Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Researchers simulate complete structure of virus -- on a computer

15.03.2006


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.

Jim Barlow | EurekAlert!
Further information:
http://www.uiuc.edu

More articles from Life Sciences:

nachricht Molecular microscopy illuminates molecular motor motion
26.07.2017 | Penn State

nachricht New virus discovered in migratory bird in Rio Grande do Sul, Brazil
26.07.2017 | Fundação de Amparo à Pesquisa do Estado de São Paulo

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Carbon Nanotubes Turn Electrical Current into Light-emitting Quasi-particles

Strong light-matter coupling in these semiconducting tubes may hold the key to electrically pumped lasers

Light-matter quasi-particles can be generated electrically in semiconducting carbon nanotubes. Material scientists and physicists from Heidelberg University...

Im Focus: Flexible proximity sensor creates smart surfaces

Fraunhofer IPA has developed a proximity sensor made from silicone and carbon nanotubes (CNT) which detects objects and determines their position. The materials and printing process used mean that the sensor is extremely flexible, economical and can be used for large surfaces. Industry and research partners can use and further develop this innovation straight away.

At first glance, the proximity sensor appears to be nothing special: a thin, elastic layer of silicone onto which black square surfaces are printed, but these...

Im Focus: 3-D scanning with water

3-D shape acquisition using water displacement as the shape sensor for the reconstruction of complex objects

A global team of computer scientists and engineers have developed an innovative technique that more completely reconstructs challenging 3D objects. An ancient...

Im Focus: Manipulating Electron Spins Without Loss of Information

Physicists have developed a new technique that uses electrical voltages to control the electron spin on a chip. The newly-developed method provides protection from spin decay, meaning that the contained information can be maintained and transmitted over comparatively large distances, as has been demonstrated by a team from the University of Basel’s Department of Physics and the Swiss Nanoscience Institute. The results have been published in Physical Review X.

For several years, researchers have been trying to use the spin of an electron to store and transmit information. The spin of each electron is always coupled...

Im Focus: The proton precisely weighted

What is the mass of a proton? Scientists from Germany and Japan successfully did an important step towards the most exact knowledge of this fundamental constant. By means of precision measurements on a single proton, they could improve the precision by a factor of three and also correct the existing value.

To determine the mass of a single proton still more accurate – a group of physicists led by Klaus Blaum and Sven Sturm of the Max Planck Institute for Nuclear...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

Closing the Sustainability Circle: Protection of Food with Biobased Materials

21.07.2017 | Event News

»We are bringing Additive Manufacturing to SMEs«

19.07.2017 | Event News

 
Latest News

CCNY physicists master unexplored electron property

26.07.2017 | Physics and Astronomy

Molecular microscopy illuminates molecular motor motion

26.07.2017 | Life Sciences

Large-Mouthed Fish Was Top Predator After Mass Extinction

26.07.2017 | Earth Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>