Test Flying a Virus
- From: "whitesickle@xxxxxxx" <whitesickle@xxxxxxx>
- Date: Tue, 14 Mar 2006 13:29:39 -0500 (EST)
Public release date: 14-Mar-2006
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Contact: Jim Barlow, Life Sciences Editor
jebarlow@xxxxxxxx
217-333-5802
University of Illinois at Urbana-Champaign
Researchers simulate complete structure of virus -- on a computer
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An overall computer-simulated view of the satellite tobacco mosaic
virus credit: University of Illinois/NCSA
Click here for a high resolution image.
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When Boeing and Airbus developed their latest aircraft, the companies'
engineers designed and tested them on a computer long before the planes
were built. Biologists are catching on. They've just completed the
first computer simulation of an entire life form -- a virus.
In their quest to study life, biologists apply engineering knowledge
somewhat differently: They "reverse engineer" life forms, test fly them
in the computer, and see if they work in silico the way they do in
vivo. This technique previously had been employed for small pieces of
living cells, such as proteins, but not for an entire life form until
now.
The accomplishment, performed by computational biologists at the
University of Illinois at Urbana-Champaign and crystallographers at the
University of California at Irvine, is detailed in the March issue of
the journal Structure.
Deeper understanding of the mechanistic properties of viruses, the
researchers say, could not only contribute to improvements in public
health, but also in the creation of artificial nanomachines made of
capsids -- a small protein shell that contains a viral building plan, a
genome, in the form of DNA or RNA.
Viruses are incredibly tiny and extremely primitive life forms that
cause myriad diseases. Biologists often refer to them as particles
rather than organisms. Viruses hijack a biological cell and make it
produce many new viruses from a single original. They've evolved
elaborate mechanisms of cell infection, proliferation and departure
from the host when it bursts from viral overcrowding.
For their first attempt to reverse engineer a life form in a computer
program, computational biologists selected the satellite tobacco mosaic
virus because of its simplicity and small size.
The satellite virus they chose is a spherical RNA sub-viral agent that
is so small and simple that it can only proliferate in a cell already
hijacked by a helper virus -- in this case the tobacco mosaic virus
that is a serious threat to tomato plants.
A computer program was used to reverse engineer the dynamics of all
atoms making up the virus and a small drop of salt water surrounding
it. The virus and water contain more than a million atoms altogether.
The necessary calculation was done at Illinois on one of the world's
largest and fastest computers operated by the National Center for
Supercomputing Applications. The computer simulations provided an
unprecedented view into the dynamics of the virus.
"The simulations followed the life of the satellite tobacco mosaic
virus, but only for a very brief time," said co-author Peter
Freddolino, a doctoral student in biophysics and computational biology
at Illinois. "Nevertheless, they elucidated the key physical properties
of the viral particle as well as providing crucial information on its
assembly."
It may take still a long time to simulate a dog wagging its tail in the
computer, said co-author Klaus Schulten, Swanlund Professor of Physics
at Illinois. "But a big first step has been taken to 'test fly' living
organisms," he said. "Naturally, this step will assist modern medicine
as we continue to learn more about how viruses live."
The computer simulations were carried out in Schulten's Theoretical and
Biophysics Group's lab at the Beckman Institute for Avanced Science and
Technology.
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Other co-authors were Anton Arkhipov, a doctoral student in physics at
Illinois, and Alexander McPherson, a professor of molecular biology and
biochemistry, and research specialist Steven Larson, both at UC-Irvine.
The work was supported by the National Institutes of Health and by
computing time from NCSA through its National Science Foundation
funding.
The Beckman Institute is an interdisciplinary research institute
devoted to basic research in the physical sciences, computation,
engineering, and biological, behavioral, and cognitive sciences.
.
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