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Primeur weekly 2011-11-14

Special

International data Grids to be highlighted by RENCI at SC11 ...

Japan's K Computer tops 10 Petaflop/s to stay atop TOP500 List ...

NASA and DOE's Lawrence Livermore National Laboratory confirm Obsidian's BGFC first order functionality ...

Adaptive Computing delivers intelligent Grid resource management to Gaea, NOAA's new climate modelling and research system ...

Exascale supercomputing

NCAR selects IBM for key components of new Supercomputing Center ...

The Cloud

Terascala announces enhanced version of proven storage management solution for fast data analysis in the Cloud and in shared resource environments ...

Terascala announces support for Lustre 2,1 ...

The Green Grid and Open Data Center Alliance form strategic collaboration to drive efficient Cloud resource standards ...

EuroFlash

Submissions for ISC research papers and tutorials now being accepted ...

Post Doc position available at INAF in Catania, Sicily ...

DataDirect Networks' groundbreaking Storage Fusion Architecture (SFA) System selected to power Europe's fastest supercomputer ...

European industry and research centres join forces to create a European Technology Platform for High Performance Computing ...

Russian Academy of Sciences expands GPU supercomputing infrastructure to accelerate scientific research ...

PRACE to issue project access 4th call for proposals for Tier-0 and Synchronized Call for Tier-1 ...

USFlash

Terascala announces membership in OpenSFS ...

Supercomputers accelerate development of advanced materials ...

Kraken set to deliver 2 billionth CPU hour, sustains 96 percent utilization ...

NEC developing next generation vector supercomputer - aiming for the world's leading energy-efficient supercomputer ...

Blacklight goes to work at the Pittsburgh Supercomputing Center ...

Fujitsu launches PRIMEHPC FX10 supercomputer ...

Platform Computing announces support for upcoming Intel Many Integrated Core architecture-based products ...

NASA selects next-generation SGI ICE HPC platform for technology upgrade ...

SDSC's Triton Resource helps develop new model for forecasting California solar power production ...

U.S. Department of Energy Laboratory selects DataDirect Networks' SFA12K Storage to enable clean energy technology insight and discovery ...

Rensselaer Polytechnic Institute researchers use supercomputer to study effects of stacking graphene nanoribbons ...

Appro has been selected for the second time to support the High Performance Computing Modernization Programme (HPCMP) to improve supercomputing capabilities ...

Chinese researchers tap GPU supercomputer for world's first simulation of complete H1N1 virus ...

For the first time, IBM brings mainframe and Windows together ...

AMD processors power leading research and academic supercomputers ...

Mali-T658 GPU extends graphics and GPU compute leadership for high performance devices ...

ORNL fundamental discovery casts enzymes in new light ...

Altera's Stratix IV FPGAs deliver unprecedented acceleration for world's most powerful reconfigurable supercomputer ...

ORNL fundamental discovery casts enzymes in new light

8 Nov 2011 Oak Ridge - A tree outside Oak Ridge National Laboratory researcher Pratul Agarwal's office window provided the inspiration for a discovery that may ultimately lead to drugs with fewer side effects, less expensive biofuels and more.

Just as a breeze causes leaves, branches and ultimately the tree to move, enzymes moving at the molecular level perform hundreds of chemical processes that have a ripple effect necessary for life. Previously, protein complexes were viewed as static entities with biological function understood in terms of direct interactions, but that isn't the case. This finding, published inPLoS Biology, may have enormous implications.

"Our discovery is allowing us to perhaps find the knobs that we can use to improve the catalytic rate of enzymes and perform a host of functions more efficiently", stated Pratul Agarwal, a member of the Department of Energy laboratory's Computer Science and Mathematics Division.

Making this discovery possible was ORNL's supercomputer, Jaguar, which allowed Pratul Agarwal and co-author Arvind Ramanathan to investigate a large number of enzymes at the atomistic scale.

The researchers found that enzymes have similar features that are entirely preserved from the smallest living organism - bacteria - to complex life forms, including humans.

"If something is important for function, then it will be present in the protein performing the same function across different species", Pratul Agarwal stated. "For example, regardless of which company makes a car, they all have wheels and brakes."

