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Gaming technology unravels 1 of the most complex entities in nature
Date:10/31/2013

periments 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 com
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Contact: Rob Dawson
rob.dawson@bbsrc.ac.uk
01-793-413-204
Biotechnology and Biological Sciences Research Council
Source:Eurekalert

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