Improving NMR Structures of RNA
| Autor: | Charles D. Schwieters, Guillermo A. Bermejo, G. Marius Clore |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Steric effects RNA Folding Magnetic Resonance Spectroscopy 030102 biochemistry & molecular biology Chemistry Stacking RNA Nuclear magnetic resonance spectroscopy Backbone conformation Force field (chemistry) Article 03 medical and health sciences Crystallography 030104 developmental biology Structural Biology Residual dipolar coupling Covalent bond Molecular Biology |
| Popis: | Here, we show that modern solution nuclear magnetic resonance (NMR) structures of RNA exhibit more steric clashes and conformational ambiguities than their crystallographic X-ray counterparts. To tackle these issues, we developed RNA-ff1, a new force field for structure calculation with Xplor-NIH. Using seven published NMR datasets, RNA-ff1 improves covalent geometry and MolProbity validation criteria for clashes and backbone conformation in most cases, relative to both the previous Xplor-NIH force field and the original structures associated with the experimental data. In addition, with smaller base-pair step rises in helical stems, RNA-ff1 structures enjoy more favorable base stacking. Finally, structural accuracy improves in the majority of cases, as supported by complete residual dipolar coupling cross-validation. Thus, the reported advances show great promise in bridging the quality gap that separates NMR and X-ray structures of RNA. |
| Databáze: | OpenAIRE |
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