Multiscale coarse-graining of monosaccharides.
A systematic multiscale coarse-graining (MS-CG) algorithm is applied to build coarse-grained models for monosaccharides in aqueous solution. The methodology is demonstrated for the example of alpha-D-glucopyranose. The nonbonded interactions are directly derived from the force-matching approach, whereas the bonded interactions are obtained through Boltzmann statistical analyses of the underlying atomistic trajectory. The MS-CG model is shown to reproduce many structural and thermodynamic properties in the constant NPT ensemble. Although the model is derived at a single temperature, pressure, and concentration, it is shown to be reasonably transferable to other thermodynamic states. In this model, long-range interactions are effectively mapped into short-range forces with a moderate cutoff and are evaluated by table look-up. As a result, molecular dynamics employing the MS-CG model is approximately 3 orders of magnitude more efficient than its atomistic counterpart. Consequently, the model is particularly suitable for simulating carbohydrate systems at large length and long time scales. Results for an alpha-(1-->4)-d-glucan with 14 glucose units are also presented, demonstrating that the MS-CG algorithm is also applicable to the coarse-graining of other saccharide systems.
Liu
Pu
P
Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA.
Izvekov
Sergei
S
Voth
Gregory A
GA
D000465:Algorithms; D005947:Glucose / Q000031:analogs & derivatives* / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D009005:Monosaccharides / Q000737:chemistry*; D012996:Solutions; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D009005:Monosaccharides; D012996:Solutions; D014867:Water; D005947:Glucose