Potential Programming

Protein modelers start out with a chain of amino acids that is already bonded toegther. They focus on nonbonded interactions between the atoms and groups of atoms in the chain, giving this chain directions to fold into the most relaxed state possible, based on its potential energy. The potential energy is a measure of the energy stored in the molecule.

The most powerful force in these interactions is the Van der Waals force. It is a stabilizing force which pulls distant atoms towards each other, but prevents them from colliding by becoming repellant in close quarters. This is the dominant force at work inside a lively molecule that contribute to the calculation of its potential energy. Modelers also incorporate the interactions between atoms and groups of differing electrical charges. You can see how this electrostatic force affects the energy level of a simple ethane molecule in the model at right.)

Scheraga's group has devised their own formula for calculating the potential energy of a molecule, building up from the behaviors of individual atoms to the folding of molecules. Researchers refer to this method as a potential function or simply a "potential." Scheraga is constantly refining their version of the potential function. The group uses the amino acid alanine, which is well understood from laboratory study, as one of the test molecules.

A Repulsive Matter: Why do rotational states (a.k.a. rotamers) of the same molecule often have different energies? A (simplified) answer to this question uses a basic fact of electrostatics--namely, that like charges repel. In a simple molecule such as ethane, the most stable rotamer is the one that maximizes the distance between the electron clouds of opposing carbon-hydrogen bonds, putting the least amount of torsional strain on the molecule. Chemists call this stable configuration the staggered conformation (when the molecule is sighted down the carbon-carbon bond, the hydrogens appear to be perfectly staggered).

You can add the electron clouds to the model by sliding the transparency control to the left. Experiment with the rest of the controls to explore the model.