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A Computational Study of Calcium(II) and Copper(II) Ion Binding to the Hyaluronate Molecule
EN-FIST Centre of Excellence, Dunajska 156, Ljubljana SI-1000, Slovenia
Faculty of Chemistry and Chemical Technology, Aškerčeva 5, 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 to whom correspondence should be addressed.
Received: 8 June 2012; in revised form: 28 August 2012 / Accepted: 6 September 2012 / Published: 20 September 2012
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.
Keywords: copper(II) ion; calcium(II) ion; hyaluronic acid; QM/MM; simulation; biopolymer
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MDPI and ACS Style
Pirc, E.T.; Zidar, J.; Bukovec, P. A Computational Study of Calcium(II) and Copper(II) Ion Binding to the Hyaluronate Molecule. Int. J. Mol. Sci. 2012, 13, 12036-12045.
Pirc ET, Zidar J, Bukovec P. A Computational Study of Calcium(II) and Copper(II) Ion Binding to the Hyaluronate Molecule. International Journal of Molecular Sciences. 2012; 13(9):12036-12045.
Pirc, Elizabeta Tratar; Zidar, Jernej; Bukovec, Peter. 2012. "A Computational Study of Calcium(II) and Copper(II) Ion Binding to the Hyaluronate Molecule." Int. J. Mol. Sci. 13, no. 9: 12036-12045.