Methods for the detection and analysis of protein-protein interactions

Proteomics. 2007 Aug;7(16):2833-42. doi: 10.1002/pmic.200700131.


A large number of methods have been developed over the years to study protein-protein interactions. Many of these techniques are now available to the nonspecialist researcher thanks to new affordable instruments and/or resource centres. A typical protein-protein interaction study usually starts with an initial screen for novel binding partners. We start this review by describing three techniques that can be used for this purpose: (i) affinity-tagged proteins (ii) the two-hybrid system and (iii) some quantitative proteomic techniques that can be used in combination with, e.g., affinity chromatography and coimmunoprecipitation for screening of protein-protein interactions. We then describe some public protein-protein interaction databases that can be searched to identify previously reported interactions for a given bait protein. Four strategies for validation of protein-protein interactions are presented: confocal microscopy for intracellular colocalization of proteins, coimmunoprecipitation, surface plasmon resonance (SPR) and spectroscopic studies. Throughout the review we focus particularly on the advantages and limitations of each method.

Publication types

  • Review

MeSH terms

  • Chromatography, Affinity
  • Databases, Protein
  • Immunoprecipitation
  • Microscopy, Confocal
  • Protein Binding
  • Proteins / isolation & purification
  • Proteins / metabolism*
  • Proteomics
  • Surface Plasmon Resonance
  • Two-Hybrid System Techniques


  • Proteins