Model Molecules

Much of Scheraga's work focuses on proteins, which are large molecules composed of amino acids. His research group uses a supercomputer to simulate the folding behavior of polyalanine, a small polypeptide (molecule with many peptide bonds). They form polyalanine by adding molecules of the amino acid alanine one at a time to a chain. Each time a piece is added to the chain they seek out the best possible shape or conformation for the new polypeptide. The problem gets more difficult each time you add a link to the chain because their method takes into consideration the interactions between each possible pair of links.

The researchers chose alanine as their model molecule because it is relatively small and because its structure and behavior are well understood through empirical study. This information based on observation gives them a basis for comparison with the results of their theoretical simulations. However, polyalanines are more difficult to build in a test tube than in a computer! The group also simulates other proteins, when they are testing and tuning their methods.

Getting To Know You: This model will introduce you to L-alanine! L-alanine is the left-handed form, and dominant form in nature, for alanine and all other amino acids. Click the ADD button to build up the molecule from its constituent groups. Moving the pointer over specific atoms and bonds will give you more information, and the buttons on the left will highlight different structures. Try the question marks for definitions.