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Wit, grit and a supercomputer yield chemical structure of HIV capsid

Researchers report that they have determined the precise chemical structure of the HIV capsid, a protein shell that protects the virus’s genetic material and is a key to its virulence.

Wit, grit and a supercomputer yield chemical structure of HIV capsid

Researchers report that they have determined the precise chemical structure of the HIV capsid, a protein shell that protects the virus’s genetic material and is a key to its virulence.

The capsid has become an attractive target for the development of new antiretroviral drugs.

The report appears in the journal Nature.

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 – 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.)

Read more at news.illinois.edu.

 

 

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