A new GROMOS force field for hexopyranose‐based carbohydrates

Abstract

A new parameter set (referred to as 45A4) is developed for the explicit-solvent simulation of hexopyranose-based carbohydrates. This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. The parametrization procedure relies on: (1) reassigning the atomic partial charges based on a fit to the quantum-mechanical electrostatic potential around a trisaccharide; (2) refining the torsional potential parameters associated with the rotations of the hydroxymethyl, hydroxyl, and anomeric alkoxy groups by fitting to corresponding quantum-mechanical profiles for hexopyranosides; (3) adapting the torsional potential parameters determining the ring conformation so as to stabilize the (experimentally predominant) (4)C(1) chair conformation. The other (van der Waals and nontorsional covalent) parameters and the rules for third and excluded neighbors are taken directly from the most recent version of the GROMOS force field (except for one additional exclusion). The new set is general enough to define parameters for any (unbranched) hexopyranose-based mono-, di-, oligo- or polysaccharide. In the present article, this force field is validated for a limited set of monosaccharides (alpha- and beta-D-glucose, alpha- and beta-D-galactose) and disaccharides (trehalose, maltose, and cellobiose) in solution, by comparing the results of simulations to available experimental data. More extensive validation will be the scope of a forthcoming article. (c) 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1400-1412, 2005.

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation

“…The combined metadynamics-umbrella sampling has been first applied to the calculation of the puckering free energy profile of β-d-Glc, employing the standard gromos 45a4 pa-rameter set 35 . In Fig.…”

“…From the point of view of the force field, the stereoisomers of glucose differ only slightly, namely (a) the order of the two central atoms involved in an improper dihedral interaction at a chiral centre has to be inverted, in order to move a residue form the equatorial to the axial conformation; (b) α anomers are distinguished from β anomers by different torsional interactions on the O5-C1-O1-H1 dihedral, and (c) those sugars having O4 and C6 located on the same side of the ring plane (galactose, talose, gulose, idose) are modeled with different parameters for the O5-C5-C6-O6 and C4-C5-C6-O6 dihedral angles 35 .…”

“…On one hand we estimated the chair conformers populations of altrose, obtained from the assignement of its 1 H NMR spectrum. On the other hand, we performed a combined metadynamicsumbrella sampling investigation 51 of the puckering properties of all α and β-d-aldopyranoses, modeled using the gromos 45a4 parameter set 35 , and identified a new set of parameters that satisfactorily reproduces the puckering free energies of the main ring conformers. This paper is organized as follows: in Sec.…”

Self-assembly of trehalose molecules on a lysozyme surface: the broken glass hypothesis

“…31 The force-field has been chosen for its adequate description of proteins as well as oligosaccharides. 29,31,32 The MD integration time-step was 2 fs, the electrostatic interactions were treated with the Reaction Field correction technique. 33 To analyse the density of sugar and water in the system, the isodensity surfaces were computed as the number of atoms occupying three-dimensional grid points and averaged over 30 ns simulation (a grid point is considered occupied if it lies inside the sphere of the atomic radius centered on any atom of any sugar or water molecule).…”

Modeling of negative Poisson’s ratio (auxetic) crystalline cellulose Iβ

“…Consequently, numerous carbohydrate-specific (Foley et al 2012) and non-carbohydrate force fields have been used to model cellulose and related carbohydrate molecules. Carbohydrate force fields include the modified AMBER (Homans 1990), GLYCAM06 (Kirschner et al 2008), CHARMM (Guvench et al 2008) and GROMOS 45a4 (Lins and Hünenberger 2005) force fields. The CHARMM and AMBER-related GLYCAM06 force fields have, for example, recently been employed in Molecular Dynamics simulations and found to be reasonably accurate in predicting the crystal structures of a range of small molecule cellulose analogues (Miyamoto et al 2016).…”