ArticleNucleic acids research2017
Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Deciphering hydration patterns across RNA conformations: Insights into water-mediated RNA recognition.Current research in structural biology · 2026Article
- RNA-binding protein RBM47 in health and disease: molecular mechanisms, preclinical evidence, and translational challenges.Frontiers in immunology · 2026Review
- The Role of RNA-Binding Proteins in Hematological Malignancies.International journal of molecular sciences · 2022Review
- In Vitro Evolution Reveals Noncationic Protein-RNA Interaction Mediated by Metal Ions.Molecular biology and evolution · 2022Article
- Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.Biophysical journal · 2021Article
- Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations.Biomolecules · 2019Article
- Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes.Cold Spring Harbor perspectives in biology · 2019Review
- Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs.FEBS open bio · 2019Article
- Specific inhibition of splicing factor activity by decoy RNA oligonucleotides.Nature communications · 2019Article
- Structural and Kinetic Profiling of Allosteric Modulation of Duplex DNA Induced by DNA-Binding Polyamide Analogues.Chemistry (Weinheim an der Bergstrasse, Germany) · 2019Article
- Structural Relaxation Processes and Collective Dynamics of Water in Biomolecular Environments.The journal of physical chemistry. B · 2019Article
- Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.PLoS computational biology · 2018Article
- 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
- Importance of amino acids Leu135 and Tyr236 for the interaction between EhCFIm25 and RNA: a molecular dynamics simulation study.Journal of molecular modeling · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- MD simulations reveal the basis for dynamic assembly of Hfq-RNA complexes.The Journal of biological chemistryArticle
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6 authors.
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Abstract
The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes.
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