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Study of protein-protein interaction by LC-MSMS(28)

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

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell

DISEASE(S): Disease Free

SUBMITTER: Wenzhang Chen

LAB HEAD: Wenzhang Chen

PROVIDER: PXD019944 | Pride | 2021-09-09

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	checksum.txt	Txt
	mapx_xlink_13-4.mgf	Mgf
	mapx_xlink_13-4.msf	Msf
	mapx_xlink_13-4.mzML	Mzml
	mapx_xlink_13-4.mzid.gz	Mzid

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1 - 5 of 6

Publications

Avidity-Based Selection of Tissue-Specific CAR-T Cells from a Combinatorial Cellular Library of CARs.

Ma Peixiang P Ren Ping P Zhang Chuyue C Tang Jiaxing J Yu Zheng Z Zhu Xuekai X Fan Kun K Li Guanglei G Zhu Wei W Sang Wei W Min Chenyu C Chen Wenzhang W Huang Xingxu X Yang Guang G Lerner Richard A RA

Advanced science (Weinheim, Baden-Wurttemberg, Germany) 20210129 6

Using T-cell chimeric antigen receptors (CAR-T) to activate and redirect T cells to tumors expressing the cognate antigen represents a powerful approach in cancer therapy. However, normal tissues with low expression of tumor-associated antigens (TAAs) can be mistargeted, resulting in severe side effects. An approach using a collection of T cells expressing a diverse, 10<sup>6</sup>-member combinatorial cellular library of CARs, in which members can be specifically enriched based on avidity for c ...[more]

PMID: 33747727

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study of protein-protein interaction by LC-MSMS

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

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

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

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Optimized cross-linking mass spectrometry for in situ interaction proteomics

Project description:ecent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking mass spectrometry (XL-MS). Here, we optimized the use of cleavable disuccinimidyl sulfoxide (DSSO) cross-linker for labeling native protein complexes in live human cells. We applied a generalized linear mixture model to calibrate cross-link peptide-spectra matching (CSM) scores to control the sensitivity and specificity of large-scale XL-MS. Using specific CSM score thresholds to control the false discovery rate, we found that higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) can both be effective for large-scale XL-MS protein interaction mapping. We found that the density and coverage of protein-protein interaction maps can be significantly improved through the use of multiple proteases. In addition, the use of sample-specific search databases can be used to improve the specificity of cross-linked peptide spectral matching. Application of this approach to human chromatin labeled in live cells recapitulated known and revealed new protein interactions of nucleosomes and other chromatin-associated complexes in situ. This optimized approach for mapping native protein interactions should be useful for a wide range of biological problems.

2019-04-03 | PXD010796 | Pride

Identifying and characterising Thrap3, Bclaf1 and Erh direct interactions using cross-linking mass spectrometry

Project description:Cross-linking mass spectrometry (XL-MS) is a powerful technology capable of yielding structural insights across the complex cellular protein interaction network. We performed XL-MS using MS-cleavable cross-linker disuccinimidyl sulfoxide (DSSO) on endogenous affinity-purified BAF complex. We identified numerous crosslinks between three BAF co-purifying proteins, namely Thrap3, Bclaf1 and Erh. Our data suggests that Bclaf1, Erh and Thrap3 interact closely and might represent a stable complex. The XL data allowed us to map interaction surfaces on Thrap3 and B, which overlap with the non-disordered portions of both proteins.

2021-09-24 | PXD027611 | Pride

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.

2023-10-04 | PXD035589 | Pride

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

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

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