Basically, any protein that exerts any kind of action, effect or influence on another protein interacts with that protein. However, in the field of life sciences, the term protein-protein interaction (PPI) is used in a more specific way:
- it has to involve direct physical contact, normally in a specific position and orientation (molecular docking), and forming a protein complex, permanent or transient
- it has to 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 ( ).
Protein-protein interactions can be classified in several ways (according to):
- 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 stability of the complex they form, as permanent or transient, and transient interactions as weak or strong.
- As most obligate interactions are permanent, and most non-obligate interactions are transient, obligate and permanent are sometimes used interchangeably in the literature.
The majority of cellular processes are regulated by transient PPI, and thus a large part of the research on PPI concentrates on this type of interaction.
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, and so on.
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 of methods: in silico, in vitro and in vivo. ():
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 hence sometimes labelled as ex vivo methods.
In vivo methods are performed in living cells or organisms. The great advantage of in vivo methods is that they preserve the native surroundings in which the interaction takes place. In addition, some of them, such as, 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.
Many of the in vivo methods mentioned above use either fluorescent or luminescent labels. Thus, 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, fluorescence microscopes, , and others. Each instrument is different in terms of performance, flexibility, throughput, sample size and, most importantly, the techniques for protein-protein interaction studies they are able to perform. Follow the link below for more information about instruments for this application.