Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

AtLEGbeta / gamma protease specificity and putative substrate characterization by HUNTER

ABSTRACT: Arabidopsis thaliana Legumain (aka VPE) beta / gamma were characterized for their cleavage specificity and putative substrates were identified by the N-termini enrichment method HUNTER.

INSTRUMENT(S): impact II

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Leaf

SUBMITTER: Fatih Demir

LAB HEAD: Pitter Florian Huesgen

PROVIDER: PXD019276 | Pride | 2020-07-29

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Structural and functional studies of <i>Arabidopsis thaliana</i> legumain beta reveal isoform specific mechanisms of activation and substrate recognition.

Dall Elfriede E Zauner Florian B FB Soh Wai Tuck WT Demir Fatih F Dahms Sven O SO Cabrele Chiara C Huesgen Pitter F PF Brandstetter Hans H

The Journal of biological chemistry 20200721 37

The vacuolar cysteine protease legumain plays important functions in seed maturation and plant programmed cell death. Because of their dual protease and ligase activity, plant legumains have become of particular biotechnological interest, <i>e.g.</i> for the synthesis of cyclic peptides for drug design or for protein engineering. However, the molecular mechanisms behind their dual protease and ligase activities are still poorly understood, limiting their applications. Here, we present the crysta ...[more]

PMID: 32719006

Similar Datasets

Mouse kidney cisplatin TAILS - The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury

Project description:Profiling of proteolytic events mouse kidneys during cisplatin-induced kidney damage. Kidneys from vehicle-treated mice are compared to cisplatin-treated mice and cisplatin treatment in animals preconditioned by hypoxia or calory restriction regimes.

2018-10-29 | PXD007186 | Pride

Mouse mitochondrial CLPP substrate identification

Project description:Identification ofputative ClpXP substrates by combination of proteome analysis and TAILS N termini profiling from wt and ClpP-deficient mouse heart mitochondria, combined with substrate trapping using catalytically inactive ClpP expressed in MEF cell culture. This dataset provides the preTAILS proteomedata

2020-06-01 | PXD018194 | Pride

Absolute quantitation of proteins by two-point quantitation using dimethylated proteotypic peptides

Project description:Absolute targeted proteomics typically employs known amounts of synthetic stable isotopically labeled peptides which are mixed with the analyte and analysed by LC-MS. In order to obtain accurate data, we evaluated the use of two different stable isotopes of the same peptide as spike-in for absolute quantification. For this purpose, peptide labeling by reductive amination was applied, which is a mild reaction for dimethylation of amine groups with very high yield and very little side reactions. Furthermore, three different forms can be generated with e.g., light and heavy labels for spike-in peptides, and medium label for endogenous peptides. The addition of the dimethylated proteotypic peptide in two different versions allows to determine the accuracy of the quantification of endogenous peptides using the relative ratio of the intensities of the two internal standards. The method was studied with peptides of apolipoprotein A-I, apolipoprotein B-100, and leucine-rich alpha-2-glycoprotein without and with serum. In serum, the endogenous protein concentrations were accurately measured across four orders of magnitude by the two-point quantitation method. Less than 20% of coefficient of variation (CV) values and strong correlation with R2 of 0.99 across three analytical replicates was observed. The results showed that the accuracy to determine the amount of endogenous peptides can be validated using two references against each other, which cannot be obtained by one-point quantitation. Because of the significant lower costs than synthetic stable isotopically labeled peptides, this approach might be particularly interesting for the absolute quantitation of multiple proteins.

2018-11-27 | PXD007894 | Pride

D. magna CT448 protease specificity

Project description:Mass developments of toxin-producing cyanobacteria are frequently observed in freshwater ecosystems due to eutrophication and global warming. These mass developments can partly be attributed to cyanobacterial toxins, such as protease inhibitors (PIs), which inhibit digestive serine proteases of Daphnia, the major herbivore of phytoplankton and cyanobacteria. To date, mechanisms of this inhibition in the gut of the crustacean Daphnia magna are not known. Here, we characterize a single serine protease, chymotrypsin 448 (CT448), which is present in the gut of the crustacean D. magna.

