ArticleJournal of biomolecular NMR2008
Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data.
Article in Journal of biomolecular NMR, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.Journal of chemical information and modeling · 2025Article
- Imino chemical shift assignments of tRNABiomolecular NMR assignments · 2024Article
- Pressure pushes tRNAProceedings of the National Academy of Sciences of the United States of America · 2023Article
- An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme.Nucleic acids research · 2021Article
- NMR Studies of Retroviral Genome Packaging.Viruses · 2020Review
- Structural Biology of the Enterovirus Replication-Linked 5'-Cloverleaf RNA and Associated Virus Proteins.Microbiology and molecular biology reviews : MMBR · 2020Review
- Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.Current opinion in structural biology · 2019Review
- Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy.Wiley interdisciplinary reviews. RNA · 2019Review
- Conformational flexibility in the enterovirus RNA replication platform.RNA (New York, N.Y.) · 2019Article
- Arginine Side-Chain Hydrogen Exchange: Quantifying Arginine Side-Chain Interactions in Solution.Chemphyschem : a European journal of chemical physics and physical chemistry · 2019Article
- Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.Structure (London, England : 1993) · 2018Article
- Structure modeling of RNA using sparse NMR constraints.Nucleic acids research · 2017Article
- Analysis of RNA structure using small-angle X-ray scattering.Methods (San Diego, Calif.) · 2017Article
- Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations.Nucleic acids research · 2016Article
- Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA.Journal of molecular biology · 2016Article
- Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.Journal of the American Chemical Society · 2015Article
- Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures.Current opinion in structural biology · 2015Review
- Conjoined use of EM and NMR in RNA structure refinement.PloS one · 2015Article
- Progress and outlook in structural biology of large viral RNAs.Virus research · 2014Review
- Evidence for a group II intron-like catalytic triplex in the spliceosome.Nature structural & molecular biology · 2014Article
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5 authors.
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Abstract
A procedure is presented for refinement of a homology model of E. coli tRNA(Val), originally based on the X-ray structure of yeast tRNA(Phe), using experimental residual dipolar coupling (RDC) and small angle X-ray scattering (SAXS) data. A spherical sampling algorithm is described for refinement against SAXS data that does not require a globbic approximation, which is particularly important for nucleic acids where such approximations are less appropriate. Substantially higher speed of the algorithm also makes its application favorable for proteins. In addition to the SAXS data, the structure refinement employed a sparse set of NMR data consisting of 24 imino N-H(N) RDCs measured with Pf1 phage alignment, and 20 imino N-H(N) RDCs obtained from magnetic field dependent alignment of tRNA(Val). The refinement strategy aims to largely retain the local geometry of the 58% identical tRNA(Phe) by ensuring that the atomic coordinates for short, overlapping segments of the ribose-phosphate backbone and the conserved base pairs remain close to those of the starting model. Local coordinate restraints are enforced using the non-crystallographic symmetry (NCS) term in the XPLOR-NIH or CNS software package, while still permitting modest movements of adjacent segments. The RDCs mainly drive the relative orientation of the helical arms, whereas the SAXS restraints ensure an overall molecular shape compatible with experimental scattering data. The resulting structure exhibits good cross-validation statistics (jack-knifed Q (free) = 14% for the Pf1 RDCs, compared to 25% for the starting model) and exhibits a larger angle between the two helical arms than observed in the X-ray structure of tRNA(Phe), in agreement with previous NMR-based tRNA(Val) models.
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