Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of Tmem81 and Izumo1-associated proteins in zebrafish sperm by IP-MS/MS

ABSTRACT: Supporting MS data for paper (doi: ) by Deneke, Blaha et al (2024), titled “A conserved fertilization complex bridges sperm and egg in vertebrates”. Related to Figure 3B, Figure S4B-C.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Danio Rerio (zebrafish) (brachydanio Rerio)

TISSUE(S): Spermatozoon

SUBMITTER: Richard Imre

LAB HEAD: Andrea Pauli

PROVIDER: PXD054632 | Pride | 2024-10-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20230116_0126_E3_RSLC6_FAIMS_Deneke_Pauli_IMP_id1012_onbead_20per_8runs_Tmem81_WT_Zebrafish_Step2_inkl_wash_noNorm_additionalLimmaRatio_3reps.pdResult	Other
	20230116_E3_RSLC6_FAIMS_Deneke_Pauli_IMP_id1012_onbead_20per_Tmem81_1.raw	Raw
	20230126_E3_RSLC6_FAIMS_Deneke_Pauli_IMP_id1012_onbead_20per_TMEM81_2.raw	Raw
	20230126_E3_RSLC6_FAIMS_Deneke_Pauli_IMP_id1012_onbead_20per_TMEM81_3.raw	Raw
	20230126_E3_RSLC6_FAIMS_Deneke_Pauli_IMP_id1012_onbead_20per_TMEM81_4.raw	Raw

Items per page:

1 - 5 of 31

Similar Datasets

Enhanced Staphylococcus aureus vaccine protection by uncoupling of the alpha-toxin-ADAM10 interaction

Project description:Staphylococcus aureus is the leading global cause of bacterial infection-associated mortality, as vaccine development has been elusive. S. aureus alpha-toxin (Hla) is an essential virulence factor in disease. In children, the anti-Hla neutralizing antibody response is the only known correlate of human protective immunity. We demonstrate that the anti-Hla response is limited in the first 2 years of life, illuminating a vaccine-targetable population. We assessed whether Hla antigenic variants would enhance vaccine-mediated immunity in neonatal mice. We identified a variant (HlaH35L/R66C/E70C, HlaHRE) that elicits a nearly 100-fold increase in the neutralizing anti-Hla antibody response compared to other candidate Hla antigens. HlaHRE immunization durably protects against skin and soft tissue infection, enhancing the T follicular helper response and germinal center B cell response. Protective immunity was also conferred to offspring following maternal immunization with HlaHRE. These findings thereby define a novel path for universal S. aureus vaccine development at the maternal-infant interface.

2024-08-13 | PXD047859 | Pride

Elucidation of molecular functions of the protocadherin CDHR5 in intestinal epithelial cells

Project description:Intestinal epithelial cells are covered by the brush border, which consists of densely packed microvilli. The Intermicrovillar Adhesion Complex (IMAC) connects the microvilli and is required for proper organization of the brush border. The protocadherin CDHR5 is an important member of the IMAC, but it is unclear whether CDHR5 has mainly structural functions or is also involved in cellular signaling. This issue was resolved with a CDHR5 knockout mouse model. Intestinal epithelial cells were isolated from the small intestine of four wild-type and four CDHR5 knockout mice. Bulk RNA sequencing was performed to provide insight into the functions of CDHR5 in cellular signaling and gene regulation.

2023-04-13 | E-MTAB-12525 | biostudies-arrayexpress

A novel interaction site determines binding between AP180 and AP2 in clathrin mediated endocytosis

Project description:The early phases of clathrin mediated endocytosis are organized through a highly complex interaction network mediated by clathrin associated sorting proteins (CLASPs) that comprise long intrinsically disordered regions (IDRs). AP180 is a CLASP exclusively expressed in neurons and comprising a long IDR of around 600 residues, whose function remains partially elusive. Using NMR spectroscopy, we now describe a novel and strong interaction of AP180 with the major adaptor protein AP2 as well as its binding dynamics at atomic resolution. We find that the 70 residue long site determines the overall interaction between AP180 and AP2 in a dynamic equilibrium between its bound and unbound sate, while weaker binding sites contributing to the overall affinity at much high concentrations of AP2. Our data suggest that this novel interaction site might play a central role in recruitment of AP2 to the clathrin coated pit, whereas more transient and promiscuous interactions allow reshaping the interaction network until cargo uptake inside a coated vesicle.

