Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dentification of Cross-linking partners of BpA modified p37 and p97 by photo cross-linking MS

ABSTRACT: we wanted to see where and how the protein p37 interacts with its partner proteins p97, PPI,Sds22 and I3. To this end p37 derivatives with genetically encoded crosslinking amino acid (p-benzoyl-L-phenylalanine) were generated. After incubation with the partner proteins, photocross-linking and tryptic digest the resulting cross-linked peptides were analysed by mass spectrometry.

INSTRUMENT(S): Orbitrap Fusion Lumos, LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Farnusch Kaschani

LAB HEAD: Farnusch Kaschani

PROVIDER: PXD021182 | Pride | 2020-10-19

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ACE_0342-02_JB02.mzML	Mzml
	ACE_0342-02_JB02.raw	Raw
	ACE_0475_JB02.mzML	Mzml
	ACE_0475_JB02.raw	Raw
	ACE_0504_JB02.fasta	Fasta

Items per page:

1 - 5 of 10

Similar Datasets

Identification of Cross-linking partners of BpA modified p97 by photo cross-linking MS

Project description:We wanted to see where and how the protein p97 interacts with its partner proteins p37, PPI,Sds22 and I3. To this end a p97 derivative with genetically encoded crosslinking amino acid (p-benzoyl-L-phenylalanine) was generated. After incubation with the partner proteins, photocross-linking and tryptic digest the resulting cross-linked peptides were analysed by mass spectrometry.

2023-07-10 | PXD039939 | Pride

In vivo cross-linking supports a head-to-tail mechanism for regulation of the plant plasma membrane P-type H+-ATPase

Project description:In higher plants, a P-type proton pumping ATPase generates the proton-motive force essential for the function of all other transporters and for proper growth and development. X-ray crystallographic studies of the plant plasma membrane proton pump have provided information on amino acids involved in ATP catalysis but provided no information on the structure of the C-terminal regulatory domain. Despite progress in elucidating enzymes involved in the signaling pathways that activate or inhibit this pump, the site of interaction of the C-terminal regulatory domain with the catalytic domains remains a mystery. Genetic studies have pointed to amino acids in various parts of the protein that may be involved but direct chemical evidence for which ones are specifically interacting with the C-terminus is lacking. In this study we used in vivo cross-linking experiments with a photo-reactive unnatural amino acid, p-benzoyl-phenylalanine (BPA) and tandem mass spectrometry, to obtain direct evidence that the carboxyl terminal regulatory domain directly interacts with amino acids located within the N-terminal actuator domain. Our observations are consistent with a mechanism in which intermolecular, rather than intramolecular, interactions are involved. Our model invokes a ‘head-to-tail’ organization of ATPase monomers in which the carboxyl terminal domain of one ATPase molecule interacts with the actuator domain of another ATPase molecule. This model serves to explain why cross-linked peptides are found only in dimers and trimers, and is consistent with prior studies suggesting that within the membrane, the protein can be organized as homopolymers, including dimers, trimers and hexamers.

2018-09-24 | PXD010892 | Pride

An UBX domain in UBXD1 organizes Ub binding at the C-terminus of the VCP/p97 AAA-ATPase

Project description:Identification of crosslinked peptides between UBXD1 and HR23b using different cross-linking approaches (chemical cross-linking with DSSO and photo crosslinking with incorporated BPA).

2023-05-25 | PXD040984 | Pride

An UBX domain in UBXD1 organizes Ub binding at the C-terminus of the VCP/p97 AAA-ATPase

Project description:Identification of crosslinked peptides between UBXD1, Ubiquitin and p97 using different cross-linking approaches (chemical cross-linking with DSSO, photo crosslinking with incorporated BPA or photo-Met)

2023-05-25 | PXD039606 | Pride

Early Scanning of Nascent Polypeptides inside the Ribosomal Tunnel by NAC

Project description:In this study, NAC was UV-crosslinked using the photo-crosslinking amino acid p-benzoyl-L-phenylalanine (pBPA) in order to determine specific interaction sites of the alphaNAC N-terminus in the native protein structure. Furthermore, quantitative chemical crosslinking coupled to mass spectrometry (q-XL-MS) was used to compare crosslink abundances of a NAC mutant versus wild type NAC in order to determine the influence of the mutated motive on the structural dynamics of NAC.

