What is a protein-protein interaction?

Protein interaction is any protein that exerts any kind of action, effect or influence on another protein. In the field of life sciences the term protein-protein interaction (PPI) is used in a more specific way:

  • It must involve direct physical contact, normally in a specific position and orientation (molecular docking) and forming permanent or transient protein complex.
  • it must be non-random, thus excluding all proteins that may bump into each other by chance.
  • It must not be generic but serves a specific purpose that differs from completely generic functions such as protein production and degradation (De las Rivas and Fontanillo 2009).

Types of protein-protein interactions

Protein-protein interactions can be classified in several ways according to Acuner-Ozbabacan et al. 2011

  • Based on affinity they can be classified as obligate (in case one or more of the proteins is unstable in vivo unless interacting and forming a specific protein complex) and non-obligate interactions (in case the proteins can exist independently).
  • Non-obligate interactions can be classified based on the stability of the complex they form, either permanent or transient with transient interactions being weak or strong.
  • Most obligate interactions are permanent and most non-obligate interactions are transient. Obligate and permanent are sometimes used interchangeably in scientific literature.


Most cellular processes are regulated by transient PPI and a large part of the research on PPI concentrates on this type of interaction.

Methods available to study protein-protein interactions

There are dozens of methods available to investigate PPI and each has several advantages and disadvantages, e.g.

  • in terms of the type of interactions they can detect
  • in terms of the type of proteins they can be used with
  • the number of false positives and false negatives they produce
  • the instrumentation required

Due to the large numbers of false positives and negatives that most methods produce it is usually necessary to confirm each interaction by using 2 or 3 different methods.

Most methods fall into one of 3 groups: in silico, in vitro and in vivo. (Srinivasa Rao et al. 2013):


In silico methods use computer models to predict protein-protein interactions. They include sequence-based approaches, structure-based approaches, chromosome proximity, gene fusion, in silico 2 hybrid, mirror tree, phylogenetic tree, and gene expression-based approaches.

In vitro methods are performed in a controlled environment outside a living organism. In vitro methods used for PPI detection include tandem affinity purification, affinity chromatography, coimmunoprecipitation, protein arrays, protein fragment complementation, phage display, X-ray crystallography, and NMR spectroscopy. In some of them, for example coimmunoprecipitation, interaction takes place in vivo but the interaction is fixed and detected after the death of the cell or organism and are sometimes labelled as ex vivo methods.

In vivo methods are performed in living cells or organisms and the advantage of in vivo methods is that they preserve the native surroundings in which the interaction takes place. Some of them, like FRET, are reversible and can be used to quantify protein-protein interactions dynamically which is highly advantageous. Follow the link below for more information about this type of methods.

Instruments used to study Protein-Protein Interactions

Many of the in vivo methods mentioned above use either fluorescent or luminescent labels and instruments able to measure fluorescence and/or luminescence are required to use them. There are many different instruments that can be used to for this kind of measurements, including microplate readers, fluorescence microscopes, in vivo imaging systems, and others. Each instrument is different in terms of performance, flexibility, throughput, sample size and most importantly the technique for protein-protein interaction studies they can perform. Follow the link below for more information about instruments for this application.


Application Notes related to Protein-Protein Interaction

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