Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteinase K digestion of Annexin A11 fibrils

ABSTRACT: Human Annexin A11 (Uniprot accession no. P50995) head domain (residues 2-196) was recombinantly expressed, purified, fibrilized, and digested by proteinase K. Products were analyzed by LC/MS/MS.

INSTRUMENT(S): LTQ XL

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Lalit Deshmukh

PROVIDER: MSV000091107 | MassIVE | Fri Jan 20 16:56:00 GMT 2023

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Publications

ALS Variants of Annexin A11's Proline-Rich Domain Impair Its S100A6-Mediated Fibril Dissolution.

Shihora Aman A Elias Ruben D RD Hammond John A JA Ghirlando Rodolfo R Deshmukh Lalit L

ACS chemical neuroscience 20230711 15

Mutations in the proline-rich domain (PRD) of annexin A11 are linked to amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease, and generate abundant neuronal A11 inclusions by an unknown mechanism. Here, we demonstrate that recombinant A11-PRD and its ALS-associated variants form liquidlike condensates that transform into β-sheet-rich amyloid fibrils. Surprisingly, these fibrils dissolved in the presence of S100A6, an A11 binding partner overexpressed in ALS. The ALS variants of ...[more]

PMID: 37433222

Similar Datasets

In vitro tyrosine phosphorylation of ALIX

Project description:Human ALIX (Uniprot accession no. Q8WUM4) Bro1 and proline-rich domains were recombinantly expressed, purified, and phosphorylated in vitro by tyrosine kinase Src. Phosphorylation products were analyzed by mass spectrometry.

| MSV000088057 | MassIVE

Broad-specificity enzymes enable fast and cost-effective digestion for in-depth proteomics and precise label free quantitation

Project description:We have devised fast and robust SP3- and STRAP-based protocols for the broad-specificity proteases subtilisin, proteinase K, and thermolysin. All three enzymes are remarkably fast, producing near-complete digests in 1-5 min, and cost 200-1000x less than proteomics-grade trypsin. Using FragPipe resolved a major challenge by drastically reducing the duration of the required "unspecific" searches. In-depth analyses of proteinase K, subtilisin, thermolysin Jurkat digests identified 7374, 8178, 8752 unique proteins with average sequence coverages of 21%, 29%, 37%, including tens of thousands of amino acids not reported in the PeptideAtlas database spanning over 2400 experiments. While we could not identify distinct cleavage patterns, machine learning could distinguish true protease products from random cleavages, potentially enabling the prediction of cleavage products. 2D runs: 20 high-pH RP-HPLC fractions analyzed by DDA LC-MS/MS mode on a timsTOF Pro2, with Evosep; 15 SPD method, 200 ng peptide loaded on-column. STRAP vs SP3: each digest prepared in triplicate with SP3 and STRAP, respectiveyl-- analyzed by DDA nano-LC-MS/MS on an Orbitrap Exploris 480, 87 min gradient, 750 ng peptide loaded on-column.

2023-11-29 | MSV000093532 | MassIVE

Comparative transcriptomic analysis of Arabidopsis plants treated with short oligogalacturonides and mock

Project description:The importance of oligogalacturonides for plant defence and growth has been described extensively in litterature. However, much of previous global transcriptome analyses for plants treated with oligogalacturonides have focused on long (>10 galacturonosyl residues) oligogalacturonides. This study focuses on the transcriptomic impact that short (<10 galacturonosyl residues) oligogalacturonides have on plant transcriptomes and overall biology. Arabidopsis seedling were grown on liquid 1/2 MS medium in 12-well culture plates in vitro for 12 days. 12 seedlings were cultured per well, and three wells were combined per biological replicate. The seedling plants were treated either with 1/2 MS medium (mock), 1/2 MS with trimeric oligogalacturonides (trimers) and a mixture of 1/2 MS and oligogalacturonides (short OG-mix) containing 2-9 residues for 3 hours. RNA was extracted from the seedlings, three biological replicates per treatment, and sequenced using the SOLiD 5500XL platform.

2015-06-05 | E-GEOD-69538 | biostudies-arrayexpress

Refined read-out: hUHRF1‑tandem Tudor prefers histone H3 containing K9me2/3 and K4me1

Project description:Histone post-translational modifications (PTMs) are an important part of chromatin signaling mechanisms. Among them, histone H3 has a prominent role, and combinations of multiple PTMs are common. We investigated binding of multiple marks on the same H3 histone by the human UHRF1-TTD (Uniprot Q96T88, residues 126-280), known to bind H3K9me2/3 histones. We verified binding to H3K9me2/3 and demonstrated stronger binding to synthetic H3 peptides containing K4me1 and K9me2/3 as well as native HepG2 mononucleosomes bearing both H3K9me2/3 and H3K4me1.

