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 Force Sensors
20.09.2017 | Max-Planck-Institut für Biochemie

nachricht Foster tadpoles trigger parental instinct in poison frogs
20.09.2017 | Veterinärmedizinische Universität Wien

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Tiny lasers from a gallery of whispers

New technique promises tunable laser devices

Whispering gallery mode (WGM) resonators are used to make tiny micro-lasers, sensors, switches, routers and other devices. These tiny structures rely on a...

Im Focus: Ultrafast snapshots of relaxing electrons in solids

Using ultrafast flashes of laser and x-ray radiation, scientists at the Max Planck Institute of Quantum Optics (Garching, Germany) took snapshots of the briefest electron motion inside a solid material to date. The electron motion lasted only 750 billionths of the billionth of a second before it fainted, setting a new record of human capability to capture ultrafast processes inside solids!

When x-rays shine onto solid materials or large molecules, an electron is pushed away from its original place near the nucleus of the atom, leaving a hole...

Im Focus: Quantum Sensors Decipher Magnetic Ordering in a New Semiconducting Material

For the first time, physicists have successfully imaged spiral magnetic ordering in a multiferroic material. These materials are considered highly promising candidates for future data storage media. The researchers were able to prove their findings using unique quantum sensors that were developed at Basel University and that can analyze electromagnetic fields on the nanometer scale. The results – obtained by scientists from the University of Basel’s Department of Physics, the Swiss Nanoscience Institute, the University of Montpellier and several laboratories from University Paris-Saclay – were recently published in the journal Nature.

Multiferroics are materials that simultaneously react to electric and magnetic fields. These two properties are rarely found together, and their combined...

Im Focus: Fast, convenient & standardized: New lab innovation for automated tissue engineering & drug

MBM ScienceBridge GmbH successfully negotiated a license agreement between University Medical Center Göttingen (UMG) and the biotech company Tissue Systems Holding GmbH about commercial use of a multi-well tissue plate for automated and reliable tissue engineering & drug testing.

MBM ScienceBridge GmbH successfully negotiated a license agreement between University Medical Center Göttingen (UMG) and the biotech company Tissue Systems...

Im Focus: Silencing bacteria

HZI researchers pave the way for new agents that render hospital pathogens mute

Pathogenic bacteria are becoming resistant to common antibiotics to an ever increasing degree. One of the most difficult germs is Pseudomonas aeruginosa, a...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

“Lasers in Composites Symposium” in Aachen – from Science to Application

19.09.2017 | Event News

I-ESA 2018 – Call for Papers

12.09.2017 | Event News

EMBO at Basel Life, a new conference on current and emerging life science research

06.09.2017 | Event News

 
Latest News

Molecular Force Sensors

20.09.2017 | Life Sciences

Producing electricity during flight

20.09.2017 | Power and Electrical Engineering

Tiny lasers from a gallery of whispers

20.09.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>