Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations.
We present a CHARMM Carbohydrate Solution Force Field (CSFF) suitable for nanosecond molecular dynamics computer simulations. The force field was derived from a recently published sugar parameter set.1 Dihedral angle parameters for the primary alcohol as well as the secondary hydroxyl groups were adjusted. Free energy profiles of the hydroxymethyl group for two monosaccharides (beta-D-glucose and beta-D-galactose) were calculated using the new parameter set and compared with similar force fields. Equilibrium rotamer populations obtained from the CSFF are in excellent agreement with NMR data (glucose gg:gt:tg approximately 66:33:1 and galactose gg:gt:tg approximately 4:75:21). In addition, the primary alcohol rotational frequency is on the nanosecond time scale, which conforms to experimental observations. Equilibrium population distributions of the primary alcohol conformers for glucose and galactose are reached within 10 nanoseconds of molecular dynamics simulations. In addition, gas phase vibrational frequencies computed for beta-D-glucose using this force field compare well with experimental frequencies. Carbohydrate parameter sets that produce both conformational energies and rotational frequencies for the pyranose primary alcohol group that are consistent with experimental observations should allow for increased accuracy in modeling the flexibility of biologically important (1-6)-linked saccharides in solution.
Kuttel
Michelle
M
Department of Chemistry, University of Cape Town, Rondebosch 7701, Cape Town, South Africa.
Brady
J W
JW
Naidoo
Kevin J
KJ
D000438:Alcohols / Q000737:chemistry*; D002236:Carbohydrate Conformation; D002241:Carbohydrates / Q000737:chemistry*; D003198:Computer Simulation; D005690:Galactose / Q000737:chemistry; D005947:Glucose / Q000737:chemistry; D008956:Models, Chemical; D015394:Molecular Structure; D013237:Stereoisomerism
D000438:Alcohols; D002241:Carbohydrates; D005947:Glucose; D005690:Galactose