Interaction experiments: A deeper dive into how protein interactions are defined and measured
Channel: Lars Juhl Jensen
Date: 2021-11-22

An introduction to the experimental assays / methods used to measure physical protein-protein interactions. The presentation first introduces the definitions of physical interactions (direct vs. co-complex interactions) and the dynamic nature of interactions (stable complexes vs. transient interactions). I then go through common experimental methods to measure protein interactions, specifically the binary yeast two-hybrid and protein fragment complementation, affinity purification mass spectrometry (AP-MS), and proximity labeling (BioID). Finally, I talk about how these different assays are best viewed as complementary and cover the challenge in representing AP-MS data as binary interaction networks.

0:00 Introduction: data availability, primary repositories like IntAct, secondary databases like STRING, and overview of the presentation
0:37 Interaction types: functional associations, co-expression, physical interactions, definitions of physical interactions, direct interactions, co-complex interactions, stable complexes, transient interactions, and co-localization
1:39 Interaction assays: 3D structures, high-throughput assays, yeast two-hybrid assay, protein fragment complementation assay, affinity purification mass spectrometry (AP-MS), tandem affinity purification, and proximity labeling (BioID).
4:46 Integrating experiments: complementary assays, different biases of assays, spoke vs. matrix representation of AP-MS data