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ProteomicsAnalysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry
Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of protei...
ORGANISM(S): Homo sapiens (Human) Xenopus laevis (African clawed frog) 
2020-10-20 | PXD020290 | Pride
Mass spectrometry Protein-dna interactions Uv-cross-linking 
ProteomicsStructural proteomics based investigation of DNA binding domain (DBD) of FOXO4 transcription factor in complex with DNA binding element (DNA)
The limited information available on the structure of complexes involving transcription factors and cognate DNA response elements represents a major obstacle in the quest to understand their mechanism of action at the molecular level. We implemented a concerted structural proteomics approach, which ...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2020-05-26 | PXD013969 | Pride
Hydrogen-deuterium exchange Transplatinum Cross-linking Protein Dna 
ProteomicsIn culture cross-linking of bacterial cells reveals large scale dynamic protein-protein interactions at the peptide level.
Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (...
ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168 
2017-05-23 | PXD006287 | Pride
Escherichia coli Bacillus subtilis Rna polymerase Membrane permeability Transcription. Bamg (bis(succinimidyl)-3-azidomethyl-glutarate) In vivo cross-linking Translation 
ProteomicsIn planta chemical crosslinking and mass spectrometry analysis of protein structure and interaction in Arabidopsis
Mass spectrometry analysis in combination with the site-specific chemical cross-linking has emerged as a powerful method in study of three-dimensional structure of protein complex and in mapping of protein-protein interactions (PPIs). Even though in vitro cross-linking experiments have been widely a...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2016-06-28 | PXD003658 | Pride
Arabidopsis Mass spectrometry Disuccinimidyl suberate In planta chemical cross-linking Interactomics Exhaustive cross-linked peptides identification tool 
ProteomicsSequential digestion with Trypsin and Elastase in cross-linking/mass spectrometry
Cross-linking/mass spectrometry has become an important approach for studying protein structures and protein-protein interactions. The amino acid composition of some protein regions impedes the detection of cross-linked residues, although it would yield invaluable information for protein modelling. ...
ORGANISM(S): Homo sapiens (Human) Schizosaccharomyces pombe 
2019-03-07 | PXD011459 | Pride
Lc-msms Cross-linking Yeast Human taf4-12 complex 
ProteomicsEpitope and paratope mapping of a SUMO-remnant antibody using cross-linking mass spectrometry and molecular docking
The small ubiquitin-like modifier (SUMO) is an important post-translational modification that regulates the function of various proteins essential for DNA damage repair, genome integrity and cell homeostasis. To identify protein SUMOylation effectively, an enrichment step is necessary, often require...
ORGANISM(S): Oryctolagus sp. 'Rabbit_OD' 
2025-02-19 | PXD055085 | Pride
Antibody Cross-linking Mass spectrometry Molecular docking Paratope mapping Sumo 
ProteomicsEpitope and paratope mapping of a SUMO-remnant antibody using cross-linking mass spectrometry and molecular docking
The small ubiquitin-like modifier (SUMO) is an important post-translational modification that regulates the function of various proteins essential for DNA damage repair, genome integrity and cell homeostasis. To identify protein SUMOylation effectively, an enrichment step is necessary, often require...
ORGANISM(S): Oryctolagus cuniculus (Rabbit) 
2025-02-19 | PXD055077 | Pride
Antibody Cross-linking Mass spectrometry Molecular docking Paratope mapping Sumo 
ProteomicsEpitope and paratope mapping of a SUMO-remnant antibody using cross-linking mass spectrometry and molecular docking
The small ubiquitin-like modifier (SUMO) is an important post-translational modification that regulates the function of various proteins essential for DNA damage repair, genome integrity and cell homeostasis. To identify protein SUMOylation effectively, an enrichment step is necessary, often require...
ORGANISM(S): Oryctolagus cuniculus (Rabbit) 
2025-02-19 | PXD060724 | Pride
Antibody Cross-linking Mass spectrometry Molecular docking Paratope mapping Sumo 
UnknownDNA-protein cross-linking by 1,2,3,4-diepoxybutane.
Not available
S-EPMC2956319 | biostudies-literature
TranscriptomicsResponse of Staphylococcus aureus to subinhibitory concentrations of a sequence-selective, DNA minor groove cross-linking pyrrolobenzodiazepine dimer.
Objectives ELB-21 is a pyrrolo[2,1-c][1,4]benzodiazepine dimer with potent antistaphylococcal activity; it binds covalently to guanine residues on opposing strands of duplex DNA, interfering with regulatory proteins and transcription elongation in a sequence-selective manner. Transcriptional and pro...
ORGANISM(S): Staphylococcus aureus 
2009-09-18 | E-BUGS-79 | biostudies-arrayexpress
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