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Primeur weekly 2016-10-10

Exascale supercomputing

The incredible shrinking particle accelerator ...

Brookhaven Lab to play major role in 2 DOE exascale computing application projects ...

Quantum computing

More stable qubits in perfectly normal silicon ...

Focus on Europe

RSC supercomputers go West ...

Hardware

Allinea tools play vital role in advancing computational research at the VSC, Austria's largest HPC facility ...

Smallest transistor ever ...

Turning to the brain to reboot computing ...

Complex materials can self-organize into circuits, may form basis for multifunction chips ...

Wireless data centre on a chip aims to cut energy use ...

Adapteva announces 28nm 64-core Epiphany-IV microprocessor chip ...

SGI introduces unique scale-out solution for SAP HANA that protects investments when moving to real-time business ...

Applications

Clemson University scientists receive $1.8 million grant to combat Type 2 diabetes ...

Climate change intensifies night-time storms over Lake Victoria ...

Computer simulations explore how Alzheimer's disease starts ...

Rice University lab explores cement's crystalline nature to boost concrete performance ...

Rice University researchers say 2D boron may be best for flexible electronics ...

Large animals, such as the imperious African elephant, most vulnerable to impact of human expansion ...

Computer simulation finds dangerous molecule activity for ageing ...

Tornadogenesis ...

As hurricane heads up coast, a RENCI supercomputer swings into action ...

New drug candidate may reduce deficits in Parkinson's disease ...

XSEDE allocations awarded to 155 research teams across U.S. ...

OSC part of NSF-funded consortium for advancing research computing practices ...

NCSA awarded NSF grant to expand computational science education in food, energy, and water ...

Crosstalk analysis of biological networks for improved pathway annotation ...

The Cloud

Nimbix collaborates with IBM and NVIDIA to launch powerful GPU Cloud offering ...

Computer simulations explore how Alzheimer's disease starts


A team of Rice University researchers built computer simulations of amyloid beta proteins to see what their energy landscapes reveal about the formation of plaques in patients with Alzheimer's disease. From left, Weihua Zheng, Min-Yeh Tsai, Peter Wolynes and Mingchen Chen. Credit: Jeff Fitlow/Rice University.
3 Oct 2016 Houston - A new Rice University study uses computer simulations to explore the initial steps of the molecular process that leads to Alzheimer's disease. The disease starts by the aggregation of a common protein called amyloid beta. The Rice study is the first to model the energy landscape of the assembly of many copies of the pathogenic protein into its toxic form.

The research led by Professor Peter Wolynes of Rice's Center for Theoretical Biological Physics is detailed in theProceedings of the National Academy of Sciences.

Peter Wolynes and his team are pioneers in the development of the energy landscape theory for proteins. All proteins start as chains of amino acids with their sequence determined by DNA, and each arrangement of the chain has a particular energy associated with it. The map of these energies and structures is called the energy landscape.

For most proteins, the energy landscape guides the protein to fold into its useful functional shape. Peter Wolynes and his colleagues, developed a computer programme, called AWSEM - associative memory, water mediated, structure and energy model, that simulates the process and can predict the most important functional structures.

A single molecule of the amyloid beta protein by itself does not fold into a definite structure and also appears to be harmless, Peter Wolynes said. The disease starts when several molecules come together to form an oligomer. The structures of such oligomers, which are thought to be the toxic agents, has been unknown, he said.

At a later stage, the oligomers change into fibrillar plaques that appear to be less toxic.

The Rice researchers used AWSEM to analyze oligomers of up to eight monomers in the prefibrillar form to see how they change into fibers.

In the oligomer made of six monomers, for instance, they found that this transition takes place when self-recognizing sequences on separate protein molecules interacted with each other rather than with their prefibrillar partners. These structures, they wrote, then form the stable core of a propagating amyloid aggregate.

"A few years ago, there were experiments on the misfolding of a beta protein called titin, and we started to study its aggregation", Peter Wolynes stated. "We discovered this interesting thing, that it wasn't the whole protein but only particular parts of the protein that were responsible for misfolding in amyloidogenic regions we found.

"It turned out there were very small lengths of about five amino acids that were extra sticky to each other", he stated. "The surprise was that while the overall molecule was foldable, there were five to 10 residues that, if you had another copy of the same molecule, would be able to stick together and cause aggregation."

