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Primeur weekly 2015-01-26

Exascale supercomputing

BSC and Intel extend research collaboration on systems behaviour analysis and prediction at Exascale R&D Lab ...

NASA scientist joins groundbreaking UK supercomputing start-up ...

Second European Exascale Software Initiative, EESI2, is organizing its final international conference ...

The Cloud

Anthem teams with IBM to strengthen IT operational performance ...

The European Space Agency builds a private Cloud platform with Red Hat ...

AccelOps' latest release delivers interactive security and performance analytics plus Cloud monitoring ...

Oracle Voice brings a mobile, speech-enabled virtual assistant to the Oracle Sales Cloud in Release 9 on smart phones ...

EuroFlash

New Head of Astroparticle Physics European Consortium appointed ...

REF signals deep impact as EPSRC announces GPB30 million for Impact Acceleration Accounts ...

New laser for computer chips ...

Graphene brings quantum effects to electronic circuits ...

Square Kilometre Array: The Cosmology Engine ...

Computer scientists from Saarbruecken improve the privacy of the Internet currency Bitcoin ...

Graphene enables all-electrical control of energy flow from light emitters ...

USFlash

DataDirect Networks again dominates as world leader in 2014/2015 TOP500 global supercomputing list ...

DataDirect Networks Storage Fusion Xcelerator (SFX) flash cache technology wins Storage Visions Award ...

UCSD study shows why protein mutations lead to familial form of Parkinson's disease ...

UC San Diego physicist Frank Würthwein joins SDSC ...

SDSC supercomputers to assist UC San Diego's 'Extreme Events' Center ...

SDSC announces UC Graduate Summer Fellowship programme ...

New wind-farm computer simulations unlock increased power generation ...

The City University of New York selects SGI to power major research projects ...

Air Force Research Laboratory's Department of Defense Supercomputer Resource Center (DSRC) to receive new supercomputer ...

Supercomputer simulations yield method for predicting behaviour of new concrete formulas ...

Oracle tackles data centre cost and complexity with next-generation engineered systems ...

A 3D view of the Greenland Ice Sheet opens window on ice history ...

Dedicated Computing joins the Intel Cluster Ready programme to offer high-performance computing cluster solutions for bioinformatics research ...

Researchers get $1.4 million to advance 'Big Data' for genomic research ...

Optimizing optimization algorithms ...

Scientists set quantum speed limit ...

New signal amplification process set to transform communications, imaging, and computing ...

UCSD study shows why protein mutations lead to familial form of Parkinson's disease

21 Jan 2015 San Diego - Researchers at the San Diego Supercomputer Center (SDSC) at the University of California, San Diego (UCSD), have shown for the first time why protein mutations lead to the familial form of Parkinson's disease. The study, available on-line in prepublication inACS Chemical Neuroscienceand partially funded by the National Institutes of Health, focuses specifically on alpha-synuclein (asyn), a protein whose function in healthy tissue is unknown but which represents the major structural component of Lewy bodies - protein clumps found in the brains of individuals with Parkinson's disease and other neurological disorders.

Parkinson's disease is characterized by impairment or deterioration of neurons in an area of the brain known as the substantia nigra. In the familial form of the disorder, a set of mutations in asyn had been identified but what was unknown was the molecular mechanism by which these mutations caused disease.

"As an unstructured protein, asyn is sometimes called 'chameleon' because it has no stable configuration and constantly changes its shape", stated lead author Igor F. Tsigelny, a research scientist with SDSC as well as the UC San Diego Moores Cancer Center and the Department of Neurosciences. "Nevertheless when these changes seem to be random on first glance, they have specific intrinsic rules that control the evolution of the asyn shape."

Using SDSC's data-intensive Gordon supercomputer to find hidden rules of the conformational changes of asyn, researchers conducted extensive calculations of the possible evolution of the protein structure.

