrostatics

847

(9)

Applications

856

(5)

Conclusion and Future Directions

861

(11)

References

862

(10)

Ligand Effects on the Protein Ensemble: Unifying the Descriptions of Ligand Binding, Local Conformational Fluctuations, and Protein Stability

Steven T. Whitten

Bertrand E. Garcia-Moreno

Vincent J. Hilser

Introduction

872

(3)

The Effect of pH on the Conformational Ensemble

875

(6)

Results and Discussion

881

(5)

Summary and Conclusions

886

(8)

References

889

(5)

Molecular Modeling of the Cytoskeleton

Xiange Zheng

David Sept

Introduction

894

(1)

Simulation Methods

894

(4)

Applications of Molecular Modeling

898

(6)

Related Methodologies

904

(3)

Conclusions

907

(5)

References

907

(5)

Mathematical Modeling of Cell Migration

Anders E. Carlsson

David Sept

Introduction

912

(1)

Cell Protrusion

912

(14)

Cell Adhesion and Retraction

926

(4)

Whole-Cell Models

930

(3)

Summary and Future Outlook

933

(6)

References

934

(5)

Index

939

(26)

Volumes in Series

965

Professor of Biochemistry and Marine Biology at Northeastern University, promoted 1996. Joined Northeastern faculty in 1987. Previously a faculty member in Dept. of Biochemistry at the University of Mississippi Medical Center, 1983-1987.Principal Investigator in the U.S. Antarctic Program since 1984. Twelve field seasons "on the ice" since 1981. Research conducted at Palmer Station, Antarctica, and McMurdo Station, Antarctica.Research areas: Biochemical, cellular, and physiological adaptation to low and high temperatures. Structure and function of cytoplasmic microtubules and microtubule-dependent motors from cold-adapted Antarctic fishes. Regulation of tubulin and globin gene expression in zebrafish and Antarctic fishes. Role of microtubules in morphogenesis of the zebrafish embryo. Developmental hemapoiesis in zebrafish and Antarctic fishes. UV-induced DNA damage and repair in Antarctic marine organisms.

Biophysical Tools for Biologists: In Vitro Techniques, Volume 84 [Kietas viršelis]

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