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Molecular dynamics of carbohydrate binding to a designed protein

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Published on May 1, 2013

The binding of a simple carbohydrate, galactose, to a rationally engineered protein, ThreeFoil (http://www.cell.com/structure/abstrac...), is examined using GPU accelerated molecular dynamics. The protein was designed to have three identical subunits, linked together in a single protein chain. As such it possesses three identical binding sites, one of which is examined here.

The molecular dynamics simulations were performed using NAMD (http://www.ks.uiuc.edu/Research/namd/) on an nVidia M2070 GPU, using AMBER forcefields (http://ambermd.org/) and solvated with ~15,000 water molecules. The total simulation time is 2 nano-seconds at 298K (~room temperature).

Rendering was performed using VMD (http://www.ks.uiuc.edu/Research/vmd/). The protein is shown as sticks, and the carbohydrate as spheres, with hydrogen atoms in white, oxygen in red, nitrogen in blue, and carbon in gray. Water is shown as a low resolution surface in transparent blue in order to illustrate the periodic solvation box used and the "solvation shell" around the protein and carbohydrate. The movements of individual atoms appear "jerky" because they occur on a far faster timescale than diffusion of the carbohydrate into the binding site.

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