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A computational study of calcium(II) and copper(II) ion binding to the hyaluronate molecule.

Pirc ET, Zidar J, Bukovec P - Int J Mol Sci (2012)

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: EN-FIST Centre of Excellence, Dunajska 156, Ljubljana SI-1000, Slovenia; E-Mail: peter.bukovec@fkkt.uni-lj.si ; Faculty of Chemistry and Chemical Technology, Aškerčeva 5, Ljubljana SI-1000, Slovenia.

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.

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Copper(II) hyaluronate complex after minimization on M06 level with basis set 6-31G* with distances to copper(II) ion indicated.
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f2-ijms-13-12036: Copper(II) hyaluronate complex after minimization on M06 level with basis set 6-31G* with distances to copper(II) ion indicated.

Mentions: The final structure of copper(II) hyaluronate after the QM/MM minimization using M06 and the basis set 6-31G* confirms the EXAFS data (see Figure 2). Four oxygen atoms are present in the equatorial plane at approximately 1.96 Å. Two oxygen atoms come from two water molecules, whereas two oxygen atoms come from the carboxylate groups of the nearby GCU residues. The axial oxygen atoms come from two water molecules. Our results indicate the nitrogen atom from the N-acetylglucosamine residue does not participate in the coordination bonding as it is located outside the first coordination sphere.


A computational study of calcium(II) and copper(II) ion binding to the hyaluronate molecule.

Pirc ET, Zidar J, Bukovec P - Int J Mol Sci (2012)

Copper(II) hyaluronate complex after minimization on M06 level with basis set 6-31G* with distances to copper(II) ion indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3472790&req=5

f2-ijms-13-12036: Copper(II) hyaluronate complex after minimization on M06 level with basis set 6-31G* with distances to copper(II) ion indicated.
Mentions: The final structure of copper(II) hyaluronate after the QM/MM minimization using M06 and the basis set 6-31G* confirms the EXAFS data (see Figure 2). Four oxygen atoms are present in the equatorial plane at approximately 1.96 Å. Two oxygen atoms come from two water molecules, whereas two oxygen atoms come from the carboxylate groups of the nearby GCU residues. The axial oxygen atoms come from two water molecules. Our results indicate the nitrogen atom from the N-acetylglucosamine residue does not participate in the coordination bonding as it is located outside the first coordination sphere.

Bottom Line: 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).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.

View Article: PubMed Central - PubMed

Affiliation: EN-FIST Centre of Excellence, Dunajska 156, Ljubljana SI-1000, Slovenia; E-Mail: peter.bukovec@fkkt.uni-lj.si ; Faculty of Chemistry and Chemical Technology, Aškerčeva 5, Ljubljana SI-1000, Slovenia.

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.

Show MeSH