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Accurate geometrical restraints for Watson–Crick base pairs

Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources...

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Autores principales: Gilski, Miroslaw, Zhao, Jianbo, Kowiel, Marcin, Brzezinski, Dariusz, Turner, Douglas H., Jaskolski, Mariusz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6457083/
https://www.ncbi.nlm.nih.gov/pubmed/32830749
http://dx.doi.org/10.1107/S2052520619002002
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author Gilski, Miroslaw
Zhao, Jianbo
Kowiel, Marcin
Brzezinski, Dariusz
Turner, Douglas H.
Jaskolski, Mariusz
author_facet Gilski, Miroslaw
Zhao, Jianbo
Kowiel, Marcin
Brzezinski, Dariusz
Turner, Douglas H.
Jaskolski, Mariusz
author_sort Gilski, Miroslaw
collection PubMed
description Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources and compared: small-molecule crystal structures in the Cambridge Structural Database (CSD), ultrahigh-resolution structures in the Protein Data Bank (PDB) and quantum-mechanical (QM) calculations. The best parameters are those based on CSD structures. After over two decades, the standard library of Parkinson et al. [(1996), Acta Cryst. D52, 57–64] is still valid, but improvements are possible with the use of the current CSD database. The CSD-derived geometry is fully compatible with Watson–Crick base pairs, as comparisons with QM results for isolated and paired bases clearly show that the CSD targets closely correspond to proper base pairing. While the QM results are capable of distinguishing between single and paired bases, their level of accuracy is, on average, nearly two times lower than for the CSD-derived targets when gauged by root-mean-square deviations from ultrahigh-resolution structures in the PDB. Nevertheless, the accuracy of QM results appears sufficient to provide stereochemical targets for synthetic base pairs where no reliable experimental structural information is available. To enable future tests for this approach, QM calculations are provided for isocytosine, isoguanine and the iCiG base pair.
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spelling pubmed-64570832019-04-19 Accurate geometrical restraints for Watson–Crick base pairs Gilski, Miroslaw Zhao, Jianbo Kowiel, Marcin Brzezinski, Dariusz Turner, Douglas H. Jaskolski, Mariusz Acta Crystallogr B Struct Sci Cryst Eng Mater Research Papers Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources and compared: small-molecule crystal structures in the Cambridge Structural Database (CSD), ultrahigh-resolution structures in the Protein Data Bank (PDB) and quantum-mechanical (QM) calculations. The best parameters are those based on CSD structures. After over two decades, the standard library of Parkinson et al. [(1996), Acta Cryst. D52, 57–64] is still valid, but improvements are possible with the use of the current CSD database. The CSD-derived geometry is fully compatible with Watson–Crick base pairs, as comparisons with QM results for isolated and paired bases clearly show that the CSD targets closely correspond to proper base pairing. While the QM results are capable of distinguishing between single and paired bases, their level of accuracy is, on average, nearly two times lower than for the CSD-derived targets when gauged by root-mean-square deviations from ultrahigh-resolution structures in the PDB. Nevertheless, the accuracy of QM results appears sufficient to provide stereochemical targets for synthetic base pairs where no reliable experimental structural information is available. To enable future tests for this approach, QM calculations are provided for isocytosine, isoguanine and the iCiG base pair. International Union of Crystallography 2019-03-27 /pmc/articles/PMC6457083/ /pubmed/32830749 http://dx.doi.org/10.1107/S2052520619002002 Text en © Miroslaw Gilski et al. 2019 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/2.0/uk/
spellingShingle Research Papers
Gilski, Miroslaw
Zhao, Jianbo
Kowiel, Marcin
Brzezinski, Dariusz
Turner, Douglas H.
Jaskolski, Mariusz
Accurate geometrical restraints for Watson–Crick base pairs
title Accurate geometrical restraints for Watson–Crick base pairs
title_full Accurate geometrical restraints for Watson–Crick base pairs
title_fullStr Accurate geometrical restraints for Watson–Crick base pairs
title_full_unstemmed Accurate geometrical restraints for Watson–Crick base pairs
title_short Accurate geometrical restraints for Watson–Crick base pairs
title_sort accurate geometrical restraints for watson–crick base pairs
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6457083/
https://www.ncbi.nlm.nih.gov/pubmed/32830749
http://dx.doi.org/10.1107/S2052520619002002
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