PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

Gaming technology unravels 1 of the most complex entities in nature

Computational research unveils secrets in the human carbohydrate bar-code

2013-10-31
(Press-News.org) Contact information: Rob Dawson
rob.dawson@bbsrc.ac.uk
01-793-413-204
Biotechnology and Biological Sciences Research Council
Gaming technology unravels 1 of the most complex entities in nature Computational research unveils secrets in the human carbohydrate bar-code BBSRC-funded researchers at the University of Manchester's Institute of Biotechnology have used the power of off-the-shelf computer gaming technology to capture previously unobservable atomic movements. The research is helping to chart one of nature's most complex entities known as "glycomes" - the entire complement of carbohydrates within a cell.

This novel solution provides a new understanding of these vital biomolecules which play a role in everything from neuronal development, inflammation and cell structure, to disease pathology and blood clotting.

Understanding the shapes of major biological molecules has revolutionised areas like drug development and medical diagnostics, but the shape of complex carbohydrates has been largely ignored.

The research, reported in a series of six peer-reviewed scientific publications (see notes) with the most recent (published today) appearing in Carbohydrate Research, provides a new view of these biochemical barcodes and present new opportunities in the science of carbohydrates, such as designing drugs or biomaterials that mimic carbohydrate shape and interpreting burgeoning functional glycomics data.

Dr Ben Sattelle from the Faculty of Life Sciences said: "Carbohydrate activity stems from 3D-shape, but the link between carbohydrate sequence and function remains unclear. Sequence-function relationships are rapidly being deciphered and it is now essential to be able to interpret these data in terms of molecular 3D-structure, as has been the case for proteins and the DNA double-helix.

"By using technology designed for computer games, we have been able to investigate the previously unseen movements of carbohydrates at an atomic scale and over longer timescales than before. The insights relate carbohydrate sequence to molecular shape and provide information that will be vital for many industries.

"Carbohydrates remain extremely difficult to characterise in 3D using experiments and advances in computer technology, which exploit computer-gaming technology, have enabled us to use and develop methods that can routinely provide accurate 3D-data for this important class of biomolecules. The ability to model atomic motions in large carbohydrate polymers promises to transform our understanding of fundamentally important biological processes. For example, our approach has potential applications in the design of carbohydrate-based biomaterials, pharmaceuticals and foods."

Modelling carbohydrate motions in water is computationally demanding, meaning that simulations have been limited to short nanosecond timescales using conventional software and central processing unit (CPU) based computers. The team from Manchester achieved simulations ranging from one microsecond (the time it takes for a strobe light to flash) to twenty-five microseconds by exploiting the extra computational power of graphics processing units (GPUs) that are commonly used in game-play to produce moving images. Compared to CPU-based computers, or even supercomputing clusters of them, GPU technology allows many more simultaneous calculations to be performed.

The researchers produced the first predictions of microsecond molecular motions in glycomic building blocks and oligosaccharides. Previously unobservable atomic movements were predicted and found to be sensitive to the carbohydrate sequence. Building on these new insights, the researchers developed a new physics-based model and GPU software that allows far more realistic simulations of long carbohydrate sequences (polymers) - on microsecond and micrometer scales. Using heparan sulphate chains (Figure 1, see notes) the researchers showed that including both flexible degrees of freedom in their model, polymer linkage and ring motions, is crucial to reproduce experimental shape data and ring dynamics were implicated in sequence-dependent biological activity.

The research has culminated in a computational GPU-based method and protocol that can now be used by other researchers to explore the 3D-landscape of largely unchartered organismal glycomes in unprecedented detail.

### END


ELSE PRESS RELEASES FROM THIS DATE:

The secret's in the (robotic) stroke

2013-10-31
The secret's in the (robotic) stroke NYU-Poly researchers tease out cues that impact schooling fish behavior Brooklyn, New York— Recent studies from two research teams at the Polytechnic Institute of New York University (NYU-Poly) demonstrate ...

Increasing rate of knee replacements linked to obesity among young, researchers say

2013-10-31
Increasing rate of knee replacements linked to obesity among young, researchers say New data show younger adults have same or greater impairment than older patients BOSTON – Contrary to popular myth, it is not the aging Baby Boomer or weekend ...

Newly identified proteins make promising targets for blocking graft-vs.-host disease

2013-10-31
Newly identified proteins make promising targets for blocking graft-vs.-host disease Finding could help improve outcomes from bone marrow transplants ANN ARBOR, Mich. — Researchers from the University of Michigan Comprehensive Cancer Center have ...

