Research at the Pittsburgh Supercomputing Center on how a new born protein changes into its mature shape has been nominated finalist for the 1999 Computerworld Smithsonian Award in Science. The project, that is a collaboration between PSC and two scientific researchers of the University of California in San Francisco, Peter Kollman and Yong Duan, is the longest-ever simulation of the folding action of a protein.
The "protein-folding problem", as it is referred to by scientists, addresses the question of how in the first few microseconds of its existence a protein transforms from a stretched-out chain of amino acids to a folded structure. It is only in its final shape, usually a bundle of complex twists, turns and helices, that a protein can do its biological job. If scientists can learn the rules governing the folding process, it will be possible in theory to design drugs for particular tasks.
Recent research for instance, suggests that certain diseases, like "mad cow" and Alzheimer's disease, are malfunctions in protein folding, that could be amenable to drug therapy. The scientists have utilized powerful computers to simulate these folding processes. Such studies helped develop new cancer drugs, for example, but the studies are severely limited by the huge amount of computing time required.
Kollman and Duan developed improved protein-simulation software that can exploit massively parallel systems, like the CRAY T3D and CRAY T3E at PSC much more effectively than in the past. Using this software, and computing resources at Pittsburgh and at Cray Research, Duan and Kollman simulated the folding of a small protein in water for a full microsecond, or at least 100 times longer than prior similar simulations.
The results, which were reported in Science, the leading United States scientific journal, offer new insight into the folding process. This protein-folding simulation is one among five projects chosen nationally as the finalists for the CWSA science award. You can find more information, including graphics, about this research at the home page of the Pittsburgh Supercomputing Center.