2019-07-25 | PXD011995 | Pride

Interaction of Hsp70 Ssb1 and atypical Hsp70 Ssz1

Project description:Our goal was to better understand the interaction between the Hsp70 Ssb1 and the atypical Hsp70 Ssz1, which we had uncovered by in vivo site-specific Bpa crosslinking. Ssz1 having Bpa incorporated was purified and incubated with purified Ssb1 and the J-domain protein Zuo1 during activation of photo cross-linking. After protein gel electrophoresis and protease digestion of excised bands, the resulting cross-linked peptides were analyzed by mass spectrometry and identified by StavroX.

2021-08-26 | PXD024065 | Pride

PTPN21 and Hook3 relieve KIF1C autoinhibition and activate intracellular transport

Project description:The kinesin-3 KIF1C is a fast organelle transporter implicated in the transport of dense core vesicles in neurons and the delivery of integrins to cell adhesions. Here we report the mechanisms of autoinhibition and release that control the activity of KIF1C. We show that the microtubule binding surface of KIF1C motor domain interacts with its stalk and that these autoinhibitory interactions are released upon binding of protein tyrosine phosphatase PTPN21. The FERM domain of PTPN21 stimulates dense core vesicle transport in primary hippocampal neurons and rescues integrin trafficking in KIF1C-depleted cells. In vitro, human full-length KIF1C is a processive, plus-end directed motor. Its landing rate onto microtubules increases in the presence of either PTPN21 FERM domain or the cargo adapter Hook3 that binds the same region of KIF1C tail. This autoinhibition release mechanism allows cargo-activated transport and might enable motors to participate in bidirectional cargo transport without undertaking a tug-of-war.

2019-06-24 | PXD013939 | Pride

Identification of HJURP binding determinants on the Mis18 complex using photo-cross-linking and mass spectrometry

Project description:In the early G1 phase of the cell cycle, human HJURP is recruited to centromeres by the Mis18 complex, which consists of Mis18α, Mis18β and M18BP1. This interaction of HJURP with the Mis18 complex is essential for CENP-A deposition and the preservation of centromere identity. To identify the binding site of HJURP on the Mis18 complex, we used the amber-codon suppression method to incorporate unnatural photo-cross-linking amino acids (Bpa, p-benzoyl-L-phenylalanine; AbK, 3’-azibutyl-N-carbamoyl-lysine) and performed UV-cross-linking and mass spectrometry (MS) experiments.

2019-08-01 | PXD013339 | Pride

Influence of cross-linker polarity on selectivity towards lysine side chains

Project description:Even though the amine reactive BS2G and DSG cross-linkers have the same length of spacer and are based on N-hydroxysuccinimidic group, our data showed that each of them formed preferentially different cross-links. We demonstrated that the choice of cross-linker can have a significant impact on the output data for structural characterization of biomolecules. Using equimolar mixtures of DSG with d6-BS2G, and BS2G with d6-DSG, we established that the polar BS2G preferentially bound to polar regions of modified molecule, whereas non-polar DSG bound to hydrophobic regions. This phenomenon established that the mixture of polar and non-polar cross-linkers acted as an efficient tool for the determination of distance constraints in proteins.

2020-02-28 | PXD017299 | Pride

DEAD-box ATPase Dbp2 mediates mRNA release after 3’-end formation - II

Project description:DEAD-box ATPases belong to an abundant class of proteins that are involved in virtually all aspects of RNA metabolism and are found in all kingdoms of life. When bound to a DEAD-box ATPase, the RNA substrate is forced into a kinked conformation that is incompatible with helical structures. Distortion of the RNA can result in unwinding of short RNA duplexes (helicase activity) or destabilize RNA-protein interactions, allowing DEAD-box ATPases to remodel mRNPs (RNPase activity). The RNPase activity makes DEAD-box ATPases suitable molecular building blocks for the implementation of checkpoints that confer directionality to the process of RNA biogenesis. Here, we provide data that characterizes the DEAD-box ATPase Dbp2 (SPBP8B7.16c) of the fission yeast Schizosaccharomyces pombe. Using calibrated RNAPII-ChIP-seq, we determined the transcription profiles of a conditional depletion strain of Dbp2 and the corresponding wild type. For this, we placed the endogenous dbp2 gene under the control of the P.nmt1 promoter, which is repressed in the presence of thiamine. Cells were crosslinked at the beginning (t0) or the end (t9) of a 9h shift to thiamine-containing YES medium. S. cerevisiae spike-in cells were added in a 1:5 OD600 ratio immediately before crosslinking.

2024-06-30 | E-MTAB-13714 | biostudies-arrayexpress

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