One problem with previous studies was that the protein concentration changes as the aggregation process proceeds, Peter Wolynes said. An important mathematical development using energy landscape theory allowed the Rice researchers to correct for that effect.

With that correction, the simulation of oligomers of various complexity predicted solubilities that matched across the board what had been seen in experiments, said Weihua Zheng, a Rice research scientist and lead author of the study.

"One of the reasons you might get Alzheimer's is that you overproduce this protein", Weihua Zheng stated. "That's why solubility is a key number: You want amyloid beta to remain soluble."

The problem may lie in the production of enzymes that keep oligomer concentrations in check, Peter Wolynes said. Inhibiting such enzymes is being explored as a route for treatment with drugs, he said.

The simulations also demonstrated that the larger the oligomer, the greater the potential for forming fibrils, Peter Wolynes said. Smaller oligomers of three or four monomers were predicted by the simulations to form cylindrins, barrel-shaped structures that other researchers have suggested could drill into and damage cell membranes. "In future work, we want to look at whether these cylindrical structures actually could penetrate a membrane in simulations", he stated.

The researchers also noticed that just at the point of conversion, oligomers slightly unfold before going fibrillar. "We call that backtracking", he stated. "It may explain a couple of things, like why these oligomers accumulate rather than all converting to the more benign fibrils."

In addition to enabling examination of the mechanism of amyloid beta aggregation, the simulations let the lab analyze the effects of point mutations - including hereditary variants called Dutch and Arctic - that are associated with early onset Alzheimer's. In both cases, the mutations seemed to make aggregation faster by exposing hydrophobic segments, though a third mutation, called Iowa, "seems to be mildly protective", Peter Wolynes stated.

The team will next simulate aggregation from amyloid beta proteins with 42 amino acids, for which structures of the fibers have recently been revealed. "It's thought that these aggregate more readily than the 40s we studied here, and we hope to see why these are different - or not", he stated.

Rice postdoctoral researcher Min-Yeh Tsai and graduate student Mingchen Chen are co-authors of the study .

The National Institute of General Medical Sciences and the D.R. Bullard-Welch Chair at Rice supported the research. The researchers used the National Science Foundation-supported DAVinCI supercomputer administered by Rice's Center for Research Computing and procured in a partnership with Rice's Ken Kennedy Institute for Information Technology.

Source: Rice University

Back to Table of contents

Primeur weekly 2016-10-10

Exascale supercomputing

The incredible shrinking particle accelerator ...

Brookhaven Lab to play major role in 2 DOE exascale computing application projects ...

Quantum computing

More stable qubits in perfectly normal silicon ...

Focus on Europe

RSC supercomputers go West ...

Hardware

Allinea tools play vital role in advancing computational research at the VSC, Austria's largest HPC facility ...

Smallest transistor ever ...

Turning to the brain to reboot computing ...

Complex materials can self-organize into circuits, may form basis for multifunction chips ...

Wireless data centre on a chip aims to cut energy use ...

Adapteva announces 28nm 64-core Epiphany-IV microprocessor chip ...

SGI introduces unique scale-out solution for SAP HANA that protects investments when moving to real-time business ...

Applications

Clemson University scientists receive $1.8 million grant to combat Type 2 diabetes ...

Climate change intensifies night-time storms over Lake Victoria ...

Computer simulations explore how Alzheimer's disease starts ...

Rice University lab explores cement's crystalline nature to boost concrete performance ...

Rice University researchers say 2D boron may be best for flexible electronics ...

Large animals, such as the imperious African elephant, most vulnerable to impact of human expansion ...

Computer simulation finds dangerous molecule activity for ageing ...

Tornadogenesis ...

As hurricane heads up coast, a RENCI supercomputer swings into action ...

New drug candidate may reduce deficits in Parkinson's disease ...

XSEDE allocations awarded to 155 research teams across U.S. ...

OSC part of NSF-funded consortium for advancing research computing practices ...

NCSA awarded NSF grant to expand computational science education in food, energy, and water ...

Crosstalk analysis of biological networks for improved pathway annotation ...

The Cloud

Nimbix collaborates with IBM and NVIDIA to launch powerful GPU Cloud offering ...