Overview of the Quantitation of Protein Interactions

John S. Philo1

1 Alliance Protein Laboratories, Thousand Oaks
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 20.1
DOI:  10.1002/0471140864.ps2001s17
Online Posting Date:  May, 2001
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The biological function of many proteins involves reversible interactions with other proteins, nucleic acids, or other non‐protein ligands. Such interactions play many different roles in a wide range of cellular processes. A few examples are: (1) storing or transporting key metabolites (e.g., O2 storage by myoglobin); (2) forming and maintaining the quaternary structure of multi‐subunit enzymes; (3) specific binding and recognition events (antigen‐antibody, hormone‐receptor, transcription factor‐promoter); and (4) self‐assembly of large structures (microtubules, chromatin). Thus, the quantitative characterization of such interactions represents an important part of understanding the function of such proteins and their role in these cellular events. This unit sets the tone for the rest of the chapter, and gives important information necessary to understand some of the topics that will be covered in future supplements, such as sedimentation equilibrium (analytical and micro‐preparative), surface plasmon resonance (SPR), size‐exclusion chromatography (SEC) with on‐line light scattering, and chemical cross‐linking.

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Table of Contents

  • Some Comments on Techniques
  • The Importance of Data Analysis Methods
  • Sensitivity to Contaminants and Protein Quality
  • The Advent of Recombinant Proteins Enhances Our Capabilities for Studying Protein Interactions
  • The Virtues of Using Multiple Techniques
  • Some Thoughts on Choosing Methods
  • Obtaining Additional Thermodynamic Information
  • Thermodynamic Linkage Relationships
  • Figures
  • Tables
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Literature Cited

Literature Cited
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Key References
   Cantor, C.R. and Schimmel, P.R. 1980. Biophysical chemistry. Part II: Techniques for the study of biological structure and function. W.H. Freeman, San Francisco.
  More advanced texts; coverage of binding equilibria and thermodynamics, spectroscopy, and centrifugation methods.
   Freifelder, D. 1982. Physical Biochemistry: Applications to Biochemistry and Molecular Biology. W.H. Freeman, New York.
  Good introductory text; strong on spectroscopy and centrifugation methods
   Johnson, M.L. and Frasier, S.G. 1985. Nonlinear least‐squares analysis. Methods Enzymol. 117:301‐342.
  Good overview of the fitting of experimental data (a key part of all protein interaction studies), with some examples for ligand binding.
   van Holde, K.E. et al. 1998. See above.
  More advanced texts; coverage of binding equilibria and thermodynamics, spectroscopy, and centrifugation methods.
   Winsor, D.J. and Sawyer, W.H. 1995. Quantitative characterization of ligand binding. John Wiley & Sons, New York.
  An excellent but heavily mathematical text covering theory, data analysis, and interpretation. Methods based on phase separation, spectral changes, affinity and gel chromatography, and competitive binding are discussed in some detail, with some coverage of sedimentation, calorimetry, and other techniques. An entire chapter is devoted to DNA‐ligand interactions (also see APPENDIX ).
Internet Resources
   rasmb-manager@bbri.org (subscriptions)
  Reversible Associations in Structural and Molecular Biology (RASMB) e‐mail list server. This e‐mail group list is for discussions and questions regarding the study of reversible interactions. The dominant focus is analytical ultracentrifugation (and nearly all the experts participate), but tremendous expertise in many other relevant areas is represented as well.
   rasmb@rasmb.bbri.org (to post questions)
  Reversible Associations in Structural and Molecular Biology (RASMB) Web site. Distributes public domain software for analytical ultracentrifugation.
  Distributes public domain software for analytical ultracentrifugation. Also maintains an archive of the RASMB discussions and tutorials on sedimentation methodology.
  This site by the Protein Interaction Facility at the Huntsman Cancer Institute nicely describes the basics of SPR, analytical ultracentrifugation, and titration calorimetry, and is the distribution point for the CLAMP package of public‐domain SPR analysis software.
  Analytical ultracentrifugation products from Beckman Coulter. Useful application notes and bibliographies.
  Calorimetry Sciences Web site. Useful calorimetry application notes and bibliographies.
  Microcal Web site. Useful calorimetry application notes and bibliographies.
  Panvera Web site (fluorescence polarization). Useful application notes and bibliographies.
  Wyatt Technologies Web site (light scattering). Useful application notes and bibliographies.
  BIAcore Web site (SPR). Useful application notes and bibliographies.
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