ArticleRNA (New York, N.Y.)2007
Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation.
Article in RNA (New York, N.Y.), 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 49 citations in OpenAlex.
- Integrated NMR and MD structure and dynamics of the stem-loop-II motif (s2m) from the Omicron variant of SARS-CoV-2.RNA (New York, N.Y.) · 2025Article
- NMR characterisation of the antibiotic resistance-mediating 32mer RNA from the 23S ribosomal RNA.Biomolecular NMR assignments · 2025Article
- Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2.Journal of the American Chemical Society · 2024Article
- NMR characterization and ligand binding site of the stem-loop 2 motif from the Delta variant of SARS-CoV-2.RNA (New York, N.Y.) · 2024Article
- Dissecting Monomer-Dimer Equilibrium of an RNase P Protein Provides Insight Into the Synergistic Flexibility of 5' Leader Pre-tRNA Recognition.Frontiers in molecular biosciences · 2021Article
- m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB.PloS one · 2019Article
- Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.RNA (New York, N.Y.) · 2018Article
- Inner-Sphere Coordination of Divalent Metal Ion with Nucleobase in Catalytic RNA.Journal of the American Chemical Society · 2017Article
- Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.Nucleic acids research · 2017Article
- The Diversity of Ribonuclease P: Protein and RNA Catalysts with Analogous Biological Functions.Biomolecules · 2016Review
- Dynamic motions of the HIV-1 frameshift site RNA.Biophysical journal · 2015Article
- Structural dynamics of a single-stranded RNA-helix junction using NMR.RNA (New York, N.Y.) · 2014Article
- Hierarchy of RNA functional dynamics.Annual review of biochemistry · 2014Review
- NMR studies of nucleic acid dynamics.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2013Article
- Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.Nucleic acids research · 2012Article
- 3D maps of RNA interhelical junctions.Nature protocols · 2011Article
- Of proteins and RNA: the RNase P/MRP family.RNA (New York, N.Y.) · 2010Review
- A divalent cation stabilizes the active conformation of the B. subtilis RNase P x pre-tRNA complex: a role for an inner-sphere metal ion in RNase P.Journal of molecular biology · 2010Article
- NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Solution NMR studies of Chlorella virus DNA ligase-adenylate.Journal of molecular biology · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The P4 helix is an essential element of ribonuclease P (RNase P) that is believed to bind catalytically important metals. Here, we applied a combination of NMR residual dipolar couplings (RDCs) and a recently introduced domain-elongation strategy for measuring "motionally decoupled" relaxation data to characterize the structural dynamics of the P4 helix from Bacillus subtilis RNase P. In the absence of divalent ions, the two P4 helical domains undergo small amplitude (approximately 13 degrees) collective motions about an average interhelical angle of 10 degrees. The highly conserved U7 bulge and helical residue C8, which are proposed to be important for substrate recognition and metal binding, are locally mobile at pico- to nanosecond timescales and together form the pivot point for the collective domain motions. Chemical shift mapping reveals significant association of Mg2+ ions at the P4 major groove near the flexible pivot point at residues (A5, G22, G23) previously identified to bind catalytically important metals. The Mg2+ ions do not, however, significantly alter the structure or dynamics of P4. Analysis of results in the context of available X-ray structures of the RNA component of RNase P and structural models that include the pre-tRNA substrate suggest that the internal motions observed in P4 likely facilitate adaptive changes in conformation that take place during folding and substrate recognition, possibly aided by interactions with Mg2+ ions. Our results add to a growing view supporting the existence of functionally important internal motions in RNA occurring at nanosecond timescales.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.