Cargando…
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...
Autores principales: | , , , , , |
---|---|
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 |
_version_ | 1783409858822799360 |
---|---|
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. |
format | Online Article Text |
id | pubmed-6457083 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT gilskimiroslaw accurategeometricalrestraintsforwatsoncrickbasepairs AT zhaojianbo accurategeometricalrestraintsforwatsoncrickbasepairs AT kowielmarcin accurategeometricalrestraintsforwatsoncrickbasepairs AT brzezinskidariusz accurategeometricalrestraintsforwatsoncrickbasepairs AT turnerdouglash accurategeometricalrestraintsforwatsoncrickbasepairs AT jaskolskimariusz accurategeometricalrestraintsforwatsoncrickbasepairs |