Simulating protein folding on a supercomputer Researchers use physical laws to simulate protein folding on supercomputer By Bill Steele Researchers at Cornell have had their best success yet in simulating the folding of a protein solely from the physical laws that govern the behavior of its atoms. A group led by Harold Scheraga, the Todd Professor of Chemistry emeritus, simulated the folding of the protein HDEA from the bacterium E. coli on Cornell's IBM supercomputer and predicted a structure consisting of a bundle of five spiral coils that matched 80 percent of the structure found by X-ray crystallography. CASP-3 is a cooperative experiment to test the accuracy of computer simulations of protein folding. Scheraga's group submitted seven structures out of the CASP list of 43 and had solid successes with two of those. The Scheraga group produced the best match to the actual structure of any simulation based solely on physical laws, although other groups found more accurate matches by using programs that compared the simulated structure with the structures of similar, already-known proteins.
Cells make proteins by stringing together long chains of organic molecules called amino acids.
The chain quickly folds into a compact shape, something like the way a piece of string will bunch up if you push the ends together. The folding is driven by the attractions and repulsions between the positive and negative electric charges of the atoms making up the molecules. That final shape determines the biological activity of the protein. Enzymes, for example, do their work because parts of them match the shapes of the molecules whose reactions they control. Being able to predict the shape from the sequence of amino acids would help biologists identify the functions of proteins made by certain genes, such as those associated with Alzheimer's disease, cystic fibrosis and other hereditary disorders.