Classification and energetics of the base-phosphate interactions in RNA

Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides....

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Main Authors:	Zirbel, Craig L., Šponer, Judit E., Šponer, Jiri, Stombaugh, Jesse, Leontis, Neocles B.
Format:	Online
Language:	English
Published:	Oxford University Press 2009
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2731888/

id	pubmed-2731888
recordtype	oai_dc
spelling	pubmed-27318882009-09-10 Classification and energetics of the base-phosphate interactions in RNA Zirbel, Craig L. Šponer, Judit E. Šponer, Jiri Stombaugh, Jesse Leontis, Neocles B. RNA Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and superimposing base-phosphate (BPh) interactions from a reduced-redundancy subset of 3D structures from the PDB, we identified recurrent phosphate-binding sites on the RNA bases. Quantum chemical calculations were carried out on model systems representing each BPh interaction. The calculations show that the centers of each cluster obtained from the structure superpositions correspond to energy minima on the potential energy hypersurface. The calculations also show that the most stable phosphate-binding sites occur on the Watson–Crick edge of guanine and the Hoogsteen edge of cytosine. We modified the ‘Find RNA 3D' (FR3D) software suite to automatically find and classify BPh interactions. Comparison of the 3D structures of the 16S and 23S rRNAs of Escherichia coli and Thermus thermophilus revealed that most BPh interactions are phylogenetically conserved and they occur primarily in hairpin, internal or junction loops or as part of tertiary interactions. Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments. Oxford University Press 2009-08 2009-06-14 /pmc/articles/PMC2731888/ /pubmed/19528080 http://dx.doi.org/10.1093/nar/gkp468 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Zirbel, Craig L. Šponer, Judit E. Šponer, Jiri Stombaugh, Jesse Leontis, Neocles B.
spellingShingle	Zirbel, Craig L. Šponer, Judit E. Šponer, Jiri Stombaugh, Jesse Leontis, Neocles B. Classification and energetics of the base-phosphate interactions in RNA
author_facet	Zirbel, Craig L. Šponer, Judit E. Šponer, Jiri Stombaugh, Jesse Leontis, Neocles B.
author_sort	Zirbel, Craig L.
title	Classification and energetics of the base-phosphate interactions in RNA
title_short	Classification and energetics of the base-phosphate interactions in RNA
title_full	Classification and energetics of the base-phosphate interactions in RNA
title_fullStr	Classification and energetics of the base-phosphate interactions in RNA
title_full_unstemmed	Classification and energetics of the base-phosphate interactions in RNA
title_sort	classification and energetics of the base-phosphate interactions in rna
description	Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and superimposing base-phosphate (BPh) interactions from a reduced-redundancy subset of 3D structures from the PDB, we identified recurrent phosphate-binding sites on the RNA bases. Quantum chemical calculations were carried out on model systems representing each BPh interaction. The calculations show that the centers of each cluster obtained from the structure superpositions correspond to energy minima on the potential energy hypersurface. The calculations also show that the most stable phosphate-binding sites occur on the Watson–Crick edge of guanine and the Hoogsteen edge of cytosine. We modified the ‘Find RNA 3D' (FR3D) software suite to automatically find and classify BPh interactions. Comparison of the 3D structures of the 16S and 23S rRNAs of Escherichia coli and Thermus thermophilus revealed that most BPh interactions are phylogenetically conserved and they occur primarily in hairpin, internal or junction loops or as part of tertiary interactions. Bases that form BPh interactions, which are conserved in the rRNA 3D structures are also conserved in homologous rRNA sequence alignments.
publisher	Oxford University Press
publishDate	2009
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2731888/
_version_	1611442755540615168

Classification and energetics of the base-phosphate interactions in RNA

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