Featured Research

from universities, journals, and other organizations

Gaming technology unravels one of the most complex entities in nature: Computational research unveils secrets in the human carbohydrate bar-code

Date:
October 31, 2013
Source:
Biotechnology and Biological Sciences Research Council
Summary:
Scientists 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.

Carbohydrate research.
Credit: Dr Ben Sattelle

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, 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 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.


Story Source:

The above story is based on materials provided by Biotechnology and Biological Sciences Research Council. Note: Materials may be edited for content and length.


Journal Reference:

  1. Benedict M. Sattelle, Andrew Almond. Shaping Up for Structural Glycomics: A Predictive Protocol for Oligosaccharide Conformational Analysis Applied to N-Linked Glycans. Carbohydrate Research, 2013; DOI: 10.1016/j.carres.2013.10.011

Cite This Page:

Biotechnology and Biological Sciences Research Council. "Gaming technology unravels one of the most complex entities in nature: Computational research unveils secrets in the human carbohydrate bar-code." ScienceDaily. ScienceDaily, 31 October 2013. <www.sciencedaily.com/releases/2013/10/131031125209.htm>.
Biotechnology and Biological Sciences Research Council. (2013, October 31). Gaming technology unravels one of the most complex entities in nature: Computational research unveils secrets in the human carbohydrate bar-code. ScienceDaily. Retrieved July 25, 2014 from www.sciencedaily.com/releases/2013/10/131031125209.htm
Biotechnology and Biological Sciences Research Council. "Gaming technology unravels one of the most complex entities in nature: Computational research unveils secrets in the human carbohydrate bar-code." ScienceDaily. www.sciencedaily.com/releases/2013/10/131031125209.htm (accessed July 25, 2014).

Share This




More Computers & Math News

Friday, July 25, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Mobile App Gives Tour of Battle of Atlanta Sites

Mobile App Gives Tour of Battle of Atlanta Sites

AP (July 25, 2014) Emory University's Center for Digital Scholarship has launched a self-guided mobile tour app to coincide with the 150th anniversary of the Civil War's Battle of Atlanta. (July 25) Video provided by AP
Powered by NewsLook.com
Bill Gates: Health, Agriculture Key to Africa's Development

Bill Gates: Health, Agriculture Key to Africa's Development

AFP (July 24, 2014) Health and agriculture development are key if African countries are to overcome poverty and grow, US software billionaire Bill Gates said Thursday, as he received an honourary degree in Ethiopia. Duration: 00:36 Video provided by AFP
Powered by NewsLook.com
Creative Makeovers for Ugly Cellphone Towers

Creative Makeovers for Ugly Cellphone Towers

AP (July 24, 2014) Mobile phone companies and communities across the country are going to new lengths to disguise those unsightly cellphone towers. From a church bell tower to a flagpole, even a pencil, some towers are trying to make a point. (July 24) Video provided by AP
Powered by NewsLook.com
Robot Parking Valet Creates Stress-Free Travel

Robot Parking Valet Creates Stress-Free Travel

AP (July 23, 2014) 'Ray' the robotic parking valet at Dusseldorf Airport in Germany lets travelers to avoid the hassle of finding a parking spot before heading to the check-in desk. (July 23) Video provided by AP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

    Health News

      Environment News

        Technology News



          Save/Print:
          Share:

          Free Subscriptions


          Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

          Get Social & Mobile


          Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

          Have Feedback?


          Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
          Mobile: iPhone Android Web
          Follow: Facebook Twitter Google+
          Subscribe: RSS Feeds Email Newsletters
          Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins