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A Tyrosine, Histidine-Selective Bifunctional Cross-linker for Protein Structure Analysis

ABSTRACT: A novel cross-linking strategy based on this cross-linker has been developed and demostrated, which provides a complementary XL-MS tool analyzing protein structure

ORGANISM(S): Homo Sapiens

SUBMITTER: Zhonglin Wei

PROVIDER: PXD036600 | iProX | Sat Dec 03 00:00:00 GMT 2022

REPOSITORIES: iProX

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A tyrosine, histidine-selective bifunctional cross-linker for protein structure analysis.

Yan Qibo Q Li Ming M Zhang Yanxin Y Liu Hailong H Liu Feng F Liao Weiwei W Wang Yingwu Y Duan Haifeng H Wei Zhonglin Z

Talanta 20230310

Chemical cross-linking mass spectrometry (XL-MS) significantly contributes to the analysis of protein structures and the elucidation of protein-protein interactions. Currently available cross-linkers mainly target N-terminus, lysine, glutamate, aspartate, and cysteine residues in protein. Herein, a bifunctional cross-linker, named [4,4'-(disulfanediylbis(ethane-2,1-diyl)) bis(1-methyl-1,2,4-triazolidine-3,5-dione)] (DBMT) has been designed and characterized aiming to extremely expand the applica ...[more]

PMID: 36913793

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A Tyrosine Reactive Cross-Linker for Probing Protein 3D Structures

Project description:Cross-linking mass spectrometry (XL-MS) has made significant progress in understanding the structure of protein and elucidating architectures of larger protein complexes. Current XL-MS applications are limited to targeting lysine, glutamic acid, aspartic acid, and cysteine residues. There remains a need for the development of novel cross-linkers enabling selectively target other amino-acid residues in proteins. Here, a novel simple cross-linker, namely [4,4'-(disulfanediylbis(ethane-2,1-diyl)) bis(1,2,4-triazolidine-3,5-dione)] (DBB), has been designed, synthesized, and characterized. This cross-linker can react selectively with tyrosine residues in protein through electrochemical click reaction. Upon tandem mass spectrometry, the DBB cross-links produced the characteristic fragments, thus permitting the simplified data analysis and accurate identification for the cross-linked products. This is the first time developing a cross-linker for targeting tyrosine residue on protein without using photoirradiation or metal catalyst. This strategy might potentially be used as a complementary tool for XL-MS to probe protein 3D structures, protein complexes, and protein-protein interaction.

2020-10-22 | PXD022121 | iProX

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

Structural surfaceomics of Nomo-1 using PhoX cross-linker with timsTOF

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). PhoX 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. PhoX having in-built phosphonate-based IMAC handle which allowed additional enrichment of cross-linked peptides.

2023-10-04 | PXD035591 | Pride

Development of an sulfoxide-based, CuAAC-enrichable cross-linker

Project description:Cross-linking of BSA with a novel cross-linker. Modification of the cross-linker containing peptides with CuAAC-chemistry to attach a cleavable biotin-derivative. Enrichment with streptavidin-beads.

2019-10-14 | PXD015080 | Pride

Cross-linking mass spectrometry analysis of human ADAR1 deaminase domain WT using an MS-cleavable cross-linker, DSBU

Project description:Cross-linking mass spectrometry analysis of human ADAR1 deaminase domain WT protein (hADAR1d WT) was carried out using an MS-cleavable cross-linker, DSBU, to support the homology model structure of hADAR1d WT.

2020-08-21 | MSV000085996 | MassIVE

Developing In Vivo Cross-linking Mass Spectrometry (XL-MS) to Decipher Protein Interaction Landscapes at the Proteome Scale

Project description:We have developed a new and robust in vivo cross-linking mass spectrometry (XL-MS) that utilizes a multifunctional MS-cleavable cross-linker to enable the efficient capture, enrichment, and identification of in vivo cross-linked peptides at the whole proteome scale.