Through computer modelling, researchers showed that asyn mostly can bind the membrane with four main sites, or zones. While binding was shown to be superficial by three of the sites, one site - Zone 2 - had a particular affinity for the membrane. Researchers found that asyn contacting the neuron membrane in that site immediately and deeply penetrated it, which led to the creation of ring oligomers in the membrane, and eventually opened pores that allowed an uncontrolled influx of ions that ultimately killed the cell. Most of the mutations changed the shape of the protein in a way that increased binding of asyn to the membrane by this zone.

These theoretical predications were confirmed by a set of experimental methods conducted in the laboratory of Eliezer Masliah, a professor in UC San Diego's Department of Neurosciences. "Previous to this study, researchers could not say why these mutations caused Parkinson's disease", stated Igor F. Tsigelny. "The discovery of Zone 2 as the distinguishing feature of the membrane-penetrating configurations of asyn paves the road to possible prevention of such a binding. Now we can affect this region with rational drug design, for example by creating compounds that would change its electrostatic profile."

In addition to Igor F. Tsigelny and Eliezer Masliah, researchers involved in the study include Yuriy Sharikov, Valentina L. Kouznetsova, and Jerry P. Greenberg from SDSC; Wolf Wrasidlo from the Moores Cancer Center; and Cassia Overk, Tania Gonzalez, Margarita Trejo, Brian Spencer, and Kori Kosberg, from the Department of Neurosciences at UC San Diego.
Source: San Diego Supercomputer Center - SDSC

Back to Table of contents

Primeur weekly 2015-01-26

Exascale supercomputing

BSC and Intel extend research collaboration on systems behaviour analysis and prediction at Exascale R&D Lab ...

NASA scientist joins groundbreaking UK supercomputing start-up ...

Second European Exascale Software Initiative, EESI2, is organizing its final international conference ...

The Cloud

Anthem teams with IBM to strengthen IT operational performance ...

The European Space Agency builds a private Cloud platform with Red Hat ...

AccelOps' latest release delivers interactive security and performance analytics plus Cloud monitoring ...

Oracle Voice brings a mobile, speech-enabled virtual assistant to the Oracle Sales Cloud in Release 9 on smart phones ...

EuroFlash

New Head of Astroparticle Physics European Consortium appointed ...

REF signals deep impact as EPSRC announces GPB30 million for Impact Acceleration Accounts ...

New laser for computer chips ...

Graphene brings quantum effects to electronic circuits ...

Square Kilometre Array: The Cosmology Engine ...

Computer scientists from Saarbruecken improve the privacy of the Internet currency Bitcoin ...

Graphene enables all-electrical control of energy flow from light emitters ...

USFlash

DataDirect Networks again dominates as world leader in 2014/2015 TOP500 global supercomputing list ...

DataDirect Networks Storage Fusion Xcelerator (SFX) flash cache technology wins Storage Visions Award ...

UCSD study shows why protein mutations lead to familial form of Parkinson's disease ...

UC San Diego physicist Frank Würthwein joins SDSC ...

SDSC supercomputers to assist UC San Diego's 'Extreme Events' Center ...

SDSC announces UC Graduate Summer Fellowship programme ...

New wind-farm computer simulations unlock increased power generation ...

The City University of New York selects SGI to power major research projects ...

Air Force Research Laboratory's Department of Defense Supercomputer Resource Center (DSRC) to receive new supercomputer ...

Supercomputer simulations yield method for predicting behaviour of new concrete formulas ...

Oracle tackles data centre cost and complexity with next-generation engineered systems ...

A 3D view of the Greenland Ice Sheet opens window on ice history ...

Dedicated Computing joins the Intel Cluster Ready programme to offer high-performance computing cluster solutions for bioinformatics research ...

Researchers get $1.4 million to advance 'Big Data' for genomic research ...

Optimizing optimization algorithms ...

Scientists set quantum speed limit ...

New signal amplification process set to transform communications, imaging, and computing ...