As a result of their importance in living organisms, proteins derived their name from the Greek word, proteios, meaning primary or first place. Made by the ribosomes in a cell, proteins are involved in many cellular processes, and the study of proteins is important when looking at living organisms. Proteomics is a fairly recent term, first coined in 1996 by Marc Wilkins, with proteome denoting “PROTEin complement of a genOME”.  In other words, the proteome is all proteins expressed by an organism, and proteomics is the study of protein composition and structure, and “includes the analysis and categorization of overall protein signatures of a genome”. Proteins interact with many components of a cell and facilitate many of the biological processes in a cell, and scientists look at these interactions, one of which is protein-protein interactions (PPI).¹

In PPIs, peptide fragments of the proteins, termed short linear motifs (SLiMs), often play the role of mediator in these interactions. SLiMs are typically 10 amino acids or less and often found in intrinsically disordered regions (IDRs). Cells can have interactions that are stable and mechanistic, but they also need adaptability and flexibility with reversible and transient interactions. These transient interactions are often mediated by SLiMs. Katrina Meyer and Matthias Selbach, in a recent publication in Molecular & Cellular Proteomics, cover different ways to analyze the interactions of SLiMs in IDR and their importance in cell biology. Affinity purification mass spectrometry (AP-MS) and quantitated AP-MS can be used to study PPIs but is not as effective in unstable or transient interactions. Meyer and Selbach cover how high throughput proteomics with Protein Interaction Screen on Peptide Matrix (PRISMA) can be a useful tool, especially with a combination of label-free and stable isotope labelled amino acids in cell culture (SILAC). Learn more by reading the reference here. ²

References

1. B. Aslam et al., Journal of Chromatographic Science, 55 (2), 182(2017).
2. K. Meyer and M. Selbach, Molecular & Cellular Proteomics, (2020).