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Isolation of Labile Multi-protein Complexes by in vivo Controlled Cellular Cross-Linking and Immuno-magnetic Affinity Chromatography

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Published on: March 9, 2010

Clickable Multitargeting Cross-Linkers Based on SuFEx for In Vivo Cross-Linking Mass Spectrometry.

Yanhong Hao¹, Moran Chen¹, Xiao Huang¹

¹The Institute for Advanced Studies, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.

Analytical Chemistry

|December 23, 2025

Summary

This summary is machine-generated.

Researchers developed novel trifunctional cross-linkers (SPSF) for in vivo cross-linking mass spectrometry (XL-MS). This technique enhances protein structure analysis by increasing amino acid coverage and identifying new cross-linking sites, including phosphorylation-associated residues.

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Area of Science:

Biochemistry
Chemical Biology
Proteomics

Background:

Cross-linking mass spectrometry (XL-MS) is crucial for studying protein structure and interactions.
Amino acid coverage in XL-MS dictates analysis depth and structural resolution accuracy.

Purpose of the Study:

To design and synthesize novel trifunctional cross-linkers (succinimidyl-propargyl-aryl sulfonyl fluoride - SPSF) for in vivo multitargeting cross-linking.
To improve the depth and accuracy of XL-MS analysis for functional protein structure determination.

Main Methods:

Synthesis of novel trifunctional cross-linkers (SPSF) with sequential reactivity (succinimide ester then sulfonyl fluoride).
In vivo cross-linking in various cellular compartments.
Enrichment strategy using click chemistry and biotin-streptavidin purification for cross-link identification.
Analysis of cross-linked sites and their functional domain enrichment.

Main Results:

SPSF demonstrated effective in vivo cross-linking across cellular compartments with minimal cellular perturbation.
Improved identification of diverse cross-links (Lys-Lys, Lys-Ser, Lys-Thr, Lys-Tyr, Lys-His) via click chemistry enrichment.
SPSF-mediated multisite cross-linking expanded coverage, especially in lysine-poor regions.
High overlap observed between cross-linked Ser, Thr, Tyr sites and phosphorylation sites.
Cross-linking sites were enriched in protein-protein interaction and nucleotide recognition domains.

Conclusions:

Novel SPSF cross-linkers offer a valuable addition to the XL-MS toolbox for enhanced functional protein structure analysis.
The approach provides deeper insights into protein functional states by mapping cross-links to functional domains.
Multisite cross-linking capability expands the scope and utility of XL-MS for complex biological systems.