2024-07-04 | PXD049300 | Pride

Fast and Accurate Disulfide Bridge Detection

Project description:Recombinant expression of proteins, propelled by therapeutic antibodies, has evolved into a multi-billion-dollar industry. Essential here is quality control assessment of critical attributes such as sequence fidelity, proper folding, and post-translational modifications (PTMs). Errors can lead to diminished bioactivity and, in the context of therapeutic proteins, an elevated risk for immunogenicity. Over the years, many techniques were developed and applied to validate proteins in a standardized and high-throughput fashion. One parameter has, however, so far been challenging to assess. Disulfide bridges, covalent bonds linking two Cysteine residues, assist in the correct folding and stability of proteins and thus have a major influence on their efficacy. Mass spectrometry promises to be an optimal technique to uncover them in a fast and accurate fashion. In this work, we present a unique combination of sample preparation, data acquisition and analysis facilitating the rapid and accurate assessment of disulfide bridges in purified proteins. Through microwave-assisted acid hydrolysis (MAAH), the proteins are digested rapidly and artifact-free into peptides, with a substantial degree of overlap over the sequence. The nonspecific nature of this procedure, however, introduces chemical background which is efficiently removed by integrating ion mobility preceding the mass spectrometric measurement. The nonspecific nature of the digestion step additionally necessitates new developments in data analysis, for which we extended the XlinkX node in Proteome Discoverer (XlinkX/PD) to efficiently process the data and ensure correctness through effective false discovery rate correction. The entire workflow can be completed within one hour, allowing for high-throughput, high-accuracy disulfide mapping

2024-04-08 | PXD046855 | Pride

Exosomes define a local and systemic communication network in healthy pancreas and in pancreatic ductal adenocarcinoma

Project description:Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease. Understanding its biology is crucial for finding effective therapies. Exosomes have been implicated in cancer, but their behavior in living systems remains poorly understood. We aimed to map the spatiotemporal distribution of exosomes from both healthy pancreas and PDAC to determine their biological significance. To achieve this, we developed a genetically engineered mouse model (ExoBow) to trace spontaneous exosomes communication. Within the PDAC microenvironment, cancer cells establish preferential communication routes with cancer associated fibroblasts and endothelial cells. The latter is a conserved event in the healthy pancreas. Inhibiting exosomes secretion in both scenarios significantly enhanced angiogenesis, underscoring the contribution of exosomes to the vascularization of the organ and to cancer. Inter-organ communication is significantly increased in PDAC, and the thymus is a sustained target in both contexts. PDAC cells also communicate with the kidneys and lungs, and the healthy pancreas with bone-marrow, brain, and intestines. In sum, we found that exosomes mediate an organized communication network in vivo that controls angiogenesis locally, both in the healthy pancreas and PDAC, and that targets the thymus also in both conditions, unravelling their potential role in central immune surveillance and anti-tumor immune response.

