Shooting a Moving Target

Proteins are large molecules made up of chains of amino acids folded into complex shapes or conformations. Once on their own in solution, these chains twist and shimmy with energy. Each atom is constantly reacting to the positions of its neighbors. However, all is not chaos. The chains tend to fold into recognizable types of conformations.

As it folds, the protein chain settles down. It seeks a shape with low energy, one in which the atoms are not repelling each other. The structure with the lowest energy is most likely to be the protein's native conformation. For example, when you build a chain of the amino acid alanine (polyalanine), this form is a coiling alpha helix.

We don't have a method yet for watching proteins fold under a microscope. Instead, researchers approach the question from two directions. They either settle for using X-ray crystallography to examine protein crystals. Or they use computers to simulate the folding process. Scheraga's group focuses on building protein chains in this virtual environment.

Spin Your Own Spiral: This model represents a chain of polyalanine that forms an alpha helix (right-handed spiral). Back off from the molecule using the zoom tool, and then change tools by clicking on the small black knob to the right of the target button. Now the tool options are switched and you will see the rotate tool (shown in the image below). Spin the molecule and discover the spiraling form for yourself. Then use the seek tool to fly down the middle of the molecule!