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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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Model hyaluronate unit. Calcium(II) ions are depicted as Van der Waals spheres. Key to atom colours: white-hydrogen, red-oxygen, cyan-carbon, blue-nitrogen, green-calcium(II) ion.
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f1-ijms-13-12036: Model hyaluronate unit. Calcium(II) ions are depicted as Van der Waals spheres. Key to atom colours: white-hydrogen, red-oxygen, cyan-carbon, blue-nitrogen, green-calcium(II) ion.

Mentions: The starting system was constructed from PDB data taking into account the fact the biologically active form is a hexamer [14,15]. The initial structure of calcium(II) hyaluronate prepared from PDB data is displayed in Figure 1, details are available elsewhere [22].


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)

Model hyaluronate unit. Calcium(II) ions are depicted as Van der Waals spheres. Key to atom colours: white-hydrogen, red-oxygen, cyan-carbon, blue-nitrogen, green-calcium(II) ion.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1-ijms-13-12036: Model hyaluronate unit. Calcium(II) ions are depicted as Van der Waals spheres. Key to atom colours: white-hydrogen, red-oxygen, cyan-carbon, blue-nitrogen, green-calcium(II) ion.
Mentions: The starting system was constructed from PDB data taking into account the fact the biologically active form is a hexamer [14,15]. The initial structure of calcium(II) hyaluronate prepared from PDB data is displayed in Figure 1, details are available elsewhere [22].

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