The structure of chymosin. The binding pocket is denoted by the black wireframe sphere.
Visualized using 3Dmol.js.

Chymosin, chemically speaking, is an aspartic endoprotease. What’s an aspartic endoprotease you ask? It’s complicated. But the gist of it is that Chymosin is an enzyme that breaks down protein in a really specific way. In our situation, the protein being broken down in a specific way is casein. Chymosin clips off the kappa-casein “hairy layer” from the casein micelles allowing them to stick together and therefore coagulate milk. That binding pocket shown in the figure above is where the magic happens. That little notch is what attacks the hairs and snips them off. To learn more, check out the previous posts on Rennet and Coagulation.

In case you need a litte coagulation review, a chunk of the coagulation post is shown below...

Coagulation

If you haven’t already, check out the previous post on milk chemistry. Specifically the section on protein. That information is crucial to understanding the rest of this post. As mentioned in the milk chemistry post, the protein of most interest in cheese making is casein. Casein micelles are covered with a negatively-charged “hairy” layer of κ-casein.

In milk, these casein micelles float around and bounce off each other. Those κ-casein hairs get in the way and prevent the casein from sticking and aggregating. Our goal in cheese making is to make those casein micelles stick together somehow. Once they stick together, a domino effect occurs, and eventually you form a mesh of casein micelles that form the structure/body of the cheese.

How we get those micelles to stick together is what coagulation is all about! The coagulation (or “clotting”) process is done to encourage those casein micelles to stick together somehow. Enzymes (e.g. Chymosin), acid, and acid/heat can all be used to encourage this process.