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Review
. 2019 Feb:48:8-18.
doi: 10.1016/j.cbpa.2018.08.006. Epub 2018 Aug 30.

Chemical cross-linking with mass spectrometry: a tool for systems structural biology

Juan D Chavez  1 , James E Bruce  2
Affiliations
Review

Chemical cross-linking with mass spectrometry: a tool for systems structural biology

Juan D Chavez et al. Curr Opin Chem Biol. 2019 Feb.

Abstract

Biological processes supporting life are orchestrated by a highly dynamic array of protein structures and interactions comprising the interactome. Defining the interactome, visualizing how structures and interactions change and function to support life is essential to improved understanding of fundamental molecular processes, but represents a challenge unmet by any single analytical technique. Chemical cross-linking with mass spectrometry provides identification of proximal amino acid residues within proteins and protein complexes, yielding low resolution structural information. This approach has predominantly been employed to provide structural insight on isolated protein complexes, and has been particularly useful for molecules that are recalcitrant to conventional structural biology studies. Here we discuss recent developments in cross-linking and mass spectrometry technologies that are providing large-scale or systems-level interactome data with successful applications to isolated organelles, cell lysates, virus particles, intact bacterial and mammalian cultured cells and tissue samples.

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Figures

Fig 1-
Fig 1-
MS analysis of non-cleavable and cleavable cross-linked peptide pairs A) MS analysis of a peptide pair cross-linked with traditional non-cleavable cross-linkers. The MSI spectrum provides the mass of the intact cross-linked species. Upon fragmentation in the MS2 a chimeric spectrum is generated comprised of fragment ions from both peptides and the masses of the individual peptides remains unknown. Searching MS data from non-cleavable cross-linked peptide pairs results in a quadratic expansion of the search space making proteome-wide searches an intractable problem. B) MS analysis of a peptide pair cross-linked with a cleavable cross-linker. The MSI spectrum provides the mass of the intact cross-linked species. Under MS2 the labile bonds in the crosslinker are selectively cleaved releasing the intact peptides allowing for accurate determination of their masses. Another round of MS analysis (MS3) allows for independent isolation and fragmentation of the released peptides greatly simplifying downstream analysis by circumventing the n2 problem and allowing for proteome wide database searches to be performed.
Fig. 2-
Fig. 2-
Overview of chemical cross-linking with mass spectrometry A) General XL-MS workflow. B) Types of questions that XL-MS can be used to address.
See this image and copyright information in PMC

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