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Conjoined Use of EM and NMR in RNA Structure Refinement
More than 40% of the RNA structures have been determined using nuclear magnetic resonance (NMR) technique. NMR mainly provides local structural information of protons and works most effectively on relatively small biomacromolecules. Hence structural characterization of large RNAs can be difficult fo...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370883/ https://www.ncbi.nlm.nih.gov/pubmed/25798848 http://dx.doi.org/10.1371/journal.pone.0120445 |
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author | Gong, Zhou Schwieters, Charles D. Tang, Chun |
author_facet | Gong, Zhou Schwieters, Charles D. Tang, Chun |
author_sort | Gong, Zhou |
collection | PubMed |
description | More than 40% of the RNA structures have been determined using nuclear magnetic resonance (NMR) technique. NMR mainly provides local structural information of protons and works most effectively on relatively small biomacromolecules. Hence structural characterization of large RNAs can be difficult for NMR alone. Electron microscopy (EM) provides global shape information of macromolecules at nanometer resolution, which should be complementary to NMR for RNA structure determination. Here we developed a new energy term in Xplor-NIH against the density map obtained by EM. We conjointly used NMR and map restraints for the structure refinement of three RNA systems — U2/U6 small-nuclear RNA, genome-packing motif (Ψ(CD))(2) from Moloney murine leukemia virus, and ribosome-binding element from turnip crinkle virus. In all three systems, we showed that the incorporation of a map restraint, either experimental or generated from known PDB structure, greatly improves structural precision and accuracy. Importantly, our method does not rely on an initial model assembled from RNA duplexes, and allows full torsional freedom for each nucleotide in the torsion angle simulated annealing refinement. As increasing number of macromolecules can be characterized by both NMR and EM, the marriage between the two techniques would enable better characterization of RNA three-dimensional structures. |
format | Online Article Text |
id | pubmed-4370883 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-43708832015-04-04 Conjoined Use of EM and NMR in RNA Structure Refinement Gong, Zhou Schwieters, Charles D. Tang, Chun PLoS One Research Article More than 40% of the RNA structures have been determined using nuclear magnetic resonance (NMR) technique. NMR mainly provides local structural information of protons and works most effectively on relatively small biomacromolecules. Hence structural characterization of large RNAs can be difficult for NMR alone. Electron microscopy (EM) provides global shape information of macromolecules at nanometer resolution, which should be complementary to NMR for RNA structure determination. Here we developed a new energy term in Xplor-NIH against the density map obtained by EM. We conjointly used NMR and map restraints for the structure refinement of three RNA systems — U2/U6 small-nuclear RNA, genome-packing motif (Ψ(CD))(2) from Moloney murine leukemia virus, and ribosome-binding element from turnip crinkle virus. In all three systems, we showed that the incorporation of a map restraint, either experimental or generated from known PDB structure, greatly improves structural precision and accuracy. Importantly, our method does not rely on an initial model assembled from RNA duplexes, and allows full torsional freedom for each nucleotide in the torsion angle simulated annealing refinement. As increasing number of macromolecules can be characterized by both NMR and EM, the marriage between the two techniques would enable better characterization of RNA three-dimensional structures. Public Library of Science 2015-03-23 /pmc/articles/PMC4370883/ /pubmed/25798848 http://dx.doi.org/10.1371/journal.pone.0120445 Text en © 2015 Gong et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Gong, Zhou Schwieters, Charles D. Tang, Chun Conjoined Use of EM and NMR in RNA Structure Refinement |
title | Conjoined Use of EM and NMR in RNA Structure Refinement |
title_full | Conjoined Use of EM and NMR in RNA Structure Refinement |
title_fullStr | Conjoined Use of EM and NMR in RNA Structure Refinement |
title_full_unstemmed | Conjoined Use of EM and NMR in RNA Structure Refinement |
title_short | Conjoined Use of EM and NMR in RNA Structure Refinement |
title_sort | conjoined use of em and nmr in rna structure refinement |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370883/ https://www.ncbi.nlm.nih.gov/pubmed/25798848 http://dx.doi.org/10.1371/journal.pone.0120445 |
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