Understanding the protein ‘interactome’

Researchers of the University of Helsinki, Finland, developed an improved method to give a detailed understanding of protein–protein interactions ­– key for deciphering regulation of cellular networks and pathways.

Proteins do not function in isolation and their interactions with other proteins define their cellular functions. These complex networks of stable and transient associations can be studied by affinity purification mass spectrometry (AP-MS) and complementary proximity-based labelling methods such as BioID. Now a research team led by Dr Markku Varjosalo from the Institute of biotechnology, University of Helsinki, has introduced an integrated approach combining AP-MS and BioID in a single workflow.

Dr Varjosalo said: "This study is a continuum of our rigorous efforts in developing new systems biology tools for studying the molecular interactions formed by proteins. We have previously proven that AP-MS is highly reproducible method, which is also suitable for large-scale and inter-laboratory studies.”

In addition to just exploiting the advantages of both strategies, the authors of the paper in Nature Communications say their approach allows identification and quantification of protein-protein interactions, identification of transient or close-proximity interactions with BioID and definition of the molecular context with MS microscopy. This can be done by using a reference dataset the team developed by identifying subcellular localisation markers. The authors also show that using MS microscopy, it is possible to assign the studied protein to it´s correct cellular or even subcellular location in even higher resolution than with confocal microscopy.

Dr Varjosalo said: “Our newly developed integrated workflow and the reference molecular context proteome map, allows an easy way to probe the molecular localization of many proteins. The developed MAC-tag and the integrated approach should empower, not only the interaction proteomics community, but also cell, molecular and structural biologists, with an experimentally proven integrated workflow for mapping in detail the physical and functional interactions and the molecular context of proteins in human cells.”