Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of Bzd Subunits / Aromatoleum sp. CIB

ABSTRACT: Identification of enriched protein subunits after SDS-PAGE separation and tryptic digest by LC-MSE

INSTRUMENT(S):

ORGANISM(S): Azoarcus Sp. Cib Escherichia Coli

SUBMITTER: Jonathan Fuchs

LAB HEAD: Prof. Dr. Matthias Boll

PROVIDER: PXD053203 | Pride | 2025-05-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	BzdN_20220610_LA_31.raw.zip	Raw
	BzdN_20220610_LA_31_IA_Log.txt	Txt
	BzdN_20220610_LA_31_IA_final_fragment.csv	Csv
	BzdN_20220610_LA_31_IA_final_peptide.csv	Csv
	BzdN_20220610_LA_31_IA_final_protein.csv	Csv

Items per page:

1 - 5 of 14

Publications

Enzymatic Birch reduction via hydrogen atom transfer at [4Fe-4S]-OH<sub>2</sub> and [8Fe-9S] clusters.

Fuchs Jonathan J Fernández-Arévalo Unai U Demmer Ulrike U Díaz Eduardo E Ullmann G Matthias GM Pierik Antonio J AJ Ermler Ulrich U Boll Matthias M

Nature communications 20250404 1

The alkali metal- and ammonia-dependent Birch reduction is the classical synthetic method for achieving dihydro additions to arenes, typically yielding 1,4-cyclodienes. A mild biological alternative to this process are 1,5-dienoyl-coenzyme A (CoA)-forming class I and II benzoyl-CoA reductases (BCRs), widely abundant key enzymes in the biodegradation of aromatic compounds at anoxic environments. To obtain a comprehensive mechanistic understanding of class I BCR catalysis, we produced the active s ...[more]

PMID: 40185728

Similar Datasets

Exoproteome analysis of Staphylococcus aureus clinical isolates belonging to different clonal complexes (C22, CC8 and CC398)

Project description:Studies on S. aureus sub-populations revealed that genomes are well conserved between isolates from the same lineages despite geographic, temporal and selective diversity. However, variation of hundreds of genes can occur between isolates from different lineages and these genes could be involved in interaction with host components. In this study, we aimed to investigate the diversity of secreted virulence factors in human and zoonotic S. aureus isolates from different clonal complexes. We focused on the S. aureus clonal complexes (CC) 8 and CC22 as dominant human lineages, and CC398 as dominant livestock-associated MRSA (LA-MRSA) which is disseminating rapidly. To study the diversity of secreted virulence factors, we compared their extracellular proteomes using label-free LC-MS/MS analysis. A common protein database was created based on DNA sequencing data and PAN genome IDs.

2018-09-11 | PXD008797 | Pride

Molecular and functional landscape of malignant serous effusions for precision oncology [MSE_baseline]

Project description:Personalized treatment for patients with advanced solid tumors critically depends on the deep characterization of tumor cells. These patients frequently develop malignant serous effusions (MSE). The value of MSE-based tumor cell characterization for guiding precision oncology is, however, currently unclear. Here, we present a comprehensive characterization of a pan-cancer cohort of 150 MSE samples at the cellular, molecular, and functional level. Our integrative analysis reveals dynamic cellular heterogeneity in MSE, and uncovers links between tumor driver mutations and ex vivo growth patterns. Strong concordance between genomic and transcriptional profiles of MSE and their corresponding solid tumors validates their use as a model system for solid tumor biology. We link baseline gene expression patterns to global ex vivo drug sensitivity, and demonstrate that drug-induced transcriptional changes in MSE are highly indicative of compound mode of action. Two case studies exemplify the utility of our approach in investigating acquired resistance to targeted therapy and identifying treatment options for relapsed solid tumors. In summary, our study provides a functional multi-omics view on a pan-cancer MSE cohort and underlines the utility of MSE-based precision oncology.

2024-08-26 | GSE240952 | GEO

Molecular and functional landscape of malignant serous effusions for precision oncology [MSE_drug_treated]

2024-08-26 | GSE240951 | GEO

Adaptive Laboratory Evolution of E. coli towards usage of fluoroindole

Project description:Although fluorine is abundant in the earth’s crust, it is scarcely found in biomolecules. Adaptive laboratory evolution (ALE) experiments were conducted to introduce organofluorine into living microorganisms. By cultivating Escherichia coli with fluorinated indole analogs, microbial cells evolved that relinquished their dependence on indole and are instead capable of utilizing either 6-fluoroindole (6Fi) or 7-fluoroindole (7Fi) for growth (TrpS-catalyzed in-situ conversion of fluoroindole into fluorotryptophan (FTrp) and TrpRS-catalyzed incorporation of FTrp in context of protein biosynthesis). Consistent and complete adaptation of microbial populations was achieved and the quantitative proteome-wide replacement of Trp by either 6FTrp or 7FTrp was confirmed by nano-LC-MSMS. The dataset comprises the ancestral strain TUB00, two positive controls W-TUB165 and Ind-TUB165 (adapted to grow on tryptophan and indole), three 6Fi adapted lineages 6TUB128-OC, 6TUB165-MB4, 6TUB165-MB3 and two 7Fi adapted lineages 7TUB165-OC and 7TUB165-MB.

