Protein interactions in 3D

Protein-protein interactions (PPIs) are essential for functioning of any living cell. While some proteins form strong interactions and bind into permanent complexes, other PPIs are of a transient nature, forming interactions of varying strength and time duration. Moreover, a cell may modulate binding affinity of a given protein:protein pair by, for instance, changing the amounts of proteins or introducing/removing post-translational modifications.

In this project, we will use bioinformatics to explore PPIs in yeast polarity protein network. Our starting point will be the proximity labelling data (TurboID), where interactors of selected polarity network proteins were identified. To distinguish between different types of interactions and to learn more about this network, we will analyze this data using various bioinformatics approaches, including mass spectrometry data analysis, performing simultaneous folding and docking of proteins (hits from TurboID) using AlphaFold2, and prediction of binding affinities, among others.

For this project, we are looking for a student interested in bioinformatics and 3D protein modelling.

Cover figure: Bem1:Cdc24 PB1 domains complex (PDB ID: 2KFK).