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ProteomicsSingle Nucleotide Resolution RNA-Protein Cross-Linking/MS: Simple Extension of the CLIR-MS Workflow
RNA-protein interactions mediate a vast number of intracellular processes. CLIR-MS (cross-linking of isotope labeled RNA and tandem mass spectrometry) is a mass spectrometric technique that allows the identification of RNA-protein interaction sites at single nucleotide/amino acid resolution in a sin...
ORGANISM(S): Homo sapiens (Human) 
2021-11-04 | PXD024010 | Pride
Protein rna cross-linking clir-ms uv xl 
UnknownSingle Nucleotide Resolution RNA-Protein Cross-Linking Mass Spectrometry: A Simple Extension of the CLIR-MS Workflow.
Not available
S-EPMC8581962 | biostudies-literature
ProteomicsRNxQuest: an extension to the xQuest pipeline enabling analysis of protein-RNA cross-linking/mass spectrometry data
The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling. The novel data type requires a bespoke data analysis approach. The n...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2023-09-06 | PXD039754 | Pride
Uv cross-linking  mbnl1  fox1  ptbp1  bsa  cross-linking  xl-ms  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
UnknownRNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein-RNA Cross-Linking/Mass Spectrometry Data.
Not available
S-EPMC10563164 | biostudies-literature
ProteomicsHybrid structural modeling of protein-RNA complexes using crosslinking of segmentally isotope labeled RNA and tandem mass spectrometry
To study protein-RNA interactions at single amino acid and single nucleotide resolution we developed a new approach, termed cross-linking of segmentally isotope labeled RNA and tandem mass spectrometry (CLIR-MS/MS). The method was developed using the PTBP1-EMCV IRES complex as a model system and add...
ORGANISM(S): Homo sapiens (Human) 
2017-03-27 | PXD005566 | Pride
Photochemical cross-linking  protein-rna cross-linking  segmental isotope labeling of rna  clir-ms/ms  ribonucleoproteins  structural proteomics  polypyrimidine tract binding protein 1  u1 snrnp 
ProteomicsIntegrative structure determination of an 85-kilodalton PTBP1-IRES complex in solution reveals a strong compaction with pronounced conformational flexibility
Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the interaction between the four RNA recognition motifs (RRMs) of the protein PTBP1 with the internal ribosome entry site (IRES) of encephalomyocarditis virus (EMCV). These results are a reanalysis of PX...
ORGANISM(S): Homo sapiens (Human) 
2023-10-24 | PXD034894 | Pride
Uv cross-linking  ptbp1  ires  rrm  splicing  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms  integrative modelling  structure 
UnknownA highly sensitive protein-RNA cross-linking mass spectrometry workflow with enhanced structural modeling potential.
Not available
S-EPMC12203917 | biostudies-literature
ProteomicsStructural requirements for photo-induced RNA-protein cross-linking
Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the UV cross-linking behavior of in vitro reconstituted FOX1 RRM in complex with its cognate RNA sequence, the Fox binding element (FBE), (U)GCAUGU. The FBE heptanucleotide was subsequently mutated, and ...
ORGANISM(S): Homo sapiens (Human) 
2022-06-09 | PXD031381 | Pride
Uv cross-linking  mbnl1  fox1  ptbp1  sf3a1  u1  u2  cross-linking  xl-ms  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
ProteomicsSequence specific recognition of U1 snRNP stem-loop 4 by the ubiquitin-like domain of U2 snRNP protein SF3A1 and its RGG motif
Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the interaction between the ubiquitin-like domain (UBL) of the protein SF3A1, a component of the U2 snRNP, with stem-loop 4 RNA (SL4) from the U1 snRNP. The complex was cross-linked and analysed both in ...
ORGANISM(S): Homo sapiens (Human) 
2022-02-22 | PXD027189 | Pride
Uv cross-linking  sf3a1  u1  u2  snrnp  splicing  spliceosome  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
UnknownStructural modeling of protein-RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS.
Not available
S-EPMC5505470 | biostudies-literature
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