2024-01-08 | PXD048225 | Pride

A maple syrup extract alleviates liver injury in type 2 diabetic model mice

Project description:A recent study showed that 54% of type 2 diabetes (T2D) patients have nonalcoholic fatty liver disease, which is a risk factor for aggravation diabetic symptoms. Previous studies suggested components in maple syrup alleviated liver injury and found polyphenols as food components to improve the symptoms and complications of diabetes. Therefore, we hypothesized that a polyphenol fraction in maple syrup improves the symptoms and complications of diabetes. To address the hypothesis, we investigated the effects of a polyphenol-rich maple syrup extract (MSE) on a T2D model mice. KK-Ay mice were fed a normal or 0.1% MSE-supplemented diet for 43 days. The results showed that the levels of serum alanine aminotransferase and aspartate aminotransferase were significantly reduced in mice that ingested MSE. Hepatic genes related to lipogenesis and lipolysis were down- and upregulated, respectively, in mice that ingested MSE. These results suggest that MSE intake alleviates liver injury and suppresses lipid accumulation in the livers of T2D mice.

2020-01-13 | GSE134185 | GEO

Characterization of the diphthamide modification of eEF2 in Arabidopsis thaliana

Project description:Diphthamide, a post-translationally modified histidine residue of eukaryotic TRANSLATION ELONGATION FACTOR2 (eEF2), is the human host cell-sensitizing target of diphtheria toxin. Diphthamide biosynthesis depends on the 4Fe-4S-cluster protein Dph1 catalyzing the first committed step, as well as Dph2 to Dph7, in yeast and mammals. Here we show that diphthamide modification of eEF2 is conserved in Arabidopsis thaliana and requires AtDPH1. Ribosomal -1 frameshifting-error rates are increased in Arabidopsis dph1 mutants, similar to yeast and mice. Compared to the wild type, shorter roots and smaller rosettes of dph1 mutants result from fewer formed cells. TARGET OF RAPAMYCIN (TOR) kinase activity is attenuated, and autophagy is activated, in dph1 mutants. Under abiotic stress diphthamide-unmodified eEF2 accumulates in wild-type seedlings, most strongly upon heavy metal excess, which is conserved in human cells. In summary, our results suggest that diphthamide contributes to the functionality of the translational machinery monitored by plants to regulate growth.

2022-08-11 | PXD034873 | Pride

Chemical Proteomics Partners identification of Cycloamphilectene

Project description:The identification of the cycloamphilectene cellular interactome has been performed, through chemical proteomics, to unambiguously define its mechanism of action and thus to understand its pharmacological effect. To achieve this goal, a small bioactive molecule (cycloamphilectene) linked to a matrix through a spacer arm “fishes out” its specific interactors from a cell lysate or a tissue extract. Once eluted, cellular partners are separated by SDS-PAGE and identified by high resolution MS and bioinformatics analysis . MS and MS/MS data were acquired using a Q-TOF Premier mass spectrometer (Waters Corp., Micromass, Manchester, United Kingdom). The five most intense ions were automatically chosen by the MassLynx (4.1) software and fragmented. After mass spectrometric measurements, data were automatically processed by ProteinLynx Global Server software to generate peak lists for protein identifications. Database searches were carried out with MASCOT server. The SwissProt human database (release 2010_11 of 02 Nov 10, 522019 sequences, 184241123 residues) was searched, allowing 2 missed cleavages, carbamidomethyl (C) as fixed modification o and oxidation (M) and phosphorylation (ST) as variable modifications. The peptide tolerance was set to 80 ppm and the MS/MS tolerance to 0.8 Da. The Raw data reported herein contains 4 different chemical proteomics experiments carried out to identify cycloamphilectene cellular partner.

2018-11-26 | PXD000106 | Pride

Proteome profile of peripheral myelin in healthy mice and in a neuropathy model

Project description:Using the sciatic nerve as a model, we biochemically purified peripheral nervous system (PNS) myelin and systematically assessed its proteome by dedicated, partly ion mobility-enhanced data-independent acquisition (DIA) workflows with alternating low and elevated energy (MSE) modes. Specifically, we used MSE for correct quantification of highest-abundance proteins, UDMSE for deep quantitative proteome coverage, and dynamic range enhancement (DRE)-UDMSE for comparative analysis, the latter mode providing a good compromise between dynamic range, identification rate and instrument run time for routine differential myelin proteome profiling. We found that integration of the proteome data with the total nerve transcriptome is suited to determine comprehensive molecular profiles in healthy nerves and in myelin-related disorders. This work provides the most comprehensive proteome resource thus far to approach development, function and pathology of peripheral myelin, and a straightforward, accurate and sensitive workflow to address myelin diversity in health and disease.

2020-02-20 | PXD015960 | Pride

Proteome profile of myelin in the zebrafish brain

Project description:While the myelin proteome is well characterized in mice, much less is known about the protein composition of myelin in non-mammalian species such as zebrafish (Danio rerio), despite its increasing popularity as model organism for myelin biology. Here, we assess the proteome of myelin biochemically purified from the brains of adult zebrafish by complementary proteomic approaches for deep qualitative and quantitative coverage. A data-independent acquisition (DIA) workflow with alternating low and elevated energy (MSE) provided the high dynamic range required for correct quantification of highest-abundance proteins. According to this analysis, the predominant Ig-CAM myelin protein zero (MPZ/P0), myelin basic protein (MBP) and the short chain dehydrogenase 36K constitute 12%, 8% and 6% of the total myelin protein, respectively. Combined with data from an ion mobility-enhanced version of the MSE mode (referred to as UDMSE) and from 1D-gel-based proteomic approaches, we provide the most comprehensive proteome resource of zebrafish myelin so far, correlate it with previously established mRNA-abundance profiles, and demonstrate both similarities and heterogeneity of myelin composition between teleost fish and rodents.

2021-03-22 | PXD023037 | Pride

Enhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator Algorithm

Project description:E.Coli Full Tryptic Digest CID Triplicate Analysis

2013-06-27 | PRD000544 | Pride