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Divide and conquer: cleavable cross-linkers to study protein conformation and protein–protein interactions

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Abstract

Chemical cross-linking combined with mass spectrometry (MS) and computational modeling has evolved as an alternative method to address fundamental questions in structural biology. The constraints revealed by the cross-links yield valuable distance information and allow one to deduce three-dimensional structural information on very large and transient protein complexes. During the past few years, technical advances in the cross-linking/MS approach have been enormous, mainly owing to the fantastic advances in MS technology, and it is easily overlooked that significant progress has been made in the design of novel cross-linking reagents. In this review, the advent of cleavable cross-linking reagents will be highlighted. In particular, gas-phase (MS-) cleavable cross-linkers offer unique properties for an automated, data-dependent assignment of cross-linked products based on the generation of characteristic fragment ion signatures in MS/MS and MS3 spectra. Therefore, MS-cleavable cross-linkers are envisioned to hold the key for proteome-wide applications of the chemical cross-linking/MS approach, not only to delineate the conformation of single proteins but also to decipher protein interaction networks.

Outline of the analytical strategy using cleavable cross-linkers in combination with MS to conduct protein conformational and protein interaction studies

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Abbreviations

Azide-A-DSBSO:

Azide-tagged, acid-cleavable disuccinimidyl bissulfoxide

BAMG:

Bis(succinimidyl)-3-azidomethyl glutarate

BID:

N-benzyliminodiacetoyloxy succinimide

BuUrBu:

4-{3-[3-(2,5-dioxo-pyrrolidine-1-yloxycarbonyl) propyl]ureido}butyric acid 2,5-dioxo-pyrrolidine-1-yl ester

CBDPS:

Cyanurbiotindipropionyl succinimide

CID:

Collision-induced dissociation

DSBU:

Disuccinimidyl dibutyric urea

DSSO:

Disuccinimidyl sulfoxide

DTSSP:

3,3′-dithiobis(sulfosuccinimidyl propionate)

ESI:

Electrospray ionization

ETD:

Electron transfer dissociation

HCD:

Higher-energy collision-induced dissociation

IRMPD:

Infrared multiphoton dissociation

LC:

Liquid chromatography

MALDI:

Matrix-assisted laser desorption/ionization

MS:

Mass spectrometry

MS/MS:

Tandem mass spectrometry

NHS:

N-hydroxysuccinimide

PIR:

Protein interaction reporter

RISE:

Reporter ion scan event

SDAD:

Succinimidyl 2-([4,4′-azipentanamido]ethyl)-1,3′-dithiopropionate

SDS-PAGE:

Sodium dodecyl polyacrylamide gel electrophoresis

SuDP:

Disuccinimidylsuccinamyl aspartyl proline

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Acknowledgments

AS gratefully acknowledges financial support from the Deutsche Forschungsgemeinschaft (DFG project Si 867/15-2), the region of Saxony-Anhalt, and the EU (COST Action BM1403). AS thanks Dr. C. Ihling for critical reading of the manuscript.

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  1. Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany

    Andrea Sinz

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Correspondence to Andrea Sinz.

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Sinz, A. Divide and conquer: cleavable cross-linkers to study protein conformation and protein–protein interactions. Anal Bioanal Chem 409, 33–44 (2017). https://doi.org/10.1007/s00216-016-9941-x

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