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DSSO,Xlink,LC-MSMS - DSSO as linker, study of protein-protein interaction by LC-MSMS

ABSTRACT: DSSO as linker, study of protein-protein interaction by LC-MSMS

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Streptococcus Pyogenes Stab901

TISSUE(S): B Cell

DISEASE(S): Disease Free

SUBMITTER: Wenzhang Chen

LAB HEAD: Wenzhang Chen

PROVIDER: PXD012466 | Pride | 2020-04-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	mapeixiang-DSSO-3.msf	Msf
	mapeixiang-DSSO-3.mzML	Mzml
	mapeixiang-DSSO-3.mzid.gz	Mzid
	mapeixiang-DSSO-3.pride.mgf.gz	Mgf
	mapeixiang-DSSO-3.raw	Raw

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Publications

Allosteric inhibition of CRISPR-Cas9 by bacteriophage-derived peptides.

Cui Yan-Ru YR Wang Shao-Jie SJ Chen Jun J Li Jie J Chen Wenzhang W Wang Shuyue S Meng Bing B Zhu Wei W Zhang Zhuhong Z Yang Bei B Jiang Biao B Yang Guang G Ma Peixiang P Liu Jia J

Genome biology 20200226 1

<h4>Background</h4>CRISPR-Cas9 has been developed as a therapeutic agent for various infectious and genetic diseases. In many clinically relevant applications, constitutively active CRISPR-Cas9 is delivered into human cells without a temporal control system. Excessive and prolonged expression of CRISPR-Cas9 can lead to elevated off-target cleavage. The need for modulating CRISPR-Cas9 activity over time and dose has created the demand of developing CRISPR-Cas off switches. Protein and small molec ...[more]

PMID: 32102684

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DSSO,Xlink,LC-MSMS - DSSO as linker, study of protein-protein interaction by LC-MSMS

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Structural surfaceomics of Nomo-1 using DSSO cross-linker with MS3 approach

Project description:The project aimed to profile the cell surface proteins of Nomo-1 (AML cell line) using structural surfaceomics for identification of protein conformation-based cancer antigens thereby expanding the toolkit for cancer target discovery for immunotherapeutic targeting. To achieve the goal, cell surface capture (CSC) was integrated with cross-linking mass spectrometry (XL-MS). DSSO was used as a cross-linker to freeze the structural conformations of protein in three-dimensional space, followed by biotinylation of cell surface proteins to enable enrichment of cell surface proteins to allow focused XL-MS analysis of those enriched proteins. DSSO being MS cleavable cross-linker, allowed higher order MS3 approach for analysis.

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Systematic Discovery of Deeply Conserved Plant Protein Complexes, DSSO-crosslinked soy (Glycine max)

Project description:The associated files are mass spec data from size exclusion chromatography fractions that were subsequently crosslinked with DSSO. The starting material was a native extract prepared from soy sprouts (Glycine max). The mass spectrometry used a data-dependent MS2-MS3 method to identify crosslinks.

2019-10-28 | PXD013704 | Pride

A3G-Vif-CBFB-CRL5 Cross-Linking with DSSO

Project description:Here we use an optimization cross-linking mass spectrometry (XL-MS) pipeline for the structural characterization of a dynamic HIV-host protein complex. Using DSSO-based XL-MS analysis, residue-protein proximity restraints based on functional genetics, and integrative modeling, we define the structure of the HIV-1 Vif protein bound to restriction factor APOBEC3G (A3G), the Cullin-5 E3 ring ligase (CRL5), and the cellular transcription factor Core Binding Factor Beta (CBFβ). Using a XL-MS3 methodology, we identify 132 inter-linked peptides and integrate the data with atomic structures of the subunits and mutagenesis data, and computed an integrative structure model of the heptameric A3G-CRL5-Vif-CBFβ complex. The resulting model ensemble quantifies the dynamic heterogenity of the A3G C-terminal domain, as well as CUL5 flexibility, and defines the interface between Vif and A3G. Our model can be used to rationalize previous structural, mutatagenesis, and functional data not included in modeling. The experimental and computational approach described here is generally applicable to other challenging host-pathogen protein complexes and provides new visualization tools for characterizing cross-linking data.

2021-11-03 | PXD025391 | Pride

Systematic Discovery of Deeply Conserved Plant Protein Complexes, Chlamydomonas reinhardtii, DSSO crosslinking

Project description:The associated files are mass spec data from size exclusion chromatography fractions that were subsequently crosslinked with DSSO and digested with one of two enzymes, Trypsin or Chymotrypsin. The starting material was a native extract prepared from Chlamydomonas reinhardtii. The mass spectrometry used a data-dependent MS2-MS3 method to identify crosslinks.

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Mapping of nanobody binding sites on human LRRK2 by CX-MS

Project description:As part of an in-depth characterization of nanobodies directed against the human Leucine-rich repeat kinase 2 (LRRK2), epitopes of the nanobodies bound to LRRK2 were mapped by chemical crosslinking combined with mass spectrometry using the CID-cleavable crosslinker disuccinimidyl sulfoxide (DSSO).

2022-02-27 | PXD030063 | Pride

Orphan quality control shapes network dynamics and gene expression

Project description:All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how composition and dynamics of complex networks are established remains poorly understood. Here, we identify the E3 ligase UBR5 as a signaling hub that helps degrade unpaired subunits of multiple transcriptional regulators that act within a network centered on the c-MYC oncoprotein. Biochemical and structural analyses show that UBR5 binds motifs that only become available upon complex dissociation. By rapidly turning over orphan transcription factor subunits, UBR5 establishes dynamic interactions between transcriptional regulators that allow cells to effectively execute gene expression, while remaining receptive to environmental signals. We conclude that orphan quality control plays an essential role in establishing dynamic protein networks, which may explain the conserved need for protein degradation during transcription and offers unique opportunities to modulate gene expression in disease. Crosslinking mass spec experiment with UBR5 HECT domain STREP-SUMO-MCRS1 and DSSO.

2023-05-30 | PXD041519 | Pride

A2M-3K DSSO cross-linking to identify the bait region position

Project description:An A2M mutant, A2M-3K, with the bait region arginines replaced with lysines, was cross-linked with DSSO. Its monomeric gel band was analyzed by XL-MS to identify the bait region position within a subunit.

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