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Study of HIV Virus Using Supercomputer May Unveil New Ways to Prevent AIDS [VIDEO]

May 30, 2013 11:58 AM EDT
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For the first time, scientists have determined the precise chemical structure of the HIV capsid, a protein shell that acts as armor for the virus’s genetic material and a key weapon when attacking the human body’s defenses.

Published in the journal Nature, the study includes detailed simulations achieved through the use of a supercomputer on a 64 million atom sample.

Called Blue Waters, the machine is one of the world’s most powerful computers and through its computing power, scientists were able to decipher in atomic-level the assemblage of the 1,300 proteins that together form the capsid.

“The sustained petascale performance of Blue Waters is precisely what enabled these talented researchers to explore new methods combined with structural and electron microscopy data to reliably model the chemical structure of the HIV capsid in great detail,” said Irene Qualters, the program manager for Advanced Cyberinfrastructure, in a press release.

At its peak performance, according to the National Science Foundation who funded the building of Blue Waters, the machine is capable of nearly 12 quadrillion floating point operations per second – 12 times the degree of operation necessary for a computer to be dubbed a petascale supercomputer.

Thus, by using Blue Waters, researchers were able to add missing pieces to the puzzle of the HIV capsid that, until they were discovered, halted reseachers searching to combat the virus.

“This is a big structure, one of the biggest structures ever solved,” said Klaus Schulten of the University of Illinois who, along with postdoctoral researcher Juan Perillia, conducted the molecular simulations that integrated data from laboratory experiments performed by colleagues at the University of Pittsburgh and Vanderbilt University.

For this reason, he said, it was clear from the beginning that the study “would require a huge amount of simulation – the largest simulation ever published – involving 64 million atoms.”

Specifically, the team discovered that, among other things, the interactions among specific regions of the proteins that were “critical for capsid assembly and stability, and for viral infectivity.”

In the end, the researchers argue, understanding such aspects of the virus can only help in the development of new antiretroviral drugs designed to suppress the HIV virus and halt the progress of AIDS.

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