Protein-Protein Interactions: An Overview

Abstract

The proteins perform their activities in a cell through their interactions, forming a complex protein-protein interaction network (PIN) that can contain tens of thousands of interactions. Knowing the interactions enables know how the organism performs its functions internally and how it interacts with the host. In Bioinformatics, by using graph theory from the computer science area, we can calculate measurements on PINs revealing relevant biological information. Knowing these measures as they are calculated, and their biological relevance is key to validating and interpreting PINs, since it is humanly impossible to analyze and extract information in complex PINs. PINs from various organisms, generated by experimental or computational methods, can be found and downloaded from the public databases for further analysis. PINs for an organism of interest can be generated by experimental methods or predicted by computational methods in both low or large scale. Knowing the biological assumptions underlying each method, whether the method is able to predict new interactions or identify previously characterized interactions, as well as advantages and disadvantages, is essential to select the method appropriate to our purpose. Regardless of the method used, biological PINs can be applied in various contexts such as hypothetical protein annotation, understanding the organism at systems biology level, identifying essential or important proteins in a biological context to be used as a target for drugs, identifying host-pathogen interactions to suggest vaccine targets, in addition to enabling research to identify a new drug class inhibiting or stabilizing interaction. PINs are generated not as the ultimate goal of a research but rather as a tool to better understand the mechanisms of action of an organism and to direct future experiments in the laboratory. In this article, we have discussed various aspects of PINs including their applications.