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Narrative
This simulation shows the protease monomers entering from the top and bottom of the screen approaching the pre-protein shown in yellow. The monomers are attracted by intermolecular forces to form the dimer around the pre-protein cleavage site shown as a blue-green part of the coil. The active site of the protease docks with the cleavage site of the pre-protein. In order for HIV to reproduce, it must cut its pre-protein.

A chemical reaction occurs. The pre-protein is cut. Once this chemical change occurs, the molecules aren't as strongly attracted to each other. The protease monomers drift off to start another cleavage cycle and the new activated protein begins its biological function.

Let's take a closer look at the pre-protein. We can show the cleavage site with different models such as this liquorice bond representation.

Here is a molecule we call an inhibitor. Like the cleavage site it attracts the protease. Unlike the pre-protein, the inhibitor is not cleaved by the protease, instead the protease tends to stay docked because no reaction has occurred to decrease the attraction.

This is important because the protease is no longer available to cut the pre-protein so HIV can't reproduce.