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Researchers
simulate complete structure of virus–on computer
Jim
Barlow, Life Sciences Editor
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Image by Anton
Arkhipov using VMD software
An overall
computer-simulated view of the satellite tobacco mosaic
virus.
Credit:
University of Illinois at Urbana-Champaign's Theoretical and
Computational Biophysics Group.
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CHAMPAIGN, Ill. —
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.
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.
Source
/ Credit: University of Illinois at Urbana-Champaign's
Theoretical and Computational Biophysics Group.
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