2023-12-12 | PXD047009 | Pride

Microglial REV-ERBα regulates inflammation and lipid droplet formation to drive tauopathy

Project description:Alzheimer’s disease is associated with disrupted circadian rhythms and clock gene expression. REV-ERBα (Nr1d1) is a circadian transcriptional repressor involved in the regulation of lipid metabolism and macrophage function. While global REV-ERBα deletion increases microglial activation and mitigates amyloid plaque formation, the cell-autonomous effects of microglial REV-ERBα deletion in healthy brain and in tauopathy are unexplored. Here, we show that microglial REV-ERBα deficient enhances inflammatory signaling, disrupts lipid metabolism, and causes lipid droplet (LD) accumulation specifically in male microglia. Inflammation and LD accumulation combine to inhibit microglial tau phagocytosis, which can be partially rescued by blockage of lipid droplet formation. Microglial REV-ERBα deletion exacerbates tau aggregation and neuroinflammation in P301S and AAV-P301L tauopathy models in male, but not female mice. These data demonstrate the importance of microglial lipid droplets in tau accumulation and reveal REV-ERBα as a therapeutically accessible, sex-dependent regulator of microglial inflammatory signaling, lipid metabolism, and tauopathy.

2023-08-09 | PXD043877 | Pride

Proteomic analysis of Monkeypox virus produced with experimentally infected Vero E6 cells.

Project description:Proteomic analysis of Monkeypox virus produced with experimentally infected Vero E6 cells using Data-Dependent Detection for a comprehensive coverage. The analysis was performed to prioritize the most responsive peptides amenable to mass spectrometry for the development of mass spectrometry-based detection methods.

2022-06-14 | PXD034494 | Pride

Plasmodium PEXEL protein processing

Project description:We identified the mature N terminials of several PEXEL protein reporters

2023-08-28 | PXD041451 | Pride

Comprehensive characterization of protein turnover by comparative SILAC labeling analysis in 3T3-L1

Project description:A balance between the synthesis and degradation of proteins is referred to as protein turnover, which is crucial for cellular protein homeostasis. Proteome-wide analysis of protein turnover in adipocytes, which are well-known for storing energy and also being associated with obesity and metabolic disorders, are yet to be carried out. Thus, with this objective in mind, our study employed comparative analysis of time-dependent SILAC labeling to evaluate the protein turnover of 3T3-L1 adipocytes ranging from 0 to 144 hours. We observed that relatively faster or slower protein half-lives in several protein groups were related to the PPAR signaling pathway, energy metabolism, extracellular matrix, ubiquitin-proteasome system, RNA splicing, Golgi complex, and lysosome. It is anticipated that these protein turnover profiles will provide greater clarity on the life cycle of adipocyte proteome and shed light on how they maintain protein homeostasis.

2023-04-18 | PXD037368 | Pride

FBXO22 as an E3 ligase supporting targeted protein degradation

Project description:Targeted protein degradation (TPD) represents a potent chemical biology paradigm that leverages the cellular degradation machinery to pharmacologically eliminate specific proteins of interest. Although multiple E3 ligases have been discovered to facilitate TPD, there exists a compelling requirement to diversify the pool of E3 ligases available for such applications. This expansion will broaden the scope of potential protein targets, accommodating those with varying subcellular localizations and expression patterns. In this study, we describe a CRISPR-based transcriptional activation screen focused on human E3 ligases, with the goal of identifying E3 ligases that can facilitate heterobifunctional compound-mediated target degradation. This approach allows us to address the limitations associated with investigating candidate degrader molecules in specific cell lines that either lack or have low levels of the desired E3 ligases. Through this approach, we identified a candidate proteolysis-targeting chimera (PROTAC), 22-SLF, that induces the degradation of FKBP12 when the FBXO22 gene transcription is activated. 22-SLF induced the degradation of endogenous FKBP12 in a FBXO22-dependent manner across multiple cancer cell lines. Subsequent mechanistic investigations revealed that 22-SLF interacts with C227 and/or C228 in FBXO22 to achieve the target degradation. Finally, we demonstrated the versatility of FBXO22-based PROTACs by effectively degrading another endogenous protein BRD4. This study uncovers FBXO22 as an E3 ligase capable of supporting ligand-induced protein degradation through electrophilic PROTACs. The platform we have developed can readily be applied to elucidate protein degradation pathways by identifying E3 ligases that facilitate either small molecule-induced or endogenous protein degradation.

2024-06-17 | PXD050270 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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