Optimized parameters for continuum solvation calculations with carbohydrates.
Continuum solvent models have been shown to be an efficient method for the calculation of the energetics of biomolecules in solution. However, for these methods to produce accurate results, an appropriate set of atomic radii or volumes is needed. While these have been developed for proteins and nucleic acids, the same is not true of carbohydrates. Here, a set of optimized parameters for continuum solvation calculations of carbohydrates in conjunction with the Carbohydrate Solution Force Field are presented. Explicit solvent free-energy perturbation simulations were performed on a set of hexapyranose sugars and used to fit atomic radii for Poisson-Boltzmann and generalized-Born calculations, and to fit atomic volumes for use with the analytical continuum electrostatics model. The solvation energetics computed with the optimized radii and a Poisson-Boltzmann model show remarkable agreement with explicit solvent simulation, with a root-mean-square error of 1.19 kcal/mol over a large test set of sugars in many conformations. The generalized-Born model gives slightly poorer agreement, but still correlates very strongly, with an error of 1.69 kcal/mol. The analytical continuum electrostatics model correlates well with the explicit solvent results, but gives a larger error of 4.71 kcal/mol. The remarkable agreement between the solvation free energies computed in explicit and implicit solvent provides strong motivation for the use of implicit solvent models in the simulation of carbohydrate-containing systems.
Green
David F
DF
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794-3600, USA. david.green@stonybrook.edu
D002241:Carbohydrates / Q000737:chemistry*; D008956:Models, Chemical; D012995:Solubility; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D014867:Water / Q000737:chemistry
D002241:Carbohydrates; D012997:Solvents; D014867:Water