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

Tratar-Pirc, Elizabeta (author), Zidar, Jernej (author), Bukovec, Peter (author)

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.

• Language: English
• Keywords: copper(II) ion, calcium(II) ion, hyaluronic acid, QM/MM, simulation, biopolymer
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Publication status: Published
• Publication version: Version of Record
• Year: 2012
• Number of pages: Str. 12036-12045
• Numbering: Vol. 13, iss. 9
• PID: 20.500.12556/RUL-129516
• UDC: 546.562:546.41:544.1:004.4
• ISSN on article: 1661-6596
• DOI: 10.3390/ijms130912036
• COBISS.SI-ID: 36212485
• Publication date in RUL: 03.09.2021

Record is a part of a journal

• Title: International journal of molecular sciences
• Shortened title: Int. j. mol. sci.
• Publisher: MDPI
• ISSN: 1661-6596
• COBISS.SI-ID: 36217605

Licences

• License: CC BY 3.0, Creative Commons Attribution 3.0 Unported
• Link: https://creativecommons.org/licenses/by/3.0/deed.en
• Description: You are free to reproduce and redistribute the material in any medium or format. You are free to remix, transform, and build upon the material for any purpose, even commercially. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.
• Licensing start date: 20.09.2012

Secondary language

• Language: Slovenian
• Keywords: anorganska kemija, bioanorganska kemija, strukturna kemija, biopolimeri, hialuronska kislina, struktura, določevanje strukture molekul, rentgenska strukturna analiza, EXAFS, vezave kovinskih ionov, računalniška študija, simulacija, QM/MM, polisaharidi, bakrov(II) ion, kalcijev(II) ion

Projects

• Funder: ARRS - Slovenian Research Agency
• Project number: P1-0012
• Name: Molekulske simulacije, bioinformatika in načrtovanje zdravilnih učinkovin

• Funder: ARRS - Slovenian Research Agency
• Project number: P1-0134
• Name: Kemija za trajnostni razvoj