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Primeur weekly 2017-01-23

Exascale supercomputing

China plans to develop powerful exascale computer ...

HiPEAC Vision 2017 finds it is 'time to reinvent computing' ...

Richard Gerber tapped to oversee NERSC's High Performance Computing Department ...

NERSC's first 'NESAP for Data' teams hit the ground running ...

ORNL plays key role in Exascale Computing Project's first year ...

Quantum computing

Seeing the quantum future... literally ...

Focus on Europe

At the vanguard of European computing systems: HiPEAC17 ...

PRACE to offer MOOCs via Future Learn ...

PRACE Summer of HPC 2017 opens for applications ...

Hardware

Hartree Centre to take delivery of powerful new generation supercomputer ...

Indiana University and international partners light 100G transatlantic link over Aqua Comms' AEConnect subsea cable ...

Nanyang Technological University and German scientists turn memory chips into processors to speed up computing tasks ...

Graphene's sleeping superconductivity awakens ...

Supercomputer market to be driven by the development of smart cities through 2021, says Technavio ...

DDN and China-based Inspur sign landmark HPC joint sales and marketing agreement ...

GW4 joins industry partners to develop 'first of its kind' supercomputer ...

Automotive safety hypervisor announced for ARM Cortex-R52 ...

Eastern Mediterranean spurred on by EUMEDCONNECT3 project extension and Lebanon capacity upgrade ...

Applications

King Faisal Prize for Würzburg physicist ...

Largest Populus SNP dataset holds promise for biofuels, materials, and metabolites ...

Glass's off-kilter harmonies: New modelling method focuses attention on amorphous material's unusual vibrational modes ...

Basel physicist Daniel Loss receives the King Faisal International Prize ...

Protein research: the computer as microscope ...

Teaching computers to recognize unhealthy guts ...

2017 International Summer School on HPC Challenges in Computational Sciences to be organized in Boulder, Colorado ...

Diamond shines in molecular dynamics simulations ...

The Cloud

Oracle Cloud Platform expands to help more organisations build and deploy high-performance applications ...

Altair to offer HPC Cloud solutions on Oracle Cloud Platform ...

Oracle buys Apiary ...

Oracle expands Cloud services globally with three new regions in North America and EMEA ...

HPE to acquire SimpliVity and expand leadership in growing hybrid IT industry ...

U.S. Army enlists IBM for $62 million Cloud deal ...

Protein research: the computer as microscope


The research team Carsten Kötting, Daniel Mann and Klaus Gerwert (left to right) sets up the measuring equipment. The detector of the spectrometer has to be cooled with liquid nitrogen. Credit: RUB, Marquard.
16 Jan 2017 Bochum - Using a combination of infrared spectroscopy and computer simulation, researchers at Ruhr-Universität Bochum (RUB) have gained new insights into the workings of protein switches. With high temporal and spatial resolution, they verified that a magnesium atom contributes significantly to switching the so-called G-proteins on and off.

G-proteins affect, for example, seeing, smelling, tasting and the regulation of blood pressure. They constitute the point of application for many drugs. "Consequently, understanding their workings in detail is not just a matter of academic interest", stated Prof. Dr. Klaus Gerwert, Head of the Department of Biophysics. Together with his colleagues, namely Bochum-based private lecturer Dr. Carsten Kötting and Daniel Mann, he published his findings in the Biophysical Journal . The journal features the subject matter as its cover story in the edition published on January 10, 2017.

GTP can bind to all G-proteins. If an enzyme cleaves a phosphate group from the bound GTP, the G-protein is switched off. This so-called GTP hydrolysis takes place in the active centre of enzymes within seconds. If the process fails, severe diseases may be triggered, such as cancer, cholera or the rare McCune-Albright syndrome, which is characterised by, for example, abnormal bone metabolism.

In order for GTP hydrolysis to take place, a magnesium atom has to be present in the enzyme's active centre. The research team observed for the first time directly in what way the magnesium affects the geometry and charge distribution in its environment. After being switched off, the atom remains in the enzyme's binding pocket. To date, researchers had assumed that the magnesium leaves the pocket after the switching off process is completed.

The new findings have been gathered thanks to a method developed at the RUB Department of Biophysics. It allows to monitor enzymatic processes at a high temporal and spatial resolution in their natural state. The method in question is a special type of spectroscopy, namely the time-resolved Fourier Transform Infrared Spectroscopy. However, the data measured with its aid do not provide any information about the precise location in the enzyme where a process is taking place. The researchers gather this information through quantum-mechanical computer simulations of structural models. "Computer simulations are crucial for decoding the information hidden in the infrared spectra", explained Carsten Kötting. The computer, so to speak, becomes a microscope.

In the current study, the RUB biophysicists also demonstrated in what way the specialised protein environment affects the acceleration of GTP hydrolysis. They analysed the role of a lysine amino acid, which is located in the same spot in many G-proteins. It binds precisely that phosphate group of the GTP molecule from which a phosphate is separated when the G-protein is switched off.

"The function of lysine is to accelerate GTP hydrolysis by transferring negative charges from the third phosphate group to the second phosphate group", elaborated Daniel Mann. "This is a crucial starting point for the development of drugs for the treatment of cancer and other severe diseases in the long term."

Source: Ruhr-Universitaet Bochum

Back to Table of contents

Primeur weekly 2017-01-23

Exascale supercomputing

China plans to develop powerful exascale computer ...

HiPEAC Vision 2017 finds it is 'time to reinvent computing' ...

Richard Gerber tapped to oversee NERSC's High Performance Computing Department ...

NERSC's first 'NESAP for Data' teams hit the ground running ...

ORNL plays key role in Exascale Computing Project's first year ...

Quantum computing

Seeing the quantum future... literally ...

Focus on Europe

At the vanguard of European computing systems: HiPEAC17 ...

PRACE to offer MOOCs via Future Learn ...

PRACE Summer of HPC 2017 opens for applications ...

Hardware

Hartree Centre to take delivery of powerful new generation supercomputer ...

Indiana University and international partners light 100G transatlantic link over Aqua Comms' AEConnect subsea cable ...

Nanyang Technological University and German scientists turn memory chips into processors to speed up computing tasks ...

Graphene's sleeping superconductivity awakens ...

Supercomputer market to be driven by the development of smart cities through 2021, says Technavio ...

DDN and China-based Inspur sign landmark HPC joint sales and marketing agreement ...

GW4 joins industry partners to develop 'first of its kind' supercomputer ...

Automotive safety hypervisor announced for ARM Cortex-R52 ...

Eastern Mediterranean spurred on by EUMEDCONNECT3 project extension and Lebanon capacity upgrade ...

Applications

King Faisal Prize for Würzburg physicist ...

Largest Populus SNP dataset holds promise for biofuels, materials, and metabolites ...

Glass's off-kilter harmonies: New modelling method focuses attention on amorphous material's unusual vibrational modes ...

Basel physicist Daniel Loss receives the King Faisal International Prize ...

Protein research: the computer as microscope ...

Teaching computers to recognize unhealthy guts ...

2017 International Summer School on HPC Challenges in Computational Sciences to be organized in Boulder, Colorado ...

Diamond shines in molecular dynamics simulations ...

The Cloud

Oracle Cloud Platform expands to help more organisations build and deploy high-performance applications ...

Altair to offer HPC Cloud solutions on Oracle Cloud Platform ...

Oracle buys Apiary ...

Oracle expands Cloud services globally with three new regions in North America and EMEA ...

HPE to acquire SimpliVity and expand leadership in growing hybrid IT industry ...

U.S. Army enlists IBM for $62 million Cloud deal ...