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Supercomputer paints electric landscape of cellular structures

Researchers create atomic-resolution maps of microtubules and ribosomes

SAN DIEGO, CA-Researchers at the University of California, San Diego have mapped key cellular structures using a new method to harness the power of supercomputing. The maps may point the way to understanding how those structures perform functions such as transporting a drug like taxol to a binding site so it can do its work in treating breast cancer.

"We've achieved a new landmark in the scale of cellular structures that we can model from a molecular perspective," said J. Andrew McCammon, Joseph E. Mayer Professor of Theoretical Chemistry at UCSD and an Howard Hughes Medical Institute investigator. "The work signals a new era of calculations on cellular-scale structures in biology."

The researchers created a new method for solving what is known as known as the Poisson-Boltzmann equation. This allowed them to increase the size of the systems they could model from less than 50,000 atoms to over an unprecedented million atoms. McCammon likened the ability to pick out one atom within such a large three-dimensional system as being able to specifically describe one cherry within an entire fruit tree.

The maps depict an atom-by-atom rendering of the electrostatic potential of structures found within cells: microtubules, which are involved in intracellular transport and shape, and ribosomes, which manufacture proteins. Electrostatics describe the way in which the landscape of electrical charge is laid out in a molecular environment, for example, the electric forces that draw a taxol molecule through a microtubule and into a binding site or that tug a tRNA molecule into place on a ribosome during translation.

The calculations were performed at the San Diego Supercomputer Center (SDSC) at UCSD on Blue Horizon, a large IBM SP supported by the National Partnership for Advanced Computational Infrastructure (NPACI). The work will appear online in the Proceedi
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Contact: Cassie Ferguson
cferguson@sdsc.edu
858 822-3622
University of California - San Diego
20-Aug-2001


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