Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Researcher uses supercomputer to model a SARS viral enzyme

17.08.2004


A Mayo Clinic researcher is the first to develop a series of three-dimensional (3D) models of an enzyme responsible for the replication of the deadly SARS (Severe Acute Respiratory syndrome) virus. These instantaneous "structures-in-time" are central to designing an anti-SARS drug -- and are therefore a welcome advance as the virus continues to threaten public health.

The structure and dynamics of the SARS viral enzyme, called chymotrypsin-like cysteine proteinase, is described in the online version of the journal Proteins: Structure, Function, and Bioinformatics. Mayo Clinic researcher Yuan-Ping Pang, Ph.D., a chemist and head of the Computer-Aided Molecular Design Laboratory, reports results produced by the terascale computer he designed, built and managed. Using 800 PC processors harnessed together, Dr. Pang analyzed the SARS viral genome and built, atom by atom, the instantaneous 3D structures of the viral enzyme -- each of which is composed of 8,113 atoms -- just 20 days after the SARS viral genome was made public.

Significance of Mayo Clinic Research



By performing exceptionally large-scale computer simulations, which his powerful computer system is capable of performing, Dr. Pang was able to quickly and correctly convert a genomic sequence into the 3D structures of a protein that encodes the blueprint for an anti-SARS drug. This ability is crucial in digesting the information available from the emerging fields of genomics and proteomics and in combating emerging infectious diseases. This work also demonstrates the successful use of low-cost, "homemade" computers for large-scale simulations of biological systems.

The Race for SARS Viral Enzyme Structure

Since the SARS outbreak emerged in early 2003, international researchers raced to obtain the 3D structure of the key SARS viral enzyme so drug design could progress. To date, three independent X-ray crystallography groups have decoded the 3D structures, which are expressed as atomic coordinates. Dr. Pang deposited computer-derived coordinates of his 3D instantaneous structures to the Protein Data Bank on April 30, 2003, and released these structures to the public on July 2, 2003 -- 27 days before the release of the first X-ray structure.

The Next Step

Now that he knows the attributes of the SARS viral enzyme, Dr. Pang uses his customized computers to assess a Mayo in-house chemicals database -- a kind of "dictionary of small molecules" -- that his team built. It contains attributes such as molecular weight, shape and polarity of 2.5 million unique chemical structures. His goal is to match their properties with the computer-revealed dynamic properties of the key SARS viral enzyme -- and by so doing, discover an anti-SARS drug. He is also pushing toward faster computer systems, aiming at petaflops speed -- that’s one thousand trillion floating-point operations per second.

Dr. Pang and Andrea Dooley, a summer undergraduate student from Massachusetts Institute of Technology, have finished this search at Mayo and just sent 20 computer-identified small molecules to Southern Research Institute in Birmingham, Ala. for further testing as anti-SARS drugs.

| EurekAlert!
Further information:
http://www.mayo.edu
http://www3.interscience.wiley.com/cgi-bin/fulltext/109593993/HTMLSTART

More articles from Life Sciences:

nachricht Hopkins researchers ID neurotransmitter that helps cancers progress
25.04.2019 | Johns Hopkins Medicine

nachricht Trigger region found for absence epileptic seizures
25.04.2019 | RIKEN

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Full speed ahead for SmartEEs at Automotive Interiors Expo 2019

Flexible, organic and printed electronics conquer everyday life. The forecasts for growth promise increasing markets and opportunities for the industry. In Europe, top institutions and companies are engaged in research and further development of these technologies for tomorrow's markets and applications. However, access by SMEs is difficult. The European project SmartEEs - Smart Emerging Electronics Servicing works on the establishment of a European innovation network, which supports both the access to competences as well as the support of the enterprises with the assumption of innovations and the progress up to the commercialization.

It surrounds us and almost unconsciously accompanies us through everyday life - printed electronics. It starts with smart labels or RFID tags in clothing, we...

Im Focus: Energy-saving new LED phosphor

The human eye is particularly sensitive to green, but less sensitive to blue and red. Chemists led by Hubert Huppertz at the University of Innsbruck have now developed a new red phosphor whose light is well perceived by the eye. This increases the light yield of white LEDs by around one sixth, which can significantly improve the energy efficiency of lighting systems.

Light emitting diodes or LEDs are only able to produce light of a certain colour. However, white light can be created using different colour mixing processes.

Im Focus: Quantum gas turns supersolid

Researchers led by Francesca Ferlaino from the University of Innsbruck and the Austrian Academy of Sciences report in Physical Review X on the observation of supersolid behavior in dipolar quantum gases of erbium and dysprosium. In the dysprosium gas these properties are unprecedentedly long-lived. This sets the stage for future investigations into the nature of this exotic phase of matter.

Supersolidity is a paradoxical state where the matter is both crystallized and superfluid. Predicted 50 years ago, such a counter-intuitive phase, featuring...

Im Focus: Explosion on Jupiter-sized star 10 times more powerful than ever seen on our sun

A stellar flare 10 times more powerful than anything seen on our sun has burst from an ultracool star almost the same size as Jupiter

  • Coolest and smallest star to produce a superflare found
  • Star is a tenth of the radius of our Sun
  • Researchers led by University of Warwick could only see...

Im Focus: Quantum simulation more stable than expected

A localization phenomenon boosts the accuracy of solving quantum many-body problems with quantum computers which are otherwise challenging for conventional computers. This brings such digital quantum simulation within reach on quantum devices available today.

Quantum computers promise to solve certain computational problems exponentially faster than any classical machine. “A particularly promising application is the...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Revered mathematicians and computer scientists converge with 200 young researchers in Heidelberg!

17.04.2019 | Event News

First dust conference in the Central Asian part of the earth’s dust belt

15.04.2019 | Event News

Fraunhofer FHR at the IEEE Radar Conference 2019 in Boston, USA

09.04.2019 | Event News

 
Latest News

High-efficiency thermoelectric materials: New insights into tin selenide

25.04.2019 | Materials Sciences

Salish seafloor mapping identifies earthquake and tsunami risks

25.04.2019 | Earth Sciences

Using DNA templates to harness the sun's energy

25.04.2019 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>