2013 JUN 10 (NewsRx) -- By a News Reporter-Staff News Editor at AIDS Weekly -- The report appears as the cover article in the journal Nature (see also HIV/AIDS).
Scientists have long sought to understand how the HIV capsid is constructed, and many studies have chipped away at its mystery. Researchers have used a variety of laboratory techniques - cryo-electron microscopy, cryo-EM tomography, nuclear magnetic resonance spectroscopy and X-ray crystallography, to name a few - to peer at individual parts of the capsid in revealing detail, or to get a sense of the whole.
Until the arrival of petascale supercomputers, however, no one could piece together the entire HIV capsid - an assemblage of more than 1,300 identical proteins forming a cone-shaped structure - in atomic-level detail. The simulations that added the missing pieces to the puzzle were conducted during testing of Blue Waters, a new supercomputer at the National Center for Supercomputing Applications at the University of Illinois.
"This is a big structure, one of the biggest structures ever solved," said U. of I. physics professor Klaus Schulten, who, with postdoctoral researcher Juan R. Perilla, conducted the molecular simulations that integrated data from laboratory experiments performed by colleagues at the University of Pittsburgh and Vanderbilt University. "It was very clear that it would require a huge amount of simulation - the largest simulation ever published - involving 64 million atoms." (Watch a video about the research.)
Previous research had established that the HIV capsid contained a number of identical proteins. Scientists knew that the proteins were arranged into pentagons and hexagons, and guessed that the pentagons formed the most tightly rounded corners of the capsid shape seen under an electron microscope. But they did not know how many of these protein building blocks were needed, or how the pentagons and hexagons fit together to form the capsid.
Keywords for this news article include: Virion, HIV/AIDS, Peptides, Proteins, Amino Acids, RNA Viruses, Nucleocapsid, Retroviridae, HIV Infections, Vertebrate Viruses, Primate Lentiviruses, Viral Sexually Transmitted Diseases, University of Illinois at Urbana-Champaign.
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