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 When Air is in Short Supply - Shedding light on plant stress reactions when oxygen runs short
23.03.2017 | Institut für Pflanzenbiochemie

nachricht WPI team grows heart tissue on spinach leaves
23.03.2017 | Worcester Polytechnic Institute

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

When Air is in Short Supply - Shedding light on plant stress reactions when oxygen runs short

23.03.2017 | Life Sciences

Researchers use light to remotely control curvature of plastics

23.03.2017 | Power and Electrical Engineering

Sea ice extent sinks to record lows at both poles

23.03.2017 | Earth Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>