A GROMOS Force Field for Furanose-Based Carbohydrates

Abstract

The article describes a GROMOS force field parameter set for molecular dynamics simulations of furanose carbohydrates. The proposed united-atom force field is designed and validated with respect to the conformational properties of furanose mono-, di-, oligo-, and polymers in aqueous solvent. The set accounts for the possibility of arbitrary glycosidic linkage connectivity between units, Oalkylation, as well as of different anomery. The compatibility with the already existing, pyranose-dedicated GROMOS 56A6 CARBO/CARBO_R set allows one to use the presently proposed extension for studying more diverse and biologically relevant carbohydrates that exploit both pyranose and furanose units. The validation performed against the quantum-mechanical and experimental data concerning the structural and conformational features shows that the newly developed set is capable to reproduce conformational equilibrium within the furanose ring, relative free energies of anomers, hydroxymethyl rotamers, and glycosidic linkage conformers. Additionally, the results concerning the conformation of the furanose ring with relation to the two-state model as well as other conformational features of furanose-containing saccharides are discussed.

The endo‐ and exo‐Anomeric Effects in Furanosides. A Computational Study

“…Finally, there exists a large number of studies that clearly indicate the importance of the endo ‐anomeric effect in the context of conformational preferences of furanose rings containing larger number of ring substituents . Furthermore, the compilation of the structural data performed for various glycosidic linkages involving furanose residues shows that conformational preferences induced by the exo ‐anomeric effect are also in accordance with our predictions.…”

“…The MM part comprised of the SPC water molecules. The interactions at the QM/MM interface were computed according to the electronic embedding scheme and the non‐bonded parameters were taken from the furanose‐dedicated edition of the GROMOS force field . The MD simulations were carried out for a duration of 130 ps and the trajectory was saved every 5 steps.…”

“…The interactions at the QM/MM interface were computed according to the electronic embedding scheme [24] and the non-bonded parameters were taken from the furanose-dedicated edition of the GROMOS force field. [25] The MD simulations were carried out for a duration of 130 ps and the trajectory was saved every 5 steps. The free energy landscapes were calculated by using the Boltzmann inversion of the respective probability distributions.…”

Three-Dimensional Structures of Carbohydrates and Where to Find Them

“…Another modification of 56A CARBO named 56A CARBO_CHT [ 189 ] was developed for chitosan and its derivatives. Recently, extensions of GROMOS 56A CARBO / CARBO_R parameter set were adapted towards charged, protonated and esterified urinates [ 190 ] and furanose-based carbohydrates [ 191 ]. GROMOS96 43A1 was reported to have good performance on glycan structure simulation in glycoproteins [ 192 , 193 ].…”

Atomic partial charge predictions for furanoses by random forest regression with atom type symmetry function

“…In the present study, we introduced atom type symmetry function (ATSF), that categorized atoms by their atom types dened in MM force elds 3,[25][26][27] and provided more detailed structural descriptions, to predict CA charges with properly trained random forest regression (RFR) models. 28 Atom type is a well-established and crucial concept embedded in common MM force elds, in which atoms are categorized beyond chemical elements and by their properties or connectivity.…”