What is a protein-protein interaction?

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 (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 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.

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, 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. (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 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 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. 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 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 techniques for protein-protein interaction studies they are able to perform. Follow the link below for more information about instruments for this application.

INSTRUMENTS to study PPI

Application Notes related to Protein-Protein Interaction

NanoBRET™ with the TriStar² S Promega NanoBRET™ protein:protein interaction system with the TriStar² S Multimode Microplate Reader

PDF | 396.4 KB

NanoBRET™ with the Mithras² Promega NanoBRET™ protein:protein interaction system with the MITHRAS² Multimode Microplate Reader

PDF | 395.5 KB

BRET Assay for 7TM Receptors Using the Mithras A Functional BRET Assay for 7TM Receptors Using the Mithras LB 940 Multimode Plate Reader

PDF | 312.0 KB

BRET-based studies of receptor dynamics with Mithras Bioluminescence Resonance Energy Transfer (BRET)-based studies of receptor dynamics in living cells with Berthold’s Mithras Multimode Microplate Reader

PDF | 334.9 KB

BRET to monitor dynamic receptor-protein interactionswith the Mithras Bioluminescence Resonance Energy Transfer (BRET) as a means of monitoring dynamic receptor-protein interactions in living cells measured on LB 940 Mithras Multimode Microplate Reader

PDF | 403.5 KB

Basic Considerations for BRET Assays with the Mithras Basic Considerations for Bioluminescence Resonance Energy Transfer (BRET) Assays for G-protein coupled receptor protein interactions in living cells

PDF | 322.0 KB

Comparison of filter sets for BRET1 using Mithras Comparison of filter sets for BRET1 assays: ß-arrestin2 (ßARR2) recruitment to the vasopressin V2 receptor using the Mithras LB 940 Multimode Microplate Reader

PDF | 187.6 KB

FRET to Study GPCR Oligomerization with Mithras FRET as a Tool to Study G-protein Coupled Receptor Oligomerization in HEK Cells.

PDF | 397.9 KB

PathHunter™ ß-arrestin assay with Mithras PathHunter™ ß-arrestin luminescence assay with Mithras LB 940 Multimode Microplate Reader

PDF | 255.0 KB

PathHunter™ ß-arrestin flash assay with Mithras PathHunter™ ß-arrestin flash luminescence assay with Mithras LB 940 Multimode Microplate Reader

PDF | 346.2 KB