2023-08-11 | GSE213741 | GEO

SWATH-MS and MRM: Quantification of Ras-related proteins in HIV-1 Infected and Methamphetamine-Exposed Human Monocyte-Derived Macrophages (hMDM)

Project description:Macrophages are involved in the immunological response to inflammatory and infectious agents, including Human Immunodeficiency Virus type 1 (HIV-1) infection. They are a primary targets of the virus and facilitate transfer across the blood brain barrier into the central nervous system. In the presence of toxic substances, such as methamphetamine (Meth), the protective functions of macrophages are further impaired. It has been shown that both HIV-1 infection and Meth induce changes in the proteome of macrophages. Therefore, in the presented study we employed a nano-liquid chromatography (nanoLC)-SWATH mass spectrometry (MS) approach to detect and quantify changes on proteome level that are induced in human monocyte derived macrophages (hMDM) that were exposed to Meth before or after HIV infection. As we focused in this study on actin and a cluster of Ras-related proteins (Rab), we selected the following proteins: actin (UniProt P60709), Ras-related protein Rab-1A (UniProt P62820), Ras-related protein Rab-2A (UniProt P61019), Ras-related protein Rab-4B (UniProt P61018), Ras-related protein Rab-7A (UniProt P51149), Ras-related protein Rab-9A (UniProt P51151), Ras-related protein Rab-11 (UniProt P62491), Ras-related protein Rab-14 (UniProt P61106), Ras-related protein Rab-22A (UniProt Q9UL26), Ras-related protein Rab-24 (UniProt Q969Q5), Ras-related protein Rab-37 (UniProt Q96AX2) for further validation, which we performed using liquid chromatography-multiple reaction monitoring (LC-MRM) MS technique. The MRM data from this study, along with LC-MRM analysis and data processing parameters, were separately described and deposited in PASSEL repository with accession number PASS01591.

2022-05-19 | PXD023291 | Pride

Quantitative phosphoproteomics of Phytophthora infestans life stages

Project description:The oomycete Phytophthora infestans is the causal agent of late blight in potato and tomato. Since the underlying processes that govern pathogenicity and development in P. infestans are largely unknown, we have performed a large-scale phosphoproteomics study of six different P. infestans life stages. We have obtained quantitative data for 2922 phosphopeptides and compared their abundance in different life stages. The samples were analysed on an LTQ Orbitrap XL ETD, operated in data dependent mode to automatically perform Orbitrap-MS and LTQ-MS/MS analysis. The raw data from the Orbitrap was converted to .mgf files using ProteoWizard. The Proteios software environment was used to search the mgf files with Mascot version 2.3.01 against a database consisting of all P. infestans proteins in UniProt as of 2010-04-22, concatenated with an equal size decoy database (random protein sequences with conserved protein length and amino acid distribution, in total 36,512 target and decoy protein entries). Search tolerances were set to 7 ppm for MS and 0.5 Da for MS/MS. One missed cleavage was allowed. Carbamidomethylation of cysteine residues was selected as a fixed modification and oxidation of methionine residues and phosphorylation of serine, threonine and tyrosine residues were selected as variable modifications. Search results were exported from Mascot as XML, including query level results, with a modification to the export script to include protein accession numbers also for the query (spectrum) level results. All search results, including the top ranked peptide for each spectrum, were imported to Proteios, where q values were calculated using the target-decoy method.

2014-03-27 | PXD000433 | Pride

A Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT

Project description:Nucleosome assembly in vivo requires assembly factors, such as histone chaperones, to bind to histones and mediate their deposition onto DNA. In yeast, the essential histone chaperone FACT (FAcilitates Chromatin Transcription) functions in nucleosome assembly and H2A-H2B deposition during transcription elongation and DNA replication. Recent studies have identified candidate histone residues that mediate FACT binding to histones, but it is not known which histone residues are important for FACT to deposit histones onto DNA during nucleosome assembly. In this study, we report that the histone H2B repression (HBR) domain within the H2B N-terminal tail is important for histone deposition by FACT. Deletion of the HBR domain causes significant defects in histone occupancy in the yeast genome, particularly at HBR-repressed genes, and a pronounced increase in H2A-H2B dimers that remain bound to FACT in vivo. Moreover, the HBR domain is required for purified FACT to efficiently assemble recombinant nucleosomes in vitro. We propose that the interaction between the highly basic HBR domain and DNA plays an important role in stabilizing the nascent nucleosome during the process of histone H2A-H2B deposition by FACT. 6 samples, 2 inputs and 4 ChIP samples for histone H2B (2 for wild-type and 2 for an H2B â30-37 mutant)

2016-08-10 | E-GEOD-80831 | biostudies-arrayexpress

Identification of targets of the protein disulfide reductase thioredoxin

Project description:Identification of targets of the protein disulfide reductase thioredoxin using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and thiol specific differential labeling with isotope-coded affinity tags (ICAT). Reduction of specific target disulfides is quantified by measuring ratios of cysteine residues labeled with the heavy (13C) and light (12C) ICAT reagents in peptides derived from tryptic digests of Trx-treated and non-treated samples. Keywords: protein, LC-MS/MS, ICAT

2008-11-20 | GSE11650 | GEO

A Basic Domain in the Histone H2B N-terminal Tail is Important for Nucleosome Assembly by FACT

2016-08-10 | GSE80831 | GEO

THP1 cell response to Mycobacterium tuberculosis infection and Mtb PAMP stimulation

Project description:To compare gene expression changes induced by infection with Mycobacterium tuberculosis (Mtb) with changes induced by purified Mtb products, we infected THP-1 cells with Mtb strain H37Rv or treated with purified Mtb products, then performed RNAseq.

2023-05-15 | GSE227851 | GEO

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