Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HeLa Cells Cross-Linked In Vivo versus as a Lysate

ABSTRACT: HeLa Cells were cross-linked with PIR either in vivo or as a lysate.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Erythrocyte, Cell Culture

SUBMITTER: Andrew Keller

LAB HEAD: James E. Bruce

PROVIDER: PXD013063 | Pride | 2019-07-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies.

Keller Andrew A Chavez Juan D JD Felt Kevin C KC Bruce James E JE

Journal of proteome research 20190717 8

Chemical cross-linking and mass spectrometry is of growing use for establishment of distance constraints on protein conformations and interactions. Whereas intraprotein cross-links can arise from proteins in isolation, interprotein cross-links reflect proximity of two interacting proteins in the sample. Prediction of expected ratios of the number of interprotein to intraprotein cross-links is hindered by lacking comprehensive knowledge on the interactome network and global occupancy levels for a ...[more]

PMID: 31267744

Similar Datasets

Mango-EcoliBDP - Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification

Project description:Dataset presented in Mango manuscript. Contains Ecoli cross-linked with BDP-NHP. Demonstration of whole proteome in-vivo cross-linking without an instrument capable of serial fragmentation.

2019-02-25 | PXD008975 | Pride

Novel roles for ribosomal histidine methylation revealed by proteomics and large-scale cross-linking mass spectrometry

Project description:The methylation of histidine residues is increasingly found to be both prevalent throughout the proteome, and also relevant to human disease. Hpm1p mono-methylates H243 in the ribosomal protein Rpl3 and represents the only histidine methyltransferase in Saccharomyces cerevisiae. Interestingly, the hpm1 deletion strain is highly pleiotropic, with many extra-ribosomal phenotypes including improved growth rates in alternative carbon sources. Here we aimed to understand how methylation of one histidine in one ribosomal protein could result in such diverse phenotypes by combining targeted mass spectrometry, growth assays, quantitative proteomics and cross-linking mass spectrometry. We confirmed the localisation and stoichiometry of the H243 site, found unreported sensitivities of Δhpm1 yeast to non-ribosomal stressors, and identified thirty differentially-abundant proteins upon hpm1 knockout, most with clear links to the coordination of sugar metabolism. We adapted the emerging technique of quantitative large scale cross-linking mass spectrometry for use in budding yeast, which resulted in the identification of 1,267 unique in vivo lysine-lysine pairs. By reproducibly monitoring over 350, we detected changes to membrane protein structure, chromatin compaction, and mitochondrial protein-protein interactions, independently of changes in protein abundance themselves. Taken together, these studies reveal a clear role for Hpm1p in the coordination of sugar metabolism, contextualise the deletion strain’s pleiotropy and illustrate how cross-linking mass spectrometry can generate mechanistic insights into complex cellular processes.

2022-08-12 | PXD027953 | Pride

In vivo protein interaction network analysis reveals porin-localized toxin inactivation in antibiotic resistant bacteria

Project description:The nosocomial pathogen Acinetobacter baumannii is a frequent cause of hospital acquired infections worldwide, and a challenge for treatment due to its evolved resistance to antibiotics, including carbapenems. To gain insight on A. baumannii antibiotic resistance mechanisms, we analyzed the protein interaction network of a multidrug-resistant A. baumannii clinical strain Ab5075. Using in vivo chemical cross-linking and mass spectrometry, we identified 2,068 non-redundant cross-linked peptide pairs containing 245 intra- and 398 inter- molecular interactions. Outer membrane proteins OmpA and YiaD, and carbapenemase Oxa-23 are hubs of the identified interaction network. Eighteen novel interactors of Oxa-23 were identified. Interactions of Oxa-23 with outer membrane porins OmpA and CarO were verified with co-immunoprecipitation analysis. Furthermore, transposon mutagenesis of oxa-23 or interactors of Oxa-23 demonstrated changes in meropenem or imipenem sensitivity in Ab5075. These results provide the first view of a porin-localized toxin inactivation model and increase understanding of bacterial antibiotic resistance mechanisms.