Biochemists find incomplete protein digestion is a useful thing for some bacteria

2013-10-31
Biochemists find incomplete protein digestion is a useful thing for some bacteria To the authors' surprise, 1 specialized replication factor was partially digested or trimmed, physically cut into shorter fragments, by an energy-dependent protease ...

Long-term use of prescription-based painkillers increases the risk of depression, SLU researcher finds

2013-10-31
Long-term use of prescription-based painkillers increases the risk of depression, SLU researcher finds ST. LOUIS – Opioid analgesics, or prescription-based narcotic pain killers, have long been known to reduce pain, but reports of adverse effects and addiction continue ...

Houston we have a problem: Microgravity accelerates biological aging

2013-10-31
Houston we have a problem: Microgravity accelerates biological aging New research in The FASEB Journal suggests that gravitational unloading significantly impairs the function of endothelial cells, as evidenced by gene expression ...

Primary GOES-R instrument ready to be installed onto spacecraft

2013-10-31
Primary GOES-R instrument ready to be installed onto spacecraft A key instrument that will fly on the Geostationary Operational Environmental Satellite – R (GOES-R) spacecraft, NOAA's next-generation of geostationary satellites, is cleared for installation ...

Lefties more likely to have psychotic disorders such as schizophrenia: Yale study

2013-10-31
Lefties more likely to have psychotic disorders such as schizophrenia: Yale study Being left-handed has been linked to many mental disorders, but Yale researcher Jadon Webb and his colleagues have found that among those with mental illnesses, people with psychotic ...

Direct link established between stimulus-response learning and substance abuse

2013-10-31
Direct link established between stimulus-response learning and substance abuse Findings from Douglas Institute neuroscientist Véronique Bohbot, PhD, neuroscientist at the Douglas Mental Health University Institute, found ...

Could a milky way supernova be visible from Earth in next 50 years?

2013-10-31
Could a milky way supernova be visible from Earth in next 50 years? Advances in cameras, new strategies for detection make it possible COLUMBUS, Ohio—Astronomers at The Ohio State University have calculated the odds that, sometime during the next 50 years, a supernova ...

LAST 30 PRESS RELEASES:

Attitudes, not income, drive energy savings at home

The playbook for perfect polaritons

‘Disease in a dish’ study of progressive MS finds critical role for unusual type of brain cell

Solar-powered method lights the way to a ‘de-fossilized’ chemical industry

Screen time linked to lower academic achievement among Ontario elementary students

One-year outcomes after traumatic brain injury and early extracranial surgery in the TRACK-TBI Study

Enduring outcomes of COVID-19 work absences on the US labor market

Affirmative action repeal and racial and ethnic diversity in us medical school admissions

Cancer progression illuminated by new multi-omics tool

Screen time and standardized academic achievement tests in elementary school

GLP-1RA order fills and out-of-pocket costs by race, ethnicity, and indication

Study finds HEPA purifiers alone may not be enough to reduce viral exposure in schools

UVA Health developing way to ID people at risk of dangerous lung scarring even before symptoms appear

How can we know when curing cancer causes myocarditis?

Male infertility in Indian men linked to lifestyle choices and hormonal imbalances

An acoustofluidic device for sample preparation and detection of small extracellular vesicles

The advent of nanotechnology has ushered in a transformative era for oncology, offering unprecedented capabilities for targeted drug delivery and controlled release. This paradigm shift enhances thera

A prototype LED as thin as wallpaper — that glows like the sun

Transnational electoral participation of undocumented Mexican immigrants in the US

A new method to build more energy-efficient memory devices for a sustainable data future

Freely levitating rotor spins out ultraprecise sensors for classical and quantum physics

‘Chinese lantern’ structure shifts into more than a dozen shapes for various applications

Towards light-controlled electronic components

Tiny architects, titanic climate impact: scientists call for October 10 to become International Coccolithophore Day

Stress sensitivity makes suicidal thoughts more extreme and persistent among the university population

Lessons from Ascension’s shark troubles could help boost conservation

Fire provides long-lasting benefits to bird populations in Sierra Nevada National Parks

Menstrual cycle affects women’s reaction time but not as much as being active

Housing associations more effective than government in supporting unemployed in deprived areas

Biochar helps composting go greener by cutting greenhouse gas emissions

[Press-News.org] Gaming technology unravels 1 of the most complex entities in nature
Computational research unveils secrets in the human carbohydrate bar-code