Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mechanism of photo-induced conformational changes in the photoenzyme fatty acid photodecarboxylase (FAP) revealed by light footprinting ion mobility mass spectrometry

ABSTRACT: To characterize and identify the fragments of fatty acid photodecarboxylase and investigate the blue light activation site using top-down proteomics and analyse the stability of fatty acid photodecarboxylase using collision-induced unfolding method.

INSTRUMENT(S):

ORGANISM(S): Chlorella Sp. Pumcc 1.1.1

TISSUE(S): Photosynthetic Cell, Cell Culture

DISEASE(S): Lipid Metabolism Disorder

SUBMITTER: Liuwei Meng

LAB HEAD: Perdita barran

PROVIDER: PXD069254 | Pride | 2025-10-15

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Native_mass_cvfap.RAW	Raw
	Raw_data.xlsx	Xlsx
	TD_of_FAP_3914_blue.RAW	Raw
	TD_of_FAP_3914_dark.RAW	Raw
	TD_of_FAP_4175_dark.RAW	Raw

Items per page:

1 - 5 of 8

Similar Datasets

The structure and target identification of the tandem RRM of yeast Npl3 bound to RNA reveal a cooperative sequence-specific recognition and an RNA chaperone role in splicing

Project description:The conserved SR-like protein Npl3 promotes the splicing of diverse pre-mRNAs. However, the RNA sequence(s) recognized by the RNA Recognition Motifs (RRM1 & RRM2) of Npl3 during the splicing reaction remain elusive. Here, we developed a split-iCRAC approach in vivo to determine the consensus sequence bound to each RRM in yeast. High-resolution NMR structures show that RRM2 recognizes a 5´-GNGG-3´ motif leading to an unusual mille-feuille topology. In addition, our data indicate a non-specific interaction of the RS domain with RNA. These structures reveal how RRM1 preferentially interacts with a CC-dinucleotide upstream of this motif, and how the inter-RRM linker and the region C-terminal to RRM2 contributes to cooperative RNA-binding. Structure-guided studies show that Npl3 genetically interacts with U2 snRNP specific factors and we provide evidence that Npl3 melts U2 snRNA stem-loop I, a prerequisite for U2/U6 duplex formation within the catalytic centre of the Bact spliceosomal complex. Our findings provide a mechanistic role for Npl3 during spliceosome active site formation.

2022-12-01 | E-MTAB-11736 | biostudies-arrayexpress

Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability

Project description:The DNA-dependent protease SPRTN maintains genome stability by degrading toxic DNA-protein crosslinks (DPCs). To understand how SPRTN’s promiscuous protease activity is confined to cleavage of crosslinked proteins, we reconstitute the repair of DPCs including their modification with SUMO and ubiquitin chains in vitro. We discover that DPC ubiquitylation strongly activates SPRTN independently of SPRTN’s known ubiquitin-binding domains. Using protein structure prediction, MD simulations and NMR spectroscopy we reveal that ubiquitin binds to SPRTN’s protease domain, promoting an open, active conformation. Replacing key interfacial residues prevents ubiquitin-dependent activation of SPRTN, leading to genomic instability and cell cycle defects in cells expressing truncated SPRTN variants that cause premature aging and liver cancer in Ruijs-Aalfs syndrome patients. Collectively, our results reveal a novel ubiquitin-dependent regulatory principle in DNA repair that ensures SPRTN activity is deployed precisely when and where it is needed.

2025-07-24 | PXD063921 | Pride

Comprehensive Analysis of Tryptic Peptides Arising from Disulfide Linkages in NISTmAb

Project description:This work presents methods for identifying and then creating a mass spectral library for disulfide-linked peptides originating from the NISTmAb, a reference material of humanized IgG1k monoclonal antibody (RM 8671). Analyses involved both partially-reduced and non-reduced samples under neutral and weakly basic conditions, followed by nanoflow liquid chromatography tandem mass spectrometry (LC-MS/MS).

2021-02-08 | PXD023358 | Pride

Epitope mapping of an anti-plasmodium pfMSP119 antibody by Intact Transition Epitope Mapping - Targeted High-Energy Rupture of Extracted Epitopes

Project description:Rapid diagnostic tests are first line assays for diagnosing infectious diseases, such as malaria. To minimize false positive and false negative test results in population screening assays, high quality reagents and well characterized antigens and antibodies are needed. An important property of antigen - antibody binding is recognition specificity which best can be estimated by mapping an antibodys epitope. The MBP-pfMSP119 antigen was chosen as mutual target for population screening. Also, since an anti-pfMSP119 antibody is planned to function as positive control in screening assays, its binding characteristics to the antigen was investigated. Intact Transition Epitope Mapping - Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE) was carried out to map the epitope of a monoclonal anti-pfMSP119 antibody, i.e. the recognized area on the MBP-pfMSP119 antigen surface. The MBP-pfMSP119 fusion protein was cloned and expressed in E.coli which then was enriched by affinity purification on amylose resin. The enriched and purified MBP-pfMSP119 fusion protein was structurally and functionally characterized before and after high pressure-assisted tryptic digestion or after GluC digestion of the reduced and alkylated fusion protein.

