Abstract
Ribonucleoproteins (RNPs) are key regulators of cellular function. We established an efficient approach, crosslinking of segmentally isotope-labeled RNA and tandem mass spectrometry (CLIR-MS/MS), to localize protein-RNA interactions simultaneously at amino acid and nucleotide resolution. The approach was tested on polypyrimidine tract binding protein 1 and U1 small nuclear RNP. Our method provides distance restraints to support integrative atomic-scale structural modeling and to gain mechanistic insights into RNP-regulated processes.
MeSH terms
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Binding Sites
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Carbon Isotopes
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Chromatography, High Pressure Liquid
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Heterogeneous-Nuclear Ribonucleoproteins / chemistry*
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Heterogeneous-Nuclear Ribonucleoproteins / genetics
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Models, Molecular*
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Nitrogen Isotopes
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Nuclear Magnetic Resonance, Biomolecular
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Nucleic Acid Conformation*
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Polypyrimidine Tract-Binding Protein / chemistry*
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Polypyrimidine Tract-Binding Protein / genetics
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Protein Binding
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RNA / chemistry*
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Ribonucleoprotein, U1 Small Nuclear / chemistry*
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Ribonucleoprotein, U1 Small Nuclear / genetics
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Software
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Tandem Mass Spectrometry
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Ultraviolet Rays
Substances
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Carbon Isotopes
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Heterogeneous-Nuclear Ribonucleoproteins
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Nitrogen Isotopes
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PTBP1 protein, human
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Ribonucleoprotein, U1 Small Nuclear
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Polypyrimidine Tract-Binding Protein
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RNA