title: A computational study of calcium(II) and copper(II) ion binding to the hyaluronate molecule.
abstract: The hyaluronate molecule is a negatively charged polysaccharide that performs a plethora of physiological functions in many cell tissues depending on its conformation. In the present paper, molecular modeling at three levels of theory and two basis sets was used to gain a deeper insight in the complex molecular structure of calcium(II) and copper(II) hyaluronate. Simulation results were compared with the experimental data (EXAFS or X-ray). It was found that B3LYP does not properly reproduce the experimental data while the HF and M06 methods do. Simulation data confirm that the N-acetyl group of the N-acetylglucosamine residue does not participate in the coordination bonding to the calcium(II) or copper(II) ion, as evident from the experimental data.
authors.affiliation: EN-FIST Centre of Excellence, Dunajska 156, Ljubljana SI-1000, Slovenia.|Faculty of Chemistry and Chemical Technology, Aškerčeva 5, Ljubljana SI-1000, Slovenia.
authors.forename: Elizabeta Tratar
authors.initials: ET
authors.lastname: Pirc
authors.affiliation: EN-FIST Centre of Excellence, Dunajska 156, Ljubljana SI-1000, Slovenia.|Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16 Connexis North, SG-138632, Singapore.|National Institute of Chemistry, Hajdrihova 19, Ljubljana SI-1000, Slovenia.
authors.forename: Jernej
authors.initials: J
authors.lastname: Zidar
authors.affiliation: EN-FIST Centre of Excellence, Dunajska 156, Ljubljana SI-1000, Slovenia.|Faculty of Chemistry and Chemical Technology, Aškerčeva 5, Ljubljana SI-1000, Slovenia.
authors.forename: Peter
authors.initials: P
authors.lastname: Bukovec
mesh_terms: D002118:Calcium / Q000737:chemistry*; D002236:Carbohydrate Conformation; D003300:Copper / Q000737:chemistry*; D006820:Hyaluronic Acid / Q000737:chemistry*; D008958:Models, Molecular
chemical_list: D003300:Copper; D006820:Hyaluronic Acid; D002118:Calcium
keywords: QM/MM; biopolymer; calcium(II) ion; copper(II) ion; hyaluronic acid; simulation