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PLink Characterizing the dynamic oligomerization of HSP90β using photo-cross-linking

ABSTRACT: Cross-linking mass spectrometry (XL-MS) is a transformative tool for probing protein structures. While conventional chemical crosslinkers exhibit well-defined chemistry for specific residues, photo-crosslinkers, despite their superior reactivity, have been hindered by incomplete mechanistic understanding and a lack of analytical frameworks. Here, we demonstrate that diazirine-based photo-crosslinks are inherently MS-cleavable—a novel property but also complicates spectral interpretation for overlapping peptide backbone and crosslinker side-chain fragments. Leveraging diagnostic side-chain fragmentation fingerprints, we developed a machine learning model that significantly improves ion coverage and reduces false discovery rates when combined with existing search algorithms. Further, we designed a homo-bifunctional diazirine crosslinker that allows for true on-demand photo-crosslinking. Empowered, we captured transient tetrameric assemblies of human HSP90β and revealed structural transitions in association equilibrium upon heat stress—features inaccessible with conventional chemical crosslinking. Together, our work establishes a new paradigm of XL-MS, combining the temporal sensitivity and precision of photo-activation with analytical confidence.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: yida jiang

LAB HEAD: Chun Tang

PROVIDER: PXD066889 | Pride | 2026-04-09

REPOSITORIES: Pride

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			Action	DRS
	HSP90-BDG_MS2_298K_R1.raw	Raw
	HSP90-BDG_MS2_298K_R2.raw	Raw
	HSP90-BDG_MS2_298K_R3.raw	Raw
	HSP90-BDG_MS2_310K_R1.raw	Raw
	HSP90-BDG_MS2_310K_R2.raw	Raw

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