2016-12-22 | PXD004236 | Pride

Chemical cross-linking mass spectrometry for systems structural biology in mouse heart tissue.

Project description:While modern structural biology technologies have greatly expanded the size and type of protein complexes that can now be studied, the ability to derive large-scale structural information on proteins and complexes as they exist within tissues is practically non-existent. Many protein properties and their involvement in disease pathways are not replicated in cell culture and some complexes are not amenable to purification. Thus, the lack of tissue-level structural information limits molecular-level insight on diseases such as heart failure. Here we demonstrate the application of XL-MS to identify protein structural features and interactions in tissue samples, providing the first systems structural biology insight on protein complexes as they exist in the mouse heart.

2017-11-30 | PXD007673 | Pride

Deciphering the architecture and interactome of the spliceosomal C complex using in vivo chemical crosslinking

Project description:We used in vivo PIR-based crosslinking to assess specific regions of interaction and protein structure of the spliceosomal C complex components hnRNPA1, A2/B1, and C, and the RALY protein. Our results indicate the interaction of proteins of the C complex via domains regions and conserved motifs, posing as evidence of a coordinated action of known regulatory sequences of RBPs. Moreover, the crosslinking information helped to model some of the RBPs, being complementary to other structural methods available.

2022-10-13 | PXD023577 | Pride

Mitochondrial protein interaction landscape of SS-31

Project description:SS-31 is a synthetic peptide that improves mitochondrial function and is currently undergoing clinical trials for treatments of heart failure, primary mitochondrial myopathy, and other mitochondrial diseases. SS-31 interacts with cardiolipin which is abundant in the inner mitochondrial membrane, but mechanistic details of its pharmacological effects are unknown. Here we apply a chemical cross-linking/mass spectrometry method to provide direct evidence for specific interactions between SS-31 and mitochondrial proteins. The identified SS-31 interactors are functional components in ATP production and 2-oxoglutarate metabolism and signaling, consistent with improved mitochondrial function resultant from SS-31 treatment. These results offer a glimpse of the protein interaction landscape of SS-31 and provide mechanistic insight relevant to SS-31 mitochondrial therapy

2020-06-12 | PXD019484 | Pride

XLinkProphet ReACT XL-MS - Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks

Project description:Control Data Crosslink ReACT Results Searched with Comet

2019-07-12 | PXD009001 | Pride

XLinkProphet Shotgun XL-MS - 9 Standard Protein Shotgun, ReACT, and Mango Search Results

Project description:9 Standard Protein Shotgun, ReACT, and Mango Search Results

2019-03-13 | PXD008941 | Pride

XLinkProphet Mango XL-MS - 9 Standard Protein Shotgun, ReACT, and Mango Search Results

Project description:9 Standard Protein Shotgun, ReACT, and Mango Search Results

2019-03-13 | PXD008951 | Pride

Effects of a phosphomimetic mutation and nucleotide binding on the interaction of Hsp90a with co-chaperone Aha1 analyzed by chemical cross-linking with mass spectrometry

Project description:Complex conformational dynamics are essential for the chaperone function of heat shock protein 90 (Hsp90), including transient, ATP-biased N-domain dimerization establishing ATPase competence. Biochemical data demonstrate that the intrinsic, but weak, ATP hydrolyzing activity of Hsp90 is markedly enhanced by the co-chaperone Aha1. However, cellular concentration of Aha1 is substoichiometric relative to Hsp90. In cells, interaction of this important co-chaperone with Hsp90 is up-regulated by posttranslational modifications (PTMs), including phosphorylation of a highly conserved tyrosine (Y313 in Hsp90a). Here we use chemical cross-linking with mass spectrometry to explore the the impacts of a phosphomimetic mutation (Y313E) and binding of a non-hydrolyzable ATP analog (AMP-PNP),on the structure Hsp90a and its interaction with Aha1.

2019-06-17 | PXD013476 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data