Protein-protein interactions: investigating the chemical interactions of a protease and its substrate.

Proteins are linear chains of amino acids. The protein backbone is made up of the same repeating group over and over again, only the side chains coming off are different. Proteases are proteins themselves, more specifically they are enzymes, and these enzymes cleave the protein backbone. However proteases don’t cleave every protein they come into contact with, they are very specific for their protein targets. When a protease does cleaves, it always cleaves at a very specific place, even though the backbone is the same everywhere. The reasoning for the difference in protease cleavage patterns is therefore not always known.

My research focuses on a protease called DegQ, and looks to determine the specific interactions the protease makes with its substrate which dictates where to cleave along the backbone. We perform experiments with the DegQ protease in vitro, or outside the cell, monitoring its cleavage with substrate. All proteins are made from a DNA template, or its gene. We employ molecular cloning to acquire the gene, which we can insert into bacteria, and exploit the bacterial machinery to make our protein. We then purify this protein to remove all other contaminants found in the bacteria. We can then start performing reactions with the protease to obtain data. Therefore, my research sits at the interface of biology and chemistry, we employ techniques of both disciplines. You will therefore gain a very good understanding of biology and chemistry, however you will be able to participate even if you have taken nothing higher than general chemistry or general biology.