The combination of hydrogen/deuterium exchange or chemical cross-linking techniques with mass spectrometry: Mapping of human 14-3-3ζ homodimer interface

Haladová, Kateřina; Mrázek, Hynek; Ječmen, Tomáš; Halada, Petr; Man, Petr; Novák, Petr; Chmelı́k, Josef; Obšil, Tomáš; Šulc, Miroslav

doi:10.1016/j.jsb.2012.04.016

Cited by 20 publications

(26 citation statements)

References 27 publications

(36 reference statements)

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“…Cysteine-specific cross-linking is also well established but usually does not yield sufficient structural information due to the low prevalence of cysteines in proteins and their involvement in the formation of disulfide bonds. Zero-length cross-linking by carbodiimide coupling (17)(18)(19) and photochemical cross-linking (20) are other strategies that have been described but have not yet found widespread application in the field.…”

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confidence: 99%

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

Leitner

Joachimiak

Unverdorben

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

223

312

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The study of proteins and protein complexes using chemical crosslinking followed by the MS identification of the cross-linked peptides has found increasingly widespread use in recent years. Thus far, such analyses have used almost exclusively homobifunctional, amine-reactive cross-linking reagents. Here we report the development and application of an orthogonal cross-linking chemistry specific for carboxyl groups. Chemical cross-linking of acidic residues is achieved using homobifunctional dihydrazides as cross-linking reagents and a coupling chemistry at neutral pH that is compatible with the structural integrity of most protein complexes. In addition to cross-links formed through insertion of the dihydrazides with different spacer lengths, zero-length cross-link products are also obtained, thereby providing additional structural information. We demonstrate the application of the reaction and the MS identification of the resulting cross-linked peptides for the chaperonin TRiC/CCT and the 26S proteasome. The results indicate that the targeting of acidic residues for cross-linking provides distance restraints that are complementary and orthogonal to those obtained from lysine cross-linking, thereby expanding the yield of structural information that can be obtained from cross-linking studies and used in hybrid modeling approaches. P roteins exert the majority of their functions in the form of protein complexes to control cellular signaling, protein synthesis, folding and degradation, and many more essential processes. Therefore, elucidating the composition and structure of such complexes has been a longstanding goal of biological research.MS-based proteomics has emerged as one of the main techniques to identify and quantify proteins and their modifications in biological samples such as isolated complexes, proteome fractions, or whole proteomes. Various MS methods now provide structural information on protein assemblies (1-3). Among them, chemical cross-linking and identification of cross-linked peptides by MS (XL-MS) has been increasingly applied to determine the subunit arrangements of biologically relevant complexes (4-6). Such XL-MS experiments indicate the locations of cross-linking sites and thus the spatial proximity of reactive groups that are connected by a covalent bond. This information is then used to determine the positioning of subunits or locate interacting regions, alone or in combination with other techniques such as NMR spectroscopy, electron microscopy, and X-ray crystallography.In the last few years, optimized protocols and new computational tools for the reliable analysis of XL-MS datasets resulted in significant advances of the XL-MS technology (4-6). These advances have contributed to the emergence of a robust, integrated XL-MS method that has been successfully applied for structure determination of a number of large protein complexes (7-11) and the detection of direct, physical interactions in whole cells (12)(13)(14). To date, the cross-linking chemistries applied in these studies have targ...

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mentioning

confidence: 99%

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

Leitner

Joachimiak

Unverdorben

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

223

312

View full text Add to dashboard Cite

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“…The initial structural informa-58 tion includes the length of cross-linker spacer and the position of 59 cross-linked amino acids in protein sequence. The cross-links 60 formed provide distance constraints which form a basis for 61 generating three dimensional models [12][13][14][15], mapping protein 62 interaction interface [16][17][18][19] or refinement of earlier resolved 63 structures [20][21][22][23]. 64 Analysis of conformational changes in proteins represents a 65 very challenging task because proteins are not static objects and 66 their structural dynamics has crucial effect on the behavior of bio-67 logical systems.…”

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confidence: 99%

Mapping protein structural changes by quantitative cross-linking

Kukačka

Rosůlek

Strohalm

et al. 2015

Methods

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“…This combination of approaches has been applied by Novak and colleagues on a variety of systems including the mapping of the 14-3-3 protein homodimer interface [127], the conformational changes this protein induces on the neutral trehalase Nth1 [128] and to generate structural models of C-type lectin-like receptors NKR-P1A [129] and NRK-P1C [130]. In this last example, HDX combined with IM-MS and cross-linking data showed that the release of one of the loops, as seen in the crystal structure, was actually an artifact, enabling the proposal of an updated model for the solution structure.…”

Section: Hdx and Covalent Labelingmentioning

confidence: 99%

Towards integrative structural mass spectrometry: Benefits from hybrid approaches

Marcoux

Cianférani

2015

Methods

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The combination of hydrogen/deuterium exchange or chemical cross-linking techniques with mass spectrometry: Mapping of human 14-3-3ζ homodimer interface

Cited by 20 publications

References 27 publications

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

Mapping protein structural changes by quantitative cross-linking

Towards integrative structural mass spectrometry: Benefits from hybrid approaches

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