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ProteomicsMonolinks Matter: Rational Modification of a Cross-Linker for Improved Flexible Protein Structure Modeling
Chemical cross-linking/mass spectrometry (XL-MS) has emerged as a complementary tool for mapping interaction sites within protein networks as well as gaining moderate-resolution native structurale insight with minimal interference. XL-MS technology mostly relies on chemoselective reactions (crosslin...
ORGANISM(S): Homo sapiens (Human) 
2025-05-06 | PXD051742 | Pride
Protein structure Alphafold Crosslink Dsso-carbamate Monolink 
ProteomicsModeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry
We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2, and conformer selection using XL-MS data. For conformer selection, w...
ORGANISM(S): Escherichia coli 
2024-05-24 | PXD046392 | Pride
Crosslinks Monolinks Alphafold2 Idr Flexible protein 
UnknownModeling Flexible Protein Structure With AlphaFold2 and Crosslinking Mass Spectrometry.
Not available
S-EPMC10884514 | biostudies-literature
UnknownRational Modification of a Cross-Linker for Improved Flexible Protein Structure Modeling.
Not available
S-EPMC11755394 | biostudies-literature
UnknownAll-in-One Pseudo-MS3 Method for the Analysis of Gas-Phase Cleavable Protein Crosslinking Reactions.
Not available
S-EPMC11250984 | biostudies-literature
ProteomicsFinding and using Diagnostic Ions in Collisional Induced Crosslinked Peptide Fragmentation Spectra
Crosslinking mass spectrometry (XL-MS) has emerged as a powerful tool in its own right for the investigation of protein structures and interactions. Utilizing standard shotgun MS mass spectrometry equipment and specialized database search software, crosslinked peptide-pairs can be identified and dir...
ORGANISM(S): Bos taurus (Bovine) 
2019-07-16 | PXD013083 | Pride
Xlinkx Crosslinking mass spectrometry Gas phase fragmentation of crosslinks 
ProteomicsComprehensive XL-MS reveals parallel orientation and versatile conformations of plant HOP2/MND1
The HOP2/MND1 heterodimer is essential for meiotic homologous recombination in plants and other eukaryotes, and promotes the repair of DNA double strand breaks. The HOP2/MND1 dimer forms via the central, split coiled coils (CC1 and CC2) present in both proteins, and the resulting complex contains se...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2015-11-05 | PXD001538 | Pride
Xl hop2 mnd1 cross link 
ProteomicsNucleotide independant as well as ATP-hydrolysis driven steps of Rea1 Linker remodelling drive the removal of assembly factors from pre-ribosomal particles: PhoX cross-linking of Rea1 in presence of ATPgS, AMP-PNP or Apo state.
The ribosome maturation factor Rea1 (or Midasin) catalyses the removal of assembly factors from large ribosomal subunit precursors and to promotes their export from the nucleus to the cytosol. Rea1 consists of nearly 5000 amino-acid residues and belongs to the AAA+ protein family. It consists of a r...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-07-29 | PXD053636 | Pride
Cross-linking mass spectrometry Structural biology Structural proteomics 
ProteomicsNotch-Jagged signaling complex defined by an interaction mosaic
The Notch signaling system links cellular fate to that of its neighbors, driving proliferation, apoptosis, and cell differentiation in metazoan organisms, whereas dysfunction leads to debilitating developmental disorders and cancers. Here we probe the molecular architecture of mammalian Notch1 full ...
ORGANISM(S): Mus musculus (Mouse) 
2021-07-08 | PXD023072 | Pride
Egf repeats Cell signaling Notch1 Cross-linking mass spectrometry Protein-protein interaction Glycoprotein Phox Xlinkx/pd Jagged1 
ProteomicsA deep XL-proteomic dataset of intact HEK293T cells using DSBSO
Cross-linking mass spectrometry is an emerging method to study protein-protein interactions (PPIs) in intact biological systems. Here, we optimized a workflow for gnerating high coverage maps of PPIs using the enrichable cross-linker Azide-A-DSBSO. This created one of the largest to-date XL-MS datas...
ORGANISM(S): Homo sapiens (Human) 
2024-10-17 | PXD043531 | Pride
Human Deep xl-ms Cell culture 
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