Researchers simulate complete structure of virus–on computer

March 14, 2006
Researchers simulate complete structure of virus–on computer
An overall computer-simulated view of the satellite tobacco mosaic virus. Credit: University of Illinois/NCSA

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.

Source: University of Illinois at Urbana-Champaign

Explore further: A passion to defeat the whitefly

Related Stories

A passion to defeat the whitefly

November 6, 2015

University of New Mexico alumna Laura Boykin (Ph.D. 2003) was recently featured in the article, "12 Badass Scientists...Who Also Happen to be Women" released by Ted Fellows, a program that falls under the purview of TED (Technology, ...

Gravity, who needs it? NASA studies your body in space

November 18, 2015

What happens to your body in space? NASA's Human Research Program has been unfolding answers for over a decade. Space is a dangerous, unfriendly place. Isolated from family and friends, exposed to radiation that could increase ...

Study adds to evidence that viruses are alive

September 25, 2015

A new analysis supports the hypothesis that viruses are living entities that share a long evolutionary history with cells, researchers report. The study offers the first reliable method for tracing viral evolution back to ...

Pacific preparedness

October 26, 2015

Not far from Tokyo's Imperial Palace, an alarm pierces the air. At a nearby elementary school, hundreds of children drop to the floor, scramble beneath their desks and hold on for dear life. It's March 9, 2012, two days before ...

Viruses join fight against harmful bacteria

September 23, 2015

In the hunt for new ways to kill harmful bacteria, scientists have turned to a natural predator: viruses that infect bacteria. By tweaking the genomes of these viruses, known as bacteriophages, researchers hope to customize ...

Recommended for you

Roboticists learn to teach robots from babies

December 1, 2015

Babies learn about the world by exploring how their bodies move in space, grabbing toys, pushing things off tables and by watching and imitating what adults are doing.

Getting into the flow on the International Space Station

December 1, 2015

Think about underground water and gas as they filter through porous materials like soil and rock beds. On Earth, gravity forces water and gas to separate as they flow through the ground, cleaning the water and storing it ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.