Simulating protein folding from physical laws

ITHACA, N.Y. -- Researchers at Cornell University 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. It was the best match of several computer-generated structures for the protein submitted to the Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP-3), which took place over the second half of 1998.

CASP-3 is a cooperative experiment to test the accuracy of computer simulations of protein folding. Researchers are given the amino-acid sequence of a number of proteins for which the shape has already been determined by X-ray crystallography or nuclear magnetic resonance techniques and asked to submit their computer solution for the structure.

Scheraga's group submitted seven structures out of the CASP list of 43 and had solid successes with two of those. In addition to HDEA, they scored high with another protein, called MarA. 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. The final shape w

Contact: Bill Steele
Cornell University News Service

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