title: Structural modeling of protein-RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS.
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.
authors.affiliation: Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
authors.forename: G
authors.initials: G
authors.lastname: Dorn
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland.
authors.forename: A
authors.initials: A
authors.lastname: Leitner
authors.affiliation: Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
authors.forename: J
authors.initials: J
authors.lastname: Boudet
authors.affiliation: Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
authors.forename: S
authors.initials: S
authors.lastname: Campagne
authors.affiliation: Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
authors.forename: C
authors.initials: C
authors.lastname: von Schroetter
authors.affiliation: Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
authors.forename: A
authors.initials: A
authors.lastname: Moursy
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland.|Faculty of Science, University of Zurich, Zürich, Switzerland.
authors.forename: R
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: Department of Biology, Institute for Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
authors.forename: F H-T
authors.initials: FH
authors.lastname: Allain
mesh_terms: D001665:Binding Sites; D002247:Carbon Isotopes; D002851:Chromatography, High Pressure Liquid; D034441:Heterogeneous-Nuclear Ribonucleoproteins / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D038941:Polypyrimidine Tract-Binding Protein / Q000737:chemistry* / Q000235:genetics; D011485:Protein Binding; D012313:RNA / Q000737:chemistry*; D017412:Ribonucleoprotein, U1 Small Nuclear / Q000737:chemistry* / Q000235:genetics; D012984:Software; D053719:Tandem Mass Spectrometry; D014466:Ultraviolet Rays
chemical_list: D002247:Carbon Isotopes; D034441:Heterogeneous-Nuclear Ribonucleoproteins; D009587:Nitrogen Isotopes; C450006:PTBP1 protein, human; D017412:Ribonucleoprotein, U1 Small Nuclear; D038941:Polypyrimidine Tract-Binding Protein; D012313:RNA