ArticleRNA (New York, N.Y.)2010
Induced fit or conformational selection for RNA/U1A folding.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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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.
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Who cites it
25 citing papers in PubMed, 49 citations in OpenAlex.
- Chemoproteomic capture of RNA binding activity in living cells.Nature communications · 2023Article
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- PTMint database of experimentally verified PTM regulation on protein-protein interaction.Bioinformatics (Oxford, England) · 2023Article
- Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model.The journal of physical chemistry. B · 2022Article
- Understanding the binding specificities of mRNA targets by the mammalian Quaking protein.Nucleic acids research · 2019Article
- Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model.Biophysical journal · 2019Article
- Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB.The Journal of chemical physics · 2018Article
- Synergistic regulation mechanism of iperoxo and LY2119620 for muscarinic acetylcholine M2 receptor.RSC advances · 2018Article
- Structural Changes of RNA in Complex with Proteins in the SRP.Frontiers in molecular biosciences · 2018Review
- Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein.Scientific reports · 2017Article
- Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode.Scientific reports · 2017Article
- Conformation Dynamics of the Intrinsically Disordered Protein c-Myb with theRSC advances · 2017Article
- Protein-RNA interactions: structural biology and computational modeling techniques.Biophysical reviews · 2016Review
- Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch.Scientific reports · 2016Article
- Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis.Journal of chemical information and modeling · 2016Article
- Global conformational selection and local induced fit for the recognition between intrinsic disordered p53 and CBP.PloS one · 2013Article
- Single-molecule observation of the induction of k-turn RNA structure on binding L7Ae protein.Biophysical journal · 2012Article
- Intrinsic flexibility of snRNA hairpin loops facilitates protein binding.RNA (New York, N.Y.) · 2012Article
- Enhancing the promiscuous phosphotriesterase activity of a thermostable lactonase (GkaP) for the efficient degradation of organophosphate pesticides.Applied and environmental microbiology · 2012Article
- Insight into the stability of cross-β amyloid fibril from VEALYL short peptide with molecular dynamics simulation.PloS one · 2012Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The hairpin II of U1 snRNA can bind U1A protein with high affinity and specificity. NMR spectra suggest that the loop region of apo-RNA is largely unstructured and undergoes a transition from unstructured to well-folded upon U1Abinding. However, the mechanism that RNA folding coupled protein binding is poorly understood. To get an insight into the mechanism, we have performed explicit-solvent molecular dynamics (MD) to study the folding kinetics of bound RNA and apo-RNA. Room-temperature MD simulations suggest that the conformation of bound RNA has significant adjustment and becomes more stable upon U1A binding. Kinetic analysis of high-temperature MD simulations shows that bound RNA and apo-RNA unfold via a two-state process, respectively. Both kinetics and free energy landscape analyses indicate that bound RNA folds in the order of RNA contracting, U1A binding, and tertiary folding. The predicted Phi-values suggest that A8, C10, A11, and G16 are key bases for bound RNA folding. Mutant Arg52Gln analysis shows that electrostatic interaction and hydrogen bonds between RNA and U1A (Arg52Gln) decrease. These results are in qualitative agreement with experiments. Furthermore, this method could be used in other studies about biomolecule folding upon receptor binding.
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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.