2020-08-24 | PXD019717 | Pride

C4PR_LIV: The SARS-CoV-2 ORF3C protein interactome in Vero cells

Project description:The SARS-CoV-2 genome encodes a multitude of accessory proteins. Using comparative genomic approaches, an additional accessory protein, ORF3c, has been predicted to be encoded within the ORF3a sgmRNA. Expression of ORF3c during infection has been confirmed independently by ribosome profiling. Despite ORF3c also being present in the 2002-2003 SARS-CoV, its function has remained unexplored. Here we show that ORF3c localises only to mitochondria during infection, where it inhibits innate immunity by restricting IFN-β production, but not NF-κB activation or JAK-STAT signalling downstream of type I IFN stimulation. We find that ORF3c acts after stimulation with cytoplasmic RNA helicases RIG-I or MDA5 or adaptor protein MAVS, but not after TRIF, TBK1 or phospho-IRF3 stimulation. ORF3c co-immunoprecipitates with the antiviral proteins MAVS and PGAM5 and induces MAVS cleavage by caspase-3. Unlike early lineage SARS-CoV-2 strains, delta variant strains lack intact ORF3c and do not cleave MAVS to the same extent. Together, these data provide insight into an uncharacterised mechanism of innate immune evasion by this important human pathogen. We suggest a model whereby ORF3c inhibits PGAM5-induced mitophagy and instead induces apoptosis, accompanied by caspase-3 activation. This repository contains data associated with the SARS-CoV-2 ORF3C SILAC AP-MS portions of this work.

2023-10-08 | PXD037765 | Pride

Evaluation of auto-antibody serum biomarkers for breast cancer screening

Project description:Using protein microarrays, derived from 642 His-tag proteins, we could distinguish sera from breast-nodule positive patients and healthy control individuals. Each Protein microarray was divided in to 4 sub-arrays. Each protein was spotted in duplicates in each sub-array. For evaluation 24 malignant, 16 benign breast cancer serum samples and 20 healthy control serum samples were used.

2011-12-21 | E-GEOD-34555 | biostudies-arrayexpress

ChAP-chip analysis of Hha binding regions in wild type and hnsstpA E. coli cells

Project description:The analysis of the distribution of Hha binding regions (His-Hha were expressed from pQE plasmid) on E. coli chromosome in E. coli W3110 (wild type) and hns/stpA mutant cells.

2013-04-02 | E-MEXP-3813 | biostudies-arrayexpress

ChIP-Seq of Myf5, MyoD, Snai1, HDAC1, HDAC2, E47 and empty vector controls in mouse skeletal myoblasts or myotubes

Project description:In skeletal myogenesis, the transcription factor MyoD activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snail-HDAC1/2 repressive complex bind and exclude MyoD from its targets. Notably, Snail binds E-box motifs that are G/C-rich in their central dinucleotides, and such sites are almost exclusively associated with genes expressed during differentiation. By contrast, Snail does not bind the A/T-rich E-boxes associated with MyoD targets in myoblasts. Thus, Snai1-HDAC1/2 prevents MyoD occupancy on differentiation-specific regulatory elements and the change from Snail- to MyoD-binding often results in enhancer switching during differentiation. Furthermore, we show that a regulatory network involving Myogenic Regulatory Factors (MRFs), Snail/2, miR-30a and miR-206 acts as a molecular switch that controls entry into myogenic differentiation. Together, these results reveal a regulatory paradigm that directs distinct gene expression programs in progenitors versus terminally differentiated cells. Genome wide binding sites of various transcription factors and chromatin modifiers in muscle cells

2012-07-04 | E-GEOD-24852 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run6)

Project description:Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish. Each loci has a control, where no Cas9/sgRNA were injected. This is amplicon sequencing with Illumina, after PCR amplification. Data was processed with ampliCan R package version 1.1.1.

2017-12-25 | E-MTAB-6310 | biostudies-arrayexpress

Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish (Run 9)

2017-12-15 | E-MTAB-6357 | biostudies-arrayexpress