Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions

Limpikirati, Patanachai; Liu, Tianying; Vachet, Richard W.

doi:10.1016/j.ymeth.2018.04.002

Cited by 90 publications

(150 citation statements)

References 160 publications

(256 reference statements)

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“…FPOP, it remains analytically challenging to determine at the residue level the site of the modification. Nevertheless, data from covalent labelling has shown promise as an input for structural modelling (36)(37)(38). To demonstrate the data input requirements for covalent labelling/ dead-end XL data we have also included example data from FPOP analysis of the protein β 2 -microglobulin (17) (see example data).…”

Section: Discriminating Between Inter-and Intra-subunit Crosslinks Inmentioning

confidence: 99%

PyXlinkViewer: a flexible tool for visualisation of protein chemical crosslinking data within the PyMOL molecular graphics system

Schiffrin

Radford

Brockwell

et al. 2020

Preprint

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Chemical crosslinking-mass spectrometry (XL-MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL-MS data yields inter-residue restraints that can be compared with high-resolution structural data.Distances greater than the crosslinker spacer-arm can reveal lowly-populated "excited" states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL-MS, there are few tools to enable rapid and facile mapping of XL-MS data onto high-resolution structures or structural models. PyXlinkViewer is a user-friendly plugin for PyMOL v2 that maps intra-protein, inter-protein and dead-end crosslinks onto protein structures/models and automates the calculation of inter-residue distances for the detected crosslinks. This enables rapid visualisation of XL-MS data, assessment of whether a set of detected crosslinks is congruent with structural data, and easy production of high-quality images for publication.

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Section: Discriminating Between Inter-and Intra-subunit Crosslinks Inmentioning

confidence: 99%

PyXlinkViewer: a flexible tool for visualisation of protein chemical crosslinking data within the PyMOL molecular graphics system

Schiffrin

Radford

Brockwell

et al. 2020

Preprint

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show abstract

“…These could include protein-RNA interactions, which can also be mediated by lysine-rich IDRs [42]. In principle, other amino acids involved in nucleic acid interactions could be analyze using similar footprinting approaches [43].…”

Section: Changes In Lysine Accessibility In Histone Proteins On Bindimentioning

confidence: 99%

DNA binding reorganizes the intrinsically disordered C-terminal region of PSC inDrosophilaPRC1

Kang

Faubert

Boulais

et al. 2020

Preprint

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Polycomb Group (PcG) proteins regulate gene expression by modifying chromatin. A key PcG complex, Polycomb Repressive Complex 1 (PRC1), has two activities: a ubiquitin ligase activity for histone H2A, and a chromatin compacting activity. In Drosophila, the Posterior Sex Combs (PSC) subunit of PRC1 is central to both activities. The N-terminal homology region (HR) of PSC assembles into PRC1, including partnering with dRING to form the ubiquitin ligase for H2A. The intrinsically disordered C-terminal region of PSC (PSC-CTR) compacts chromatin, and inhibits chromatin remodeling and transcription in vitro. Both the PSC-HR and the PSC-CTR are essential in vivo. To understand how these two activities may be coordinated in PRC1, we used cross-linking mass spectrometry (XL-MS) to analyze the conformations of the PSC-CTR in PRC1 and how they change on binding DNA. XL-MS identifies interactions between the PSC-CTR and the core of PRC1, including between the PSC-CTR and PSC-HR. New contacts and overall more compacted PSC-CTR conformations are induced by DNA binding. Protein footprinting of accessible lysine residues in the PSC-CTR reveals an extended, bipartite candidate DNA/chromatin binding surface. Our data suggest a model in which DNA (or chromatin) follows a long path on the flexible PSC-CTR. Intramolecular interactions of the PSC-CTR detected by XL-MS can bring the high affinity DNA/chromatin binding region close to the core of PRC1 without disrupting the interface between the ubiquitin ligase and the nucleosome. Our approach may be applicable to understanding the global organization of other large IDRs that bind nucleic acids.

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“…CL-MS techniques using hydroxyl radicals, DEPC, and carbenes rely on the formation of new covalent bonds with solvent accessible amino acid side chains providing information on the proteins surface structure. 96…”

Section: Covalent Labelingmentioning

confidence: 99%

Evolution of Structural Biology through the Lens of Mass Spectrometry

et al. 2018

View full text Add to dashboard Cite

Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions

Cited by 90 publications

References 160 publications

PyXlinkViewer: a flexible tool for visualisation of protein chemical crosslinking data within the PyMOL molecular graphics system

PyXlinkViewer: a flexible tool for visualisation of protein chemical crosslinking data within the PyMOL molecular graphics system

DNA binding reorganizes the intrinsically disordered C-terminal region of PSC inDrosophilaPRC1

Evolution of Structural Biology through the Lens of Mass Spectrometry

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