Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

0560262 - BTÚ 2023 RIV GB eng J - Článek v odborném periodiku
Biedermannová, Lada - Černý, Jiří - Malý, Michal - Nekardová, Michaela - Schneider, Bohdan
Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks.
Acta Crystallographica Section D-Biological Crystallography. Roč. 78, AUG 1 2022 (2022), s. 1032-1045. ISSN 1399-0047. E-ISSN 2059-7983
Grant CEP: GA MŠMT(CZ) LTAUSA18197; GA MŠMT(CZ) LM2018131
Institucionální podpora: RVO:86652036
Klíčová slova: DNA hydration * water * dinucleotide fragments * knowledge-based prediction * WatNA
Obor OECD: Analytical chemistry
Impakt faktor: 2.2, rok: 2022
Způsob publikování: Open access
https://scripts.iucr.org/cgi-bin/paper?S2059798322006234

Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 angstrom) and correctly reproduced the known features of DNA hydration, for example the 'spine of hydration' in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.
Trvalý link: https://hdl.handle.net/11104/0333870