Number of the records: 1
Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution
- 1.
SYSNO ASEP 0570656 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution Author(s) Schrenková, Věra (UOCHB-X)
Para Kkadan, Mohammed Siddhique (UOCHB-X)
Kessler, Jiří (UOCHB-X) RID, ORCID
Kapitán, J. (CZ)
Bouř, Petr (UOCHB-X) RID, ORCIDSource Title Physical Chemistry Chemical Physics. - : Royal Society of Chemistry - ISSN 1463-9076
Roč. 25, č. 11 (2023), s. 8198-8208Number of pages 11 s. Language eng - English Country GB - United Kingdom Keywords vibrational circular dichroism ; nucleic acids ; free energies OECD category Physical chemistry R&D Projects GA22-04669S GA ČR - Czech Science Foundation (CSF) EF16_019/0000729 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Research Infrastructure e-INFRA CZ - 90140 - CESNET, zájmové sdružení právnických osob Method of publishing Open access Institutional support UOCHB-X - RVO:61388963 UT WOS 000945121700001 EID SCOPUS 85149820017 DOI 10.1039/d2cp05756e Annotation 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. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418 Year of Publishing 2024 Electronic address https://doi.org/10.1039/D2CP05756E
Number of the records: 1