2021-07-30 | PXD012788 | 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

Cross-linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics

Project description:The combination of cross-linking/mass spectrometry (XL-MS) and ion mobility is still underexplored for conducting protein conformational and protein-protein interaction studies. We present a method for analyzing cross-linking mixtures on a timsTOF Pro mass spectrometer that allows separating ions based on their gas phase mobilities. Cross-linking was performed with three urea-based MS-cleavable cross-linkers that deliver distinct fragmentation patterns for cross-linked species upon collisional activation. The discrimination of cross-linked species from non-cross-linked peptides was readily performed based on their collisional cross sections. We demonstrate the general feasibility of our combined XL-MS/ion mobility approach for three protein systems of increasing complexity: (i) Bovine serum albumin, (ii) E. coli ribosome, and (iii) HEK293T cell nuclear extracts. We identified a total of 623 unique cross-linking sites for BSA, 670 for the E. coli ribosome, and 1,617 unique cross-links for nuclear extracts, corresponding to 1,088 intra- and 529 interprotein interactions and yielding 564 distinct protein-protein interactions. Our results underline the strength of combining XL-MS with ion mobility not only for deriving 3D-structures of single proteins, but also for performing system-wide protein interaction studies.

2022-03-17 | PXD027234 | Pride

Expanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS

Project description:In cross-linking mass spectrometry (XL-MS), the depth and sensitivity of cross-link detection is often limited by the low abundance of cross-links compared to non-cross-linked peptides in the digestion mixture. To improve the identification efficiency of cross-links, here we present a gas-phase separation strategy using high field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to the Orbitrap Tribrid mass spectrometers. By enabling an additional peptide separation step in gas phase using the FAIMS device, we increase the number of cross-link identification by 22% for a medium complex sample and 59% for strong cation exchange-fractionated HEK293T cell lysate in XL-MS experiments using disuccinimidyl sulfoxide (DSSO) cross-linker. When disuccinimidyl suberate (DSS) cross-linker is in use, we are able to boost cross-link identification by 89% for the medium and 100% for the highly complex sample comparing to the analyses without FAIMS . Furthermore, we show that for medium complex samples, FAIMS enables the collection of single-shot XL-MS data with comparable depth to the corresponding sample fractionated by chromatography-based approaches. Altogether, we demonstrate FAIMS is highly beneficial for XL-MS studies by expanding the proteome coverage of cross-links while improving the efficiency and confidence of cross-link identification.

2020-07-22 | PXD019926 | Pride

A Glycosidic-Bond-Based Mass-Spectrometry-Cleavable Cross-linker Enables In Vivo Cross-linking for Protein Complex Analysis

Project description:Chemical cross-linking mass spectrometry (CXMS) has emerged as a powerful technology to analyze protein complex structure and interaction. However, the spectral fragmentation behavior and spectral data retrieval of cross-linked peptides are more complex than single peptides. In this study, we designed and synthesized a trehalose-based MS-cleavable cross-linker, Trehalose Disuccinimidyl Ester (TDS), which possesses a CID/HCD-cleavable glycosidic bond and has good bioorthogonality and amphipathicity. Using TDS, the cross-linked peptides were simplified into conventional single peptides via the selective cleavage between glycosidic and peptide bonds under individual MS collision energy, which enhances the matching degree and retrieval throughput of spectral identification. The deep coverage of the TDS method facilitated the accurate resolution of the structural dynamics of purified proteins with different physicochemical properties and yeast 26S proteasome complex. Additionally, the bioorthogonality and amphipathicity of TDS enabled the cross-linking reaction to occur in vivo without the introduction of any organic solvent. Through coinciding with this feature and MS-cleavable capacity, TDS provided us a high throughput snapshot of the structural architecture of protein complex in live cells. These results provide a promising TDS toolkit to study CXMS and decipher the protein conformations and interactions with high accuracy and easy portability for cross-linker design.

2023-12-06 | PXD047554 | iProX

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