Similarly, scientists have known for decades that certain structural features of the enzyme are also preserved because of their important function. Pratul Agarwal and Arvind Ramanathan believe the same is true for enzyme flexibility.

"The importance of the structure of enzymes has been known for more than 100 years, but only recently have we started to understand that the internal motions may be the missing piece of the puzzle to understand how enzymes work", Pratul Agarwal stated. "If we think of the tree as the model, the protein move at the molecular level with the side-chain and residues being the leaves and the protein backbone being the entire stem."

This research builds on previous work in which Agarwal identified a network of protein vibrations in the enzyme Cyclphilin A, which is involved in many biological reactions, including AIDS-causing HIV-1.

While Pratul Agarwal sees this research perhaps leading to medicines able to target hard to cure diseases such as AIDS, he is also excited about its energy applications, specifically in the area of cellulosic ethanol. Highly efficient enzymes could bring down the cost of biofuels, making them a more attractive option.

Funding for this research was provided by ORNL's Laboratory Directed Research and Development program. Arvind Ramanathan was a graduate student at Carnegie Mellon University when this work began and now also works at ORNL. The paper is titled "Evolutionarily conserved linkage between enzyme fold, flexibility and catalysis".
Source: DOE/Oak Ridge National Laboratory

Back to Table of contents

Primeur weekly 2011-11-14

Special

International data Grids to be highlighted by RENCI at SC11 ...

Japan's K Computer tops 10 Petaflop/s to stay atop TOP500 List ...

NASA and DOE's Lawrence Livermore National Laboratory confirm Obsidian's BGFC first order functionality ...

Adaptive Computing delivers intelligent Grid resource management to Gaea, NOAA's new climate modelling and research system ...

Exascale supercomputing

NCAR selects IBM for key components of new Supercomputing Center ...

The Cloud

Terascala announces enhanced version of proven storage management solution for fast data analysis in the Cloud and in shared resource environments ...

Terascala announces support for Lustre 2,1 ...

The Green Grid and Open Data Center Alliance form strategic collaboration to drive efficient Cloud resource standards ...

EuroFlash

Submissions for ISC research papers and tutorials now being accepted ...

Post Doc position available at INAF in Catania, Sicily ...

DataDirect Networks' groundbreaking Storage Fusion Architecture (SFA) System selected to power Europe's fastest supercomputer ...

European industry and research centres join forces to create a European Technology Platform for High Performance Computing ...

Russian Academy of Sciences expands GPU supercomputing infrastructure to accelerate scientific research ...

PRACE to issue project access 4th call for proposals for Tier-0 and Synchronized Call for Tier-1 ...

USFlash

Terascala announces membership in OpenSFS ...

Supercomputers accelerate development of advanced materials ...

Kraken set to deliver 2 billionth CPU hour, sustains 96 percent utilization ...

NEC developing next generation vector supercomputer - aiming for the world's leading energy-efficient supercomputer ...

Blacklight goes to work at the Pittsburgh Supercomputing Center ...

Fujitsu launches PRIMEHPC FX10 supercomputer ...

Platform Computing announces support for upcoming Intel Many Integrated Core architecture-based products ...

NASA selects next-generation SGI ICE HPC platform for technology upgrade ...

SDSC's Triton Resource helps develop new model for forecasting California solar power production ...

U.S. Department of Energy Laboratory selects DataDirect Networks' SFA12K Storage to enable clean energy technology insight and discovery ...

Rensselaer Polytechnic Institute researchers use supercomputer to study effects of stacking graphene nanoribbons ...

Appro has been selected for the second time to support the High Performance Computing Modernization Programme (HPCMP) to improve supercomputing capabilities ...

Chinese researchers tap GPU supercomputer for world's first simulation of complete H1N1 virus ...

For the first time, IBM brings mainframe and Windows together ...

AMD processors power leading research and academic supercomputers ...

Mali-T658 GPU extends graphics and GPU compute leadership for high performance devices ...

ORNL fundamental discovery casts enzymes in new light ...

Altera's Stratix IV FPGAs deliver unprecedented acceleration for world's most powerful reconfigurable supercomputer ...