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6.9 MB, 109 seconds File: MOVIES/HIV/HIVC.MOV

Voiceover
There are many ways to model a molecule like the protease. You have already seen three ways. The least detailed models show whole protein molecules as simple solids like spheres.

The coil model is the simplest model that shows the structure of the protein. The coil is like a rope which runs through the protein's amino acid backbone. The active site of the enzyme is shown in red.

To see the orientation of the backbone atoms we can use a ribbon-like model.

This liquorice bond model depicts atoms in the protease by color coding the ends of tubes that represent chemical bonds.

Color coded spheres that are proportionally sized are added to represent each atom in this model, showing greater detail.

In this model the atoms appear as spheres that represent how the molecules look as they fill up space. But this model is hard to understand because it has so much detail.

So we compromise and use a model that has a mixture of detail. In the conventional view shown here the ribbons and coils illustrate the relationship of structure to the cleavage function.

Looking through the opening in the dimer, the active site is clearly visible.

Looking at the edge of the protease emphasizes its relationship to the pre-protein during docking and cleavage.