ArticleJournal of molecular biology2009
Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping.
Article in Journal of molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Beyond structures: solution NMR as the quantitative engine of integrated structural biology.Frontiers in molecular biosciences · 2026Review
- Revealing hidden protonated conformational states in RNA dynamic ensembles.Nucleic acids research · 2025Article
- Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent.ACS omega · 2025Article
- Thermodynamic examination of pH and magnesium effect on U6 RNA internal loop.RNA (New York, N.Y.) · 2019Article
- An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch.Nucleic acids research · 2018Article
- The life of U6 small nuclear RNA, from cradle to grave.RNA (New York, N.Y.) · 2018Review
- Structural Roles of Noncoding RNAs in the Heart of Enzymatic Complexes.Biochemistry · 2017Article
- Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core.Acta crystallographica. Section D, Structural biology · 2017Article
- Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.Chemical reviews · 2016Review
- Characterizing RNA Excited States Using NMR Relaxation Dispersion.Methods in enzymology · 2015Article
- Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution.Nature structural & molecular biology · 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
- RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core.The EMBO journal · 2013Article
- Hidden Conformation Events in DNA Base Extrusions: A Generalized Ensemble Path Optimization and Equilibrium Simulation Study.Journal of chemical theory and computation · 2013Article
- Structural analyses of the pre-mRNA splicing machinery.Protein science : a publication of the Protein Society · 2013Review
- Structure of the yeast U2/U6 snRNA complex.RNA (New York, N.Y.) · 2012Article
- Review
- Primordial soup or vinaigrette: did the RNA world evolve at acidic pH?Biology direct · 2012Article
- Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.Nature methods · 2011Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The U6 RNA internal stem-loop (U6 ISL) is a highly conserved domain of the spliceosome that is important for pre-mRNA splicing. The U6 ISL contains an internal loop that is in equilibrium between two conformations controlled by the protonation state of an adenine (pK(a)=6.5). Lower pH favors formation of a protonated C-A(+) wobble pair and base flipping of the adjacent uracil. Higher pH favors stacking of the uracil and allows an essential metal ion to bind at this position. Here, we define the minimal-energy path for this conformational transition. To do this, we solved the U6 ISL structure at higher pH (8.0) in order to eliminate interference from the low-pH conformer. This structure reveals disruption of the protonated C-A(+) pair and formation of a new C-U pair, which explains the preference for a stacked uracil at higher pH. Next, we used nudged elastic band molecular dynamics simulations to calculate the minimum-energy path between the two conformations. Our results indicate that the C-U pair is dynamic, which allows formation of the more stable C-A(+) pair upon adenine protonation. After formation of the C-A(+) pair, the unpaired uracil follows a minor-groove base-flipping pathway. Molecular dynamics simulations suggest that the extrahelical uracil is stabilized by contacts with the adjacent helix.
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Registered trials
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