PROTEIN – PROTEIN INTERACTION ANALYSIS
The function of a protein is functional through multiple protein interactions, so creating an interaction network between proteins can help us understand the composition of a protein complex or the up-and-downstream relationship between different proteins. The most common methods to identify protein interaction is yeast two-hybrid (Y2H) and Affinity-purification mass spectrometry (AP/MS). Y2H uses two proteins to see if they can interact and induce the yeast to express its reporter gene to identify. AP/MS, on the other hand, identifies the composition of the protein complex. AP/MS analysis the whole interactome and can investigate the relationship between proteins, not just to understand if two proteins can interact.
EPITOPE MAPPING (HDX)
Hydrogen-deuterium exchange mass spectrometry (HDX MS) is a method to study protein structure and its dynamic changes. We can identify the protein interaction site, epitope mapping, and protein active site identification..etc. The principle of this method is to soak the protein into deuterium solution, which the hydrogen of the protein will be exchanged with deuterium in a neuteral environment, and the speed of hydrogen-deuterium exchange at the surface of the protein is faster than the exchange rate inside the protein, using mass spectrometry to identify the different exchange rates between different peptides will allow us to identify the structure of the protein. An easier way to understand this method is to throw two balls that are stuck together into a colored water tub and take them back out, when you pull them apart you will see that the only site that the balls are not colored are the site where they stuck together. This same method can also be used to understand drug-protein interaction or antibody-protein interaction site.