Biophysical Tools for Biologists: In Vitro 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. Biophysical Tools for Biologists 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 problemsDelineates critical steps and potential pitfalls for each methodIncludes full-color plates to illustrate techniques

Part I: History and Reflections

Section 1. Solution Methods

1. Binding: A Polemic and Rough Guide
Nichola C. Garbett, Jonathan B. Chaires

2. Linked Equilibria in Regulation of Transcription Initiation
Dorothy Beckett

3. Biosensor-Surface Plasmon Resonance Methods for Quantitative Analysis of Biomolecular Interactions
Farial A. Tanious, Binh Nguyen, and W. David Wilson

4. Isothermal Titration Calorimetry: Experimental Design, Data Analysis, and Probing Macromolecule/Ligand Binding and Kinetic Interactions
Matthew W. Freyer and Edwin A. Lewis

5. Differential Scanning Calorimetry
Charles H. Spink

6. Analytical Ultracentrifugation: A) Sedimentation Velocity, B) Sedimentation Equilibrium
Tom Laue, Tom Moody, James Cole, and Jeff Lary

7. Determination of membrane protein molecular weights and association equilibrium constants using sedimentation equilibrium and sedimentation velocity
Nancy K. Burgess, Ann Marie Stanley, and Karen G. Fleming

8. Basic Aspects of Absorption and Fluorescence Spectroscopy and Resonance Energy Transfer Methods
Susan Bane and Natasha Shanker

9. Applications of Fluorescence Anisotropy to the Study of Protein-DNA Interactions
Vince J. LiCata and Andy J. Wowor

10. Circular Dichroism and Its Application to the Study of Biomolecules
Stephen R. Martin and Maria J. Schilstra

11. Folding and Stability
Timothy O. Street, Naomi Courtemanche and Doug Barrick

12. Hydrodynamic shape modelling of analytical ultracentrifugation data
Olwyn Byron

13. X-ray and neutron scattering data and their constrained molecular modelling
Stephen J Perkins, Azubuike I. Okemefuna, Anira N. Fernando, Alexandra Bonner, Hannah E. Gilbert and Patricia B. Furtado

14. Structural Investigations into Microtubule-MAP Complexes
Andreas Hoenger and Heinz Gross

15. Rapid Kinetic Techniques
John F. Eccleston, Stephen Martin, and Maria J. Schilstra

16. Mutagenic Analysis of the Membrane Protein Functional Mechanisms: Bacteriorhodopsin as a Model Example
George J. Turner

17. Quantifying DNA-protein interactions by single molecule stretching
Mark C. Williams, Ioulia Rouzina, and Richard L. Karpel

18. Isotopomer-based metabolomic analysis by NMR and mass spectrometry
Andrew N Lane, Teresa W-M. Fan, and Richard M. Higashi

19. Following molecular transitions with single residue spatial
and millisecond time resolution
Inna Shcherbakova, Somdeb Mitra, Robert Beer and Michael Brenowitz

20. Methods and applications of site-directed spin labeling EPR spectroscopy
Candice S. Klug and Jimmy B. Feix

21. Fluorescence Correlation Spectroscopy and its application to the characterization of molecular properties and interactions
Hacène Boukari and Dan L. Sackett

22. Practical Guide to Osmolytes
Jorg Rosgen and Daniel Harries

23. Stupid Statistics
Joel Tellinghuisen

24. Nonlinear Least Squares Fitting Methods
Michael L. Johnson

25. Methods for Simulating the Dynamics of Complex Biological Processes
Maria J Schilstra, Stephen R. Martin, and Sarah M. Keating

26. Computational Methods for Biomolecular Electrostatics
Feng Dong, Brett Olsen and Nathan A. Baker

27. Ligand effects on the protein ensemble: Unifying the descriptions of ligand binding, local conformational fluctuations, and protein stability
Steven T Whitten, Bertrand García-Moreno E., and Vincent J. Hilser

28. Molecular Modeling of Cytoskeletal Proteins
Xiange Zheng and David Sept

29. Mathematical Modeling of Cell Motility
Anders E. Carlsson and David Sept