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Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution
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SYSNO ASEP 0570656 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution Tvůrce(i) Schrenková, Věra (UOCHB-X)
Para Kkadan, Mohammed Siddhique (UOCHB-X)
Kessler, Jiří (UOCHB-X) RID, ORCID
Kapitán, J. (CZ)
Bouř, Petr (UOCHB-X) RID, ORCIDZdroj.dok. Physical Chemistry Chemical Physics. - : Royal Society of Chemistry - ISSN 1463-9076
Roč. 25, č. 11 (2023), s. 8198-8208Poč.str. 11 s. Jazyk dok. eng - angličtina Země vyd. GB - Velká Británie Klíč. slova vibrational circular dichroism ; nucleic acids ; free energies Obor OECD Physical chemistry CEP GA22-04669S GA ČR - Grantová agentura ČR EF16_019/0000729 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy Výzkumná infrastruktura e-INFRA CZ - 90140 - CESNET, zájmové sdružení právnických osob Způsob publikování Open access Institucionální podpora UOCHB-X - RVO:61388963 UT WOS 000945121700001 EID SCOPUS 85149820017 DOI 10.1039/d2cp05756e Anotace Nucleotide conformational flexibility affects their biological functions. Although the spectroscopy of Raman optical activity (ROA) is well suited to structural analyses in aqueous solutions, the link between the spectral shape and the nucleotide geometry is not fully understood. We recorded the Raman and ROA spectra of model nucleotides (rAMP, rGMP, rCMP, and dTMP) and interpreted them on the basis of molecular dynamics (MD) combined with density functional theory (DFT). The relation between the sugar puckering, base conformation and spectral intensities is discussed. Hydrogen bonds between the sugar's C3′ hydroxyl and the phosphate groups were found to be important for the sugar puckering. The simulated spectra correlated well with the experimental data and provided an understanding of the dependence of the spectral shapes on conformational dynamics. Most of the strongest spectral bands could be assigned to vibrational molecular motions. Decomposition of the experimental spectra into calculated subspectra based on arbitrary maps of free energies provided experimental conformer populations, which could be used to verify and improve the MD predictions. The analyses indicate some flaws of common MD force fields, such as being unable to describe the fine conformer distribution. Also the accuracy of conformer populations obtained from the spectroscopic data depends on the simulations, improvement of which is desirable for gaining a more detailed insight in the future. Improvement of the spectroscopic and computational methodology for nucleotides also provides opportunities for its application to larger nucleic acids. Pracoviště Ústav organické chemie a biochemie Kontakt asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434 Rok sběru 2024 Elektronická adresa https://doi.org/10.1039/D2CP05756E
Počet záznamů: 1