From Experimental Approaches to Computational Techniques: A Review on the Prediction of Protein-Protein Interactions
Table 2
An overview of large-scale experimental methods applied for the detection of PPIs on an interactome-wide scale. The first column states the name of the experiment followed by a description and a reference.
Technique
Description
Reference
Y2H
The Y2H employs a “two-plasmid” approach in yeast. The yeast protein GAL4 is a transcriptional activator consisting of two domains. The domains must be in close proximity to start the transcription process. The two plasmids are placed into a cell. A physical interaction occurs if the GAL4 binding and activation domains come together if physical interaction occurs, demonstrating that the “bait” and “target” bind [37]. This technique provides evidence of direct physical interactions between proteins.
Affinity tags are attached to a protein of interest (target), systematic precipitation of bait proteins is performed. Proteins are separated according to their mass to uncover purified protein complexes. Proteins are removed from a gel and analysed by MS techniques [40]. This technique provides evidence of direct physical interactions between proteins.
Gene expression profiles can be obtained from cell cycle experiments and the measurement of gene expression levels when the cell is under different conditions [41]. Gene expression similarity values may be calculated as the Pearson correlation co-efficient between expression levels of two proteins Protein pairs that are coexpressed are more likely to be interacting proteins [35, 42]. This technique provides indirect evidence of interactions between proteins.
This method involves the deletion or mutation of two genes which are viable alone, but cause lethality when combined in a cell under specific conditions [36, 43]. Synthetic interactions may detect PPIs between gene products, their occurrence in a pathway or participation in a function [40]. This technique provides indirect evidence of interactions between proteins.