PROTEIN FOLDING ON A CHIP

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PROTEIN FOLDING ON A CHIP
12 May 2007 - DOE/Brookhaven National Laboratory

Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory are proposing to use a supercomputer originally developed to simulate elementary particles in high-energy physics to help determine the structures and functions of proteins, including, for example, the 30,000 or so proteins encoded by the human genome. Structural information will help scientists better understand proteins’ role in disease and health, and may lead to new diagnostic and therapeutic agents.

Unlike typical parallel processors, the 10,000 processors in this supercomputer (called Quantum Chromodynamics on a Chip, or QCDOC, for its original application in physics) each contain their own memory and the equivalent of a 24-lane superhighway for communicating with one another in six dimensions. This configuration allows the supercomputer to break the task of deciphering the three-dimensional arrangement of a protein’s atoms, 100,000 in a typical protein, into smaller chunks of 10 atoms per processor. Working together, the chips effectively cut the computing time needed to solve a protein’s structure by a factor of 1000, says James Davenport, a physicist at Brookhaven. This would reduce the time for a simulation from approximately 20 years to 1 week.

“The computer analyzes the forces of attraction and repulsion between atoms, depending on their positions, distances, and angles. It shuffles through all the possible arrangements to arrive at the most stable three-dimensional configuration,” Davenport says.

The technique is complementary to other methods of protein-structure determination, such as x-ray crystallography, where the pattern of x-rays scattering off atoms in crystallized proteins is used to determine structure. It will be particularly useful for proteins that are impossible or difficult to crystallize, such as those that control the movement of molecules across the cellular membrane. The high-speed analysis will also allow scientists to study how proteins change as they interact or undergo other biochemical processes, which will give them more information about the proteins’ functions than available from structural studies alone.

Davenport and colleagues at Stony Brook University will test their application on a QCDOC machine that has been developed for physics applications at Brookhaven by Columbia University, IBM, and the RIKEN/BNL Research Center.

http://www.bnl.gov

About: DOE/Brookhaven National Laboratory
Established in 1947 on Long Island, Upton, New York, Brookhaven is a multi-program national laboratory operated by Brookhaven Science Associates for the US Department of Energy (DOE). Six Nobel Prizes have been awarded for discoveries made at the Lab.

Brookhaven has a staff of approximately 3,000 scientists, engineers, technicians and support staff and over 4,000 guest researchers annually.

Brookhaven National Laboratory's role for the DOE is to produce excellent science and advanced technology with the cooperation, support, and appropriate involvement of our scientific and local communities. The fundamental elements of the Laboratory's role in support of the four DOE strategic missions are the following:

To conceive, design, construct, and operate complex, leading edge, user-oriented facilities in response to the needs of the DOE and the international community of users.

To carry out basic and applied research in long-term, high-risk programs at the frontier of science.

To develop advanced technologies that address national needs and to transfer them to other organizations and to the commercial sector.

To disseminate technical knowledge, to educate new generations of scientists and engineers, to maintain technical capabilities in the nation's workforce, and to encourage scientific awareness in the general public.

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