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 New Test for Rare Immunodeficiency
23.08.2017 | Universität Basel

nachricht Repairing damaged hearts with self-healing heart cells
22.08.2017 | National University Health System

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

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

26.07.2017 | Event News

 
Latest News

Cholesterol-lowering drugs may fight infectious disease

22.08.2017 | Health and Medicine

Meter-sized single-crystal graphene growth becomes possible

22.08.2017 | Materials Sciences

Repairing damaged hearts with self-healing heart cells

22.08.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>