2018-10-04 | PXD010978 | Pride

HUNTER N-termini profiling of Arabidopsis thaliana wt and vpe0 mutants

Project description:Comparison of protein termini in Arabidopsis thaliana vpe0 quadruple mutant and wildtype seedlings shortly after germination to identify differential processed proteins.

2019-09-03 | PXD012804 | Pride

HUNTER N-termini profiling of Arabidopsis thaliana leaves using different proteases

Project description:Comparison of protein N-termini in Arabidopsis thaliana leaves by the HUNTER method; the corresponding digestion was performed with legumain, GluC and trypsin.

2020-01-20 | PXD014697 | Pride

Gene expression profiling of primary human retinoblastoma

Project description:Background Retinoblastoma is a pediatric eye cancer associated with RB1 loss or MYCN amplification (RB1+/+MYCNA). There are controversies concerning the existence of molecular subtypes within RB1-/- retinoblastoma. To test whether these molecular subtypes exist, we performed molecular profiling. Methods Genome-wide mRNA expression profiling was performed on 76 primary human retinoblastomas. Expression profiling was complemented by genome-wide DNA profiling and clinical, histopathological, and ex vivo drug sensitivity data. Findings RNA and DNA profiling identified major variability between retinoblastomas. While gene expression differences between RB1+/+MYCNA and RB1-/- tumors seemed more dichotomous, differences within the RB1-/- tumors were gradual. Tumors with high expression of a photoreceptor gene signature were highly differentiated, smaller in volume and diagnosed at younger age compared to tumors with low photoreceptor signature expression. Tumors with lower photoreceptor expression showed increased expression of genes involved in M-phase and mRNA and ribosome synthesis and increased frequencies of somatic copy number alterations. Interpretation Molecular, clinical and histopathological differences between RB1-/- tumors are best explained by tumor progression, reflected by a gradual loss of differentiation and photoreceptor expression signature. Since copy number alterations were more frequent in tumors with less photoreceptorness, genomic alterations might be drivers of tumor progression. Fresh frozen material from 76 primary human retinoblastoma samples were profiled with Affymetrix human genome u133 plus 2.0 PM microarray

2015-07-01 | E-GEOD-59983 | biostudies-arrayexpress

Optimization of HUNTER N-termini profiling using rat brain proteome extracts

Project description:Optimization hydrophobic tagging reaction time (30 min to 2h) and evaluation of the HUNTER protocol performance with different amounts (25 ug to 400 ug) of purified rat brain proteome as starting material.

2019-09-03 | PXD012844 | Pride

Optimization of HUNTER N-termini profiling using Arabidopsis thaliana Col-8 wt leaf proteome extracts

Project description:Optimization hydrophobic tagging reagent (hexadecanal or undecanal), reaction time (30 min to 16h) and evaluation of the HUNTER protocol performance with different amounts (25 ug to 400 ug) of purified Arabidopsis thaliana Col-8 wt leaf proteome as starting material.

2019-09-03 | PXD012821 | Pride

Brown bear skeletal muscle quantitative LC-MSMS

Project description:Muscle atrophy is one of the main deleterious consequences of ageing and physical inactivity. Although basic knowledge regarding the underlying mechanisms of muscle atrophy is continuously growing, there are still no efficient therapeutic strategies for its prevention and treatment. Hibernating bears exhibit a strong and unique ability to preserve muscle mass in conditions where muscle atrophy is observed in humans. However, underlying mechanisms have not been understood yet. To fill this gap, the aim of this study was to characterize changes in the bear muscle proteome during hibernation versus the active period. Muscle biopsies were obtained from Ursus arctos bears.

2019-05-14 | PXD004908 | 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