Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes

doi:10.1007/978-1-4939-9822-7_18

. 2020:2062:383-400.

doi: 10.1007/978-1-4939-9822-7_18.

Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes

Yufei Xiang¹, Zhuolun Shen^{1

2}, Yi Shi¹

Affiliations

¹ Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
² School of Medicine, Tsinghua University, Beijing, China.

PMID: 31768986
DOI: 10.1007/978-1-4939-9822-7_18

Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes

Yufei Xiang et al. Methods Mol Biol. 2020.

. 2020:2062:383-400.

doi: 10.1007/978-1-4939-9822-7_18.

Authors

Yufei Xiang¹, Zhuolun Shen^{1

2}, Yi Shi¹

Affiliations

¹ Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
² School of Medicine, Tsinghua University, Beijing, China.

PMID: 31768986
DOI: 10.1007/978-1-4939-9822-7_18

Abstract

Chemical cross-linking and mass spectrometric readout (CX-MS) has become a useful toolkit for structural analysis of protein complexes. CX-MS enables rapid detection of a larger number of cross-link peptides from the chemically cross-linked protein assembly, providing invaluable cross-link spatial restraints to understand the architecture of the complex. Since CX-MS is complementary with other structural and computational modeling tools, it can be used for integrative structural determination of large native protein assemblies. However, due to technical limitations, current CX-MS applications have still been predominantly confined to complexes reconstituted from recombinant proteins where large amount of purified materials are available. Cross-linking and hybrid structural proteomic analysis of endogenous protein complexes remains a challenge. In this chapter, we present a protocol that efficiently couples affinity capture of endogenous complexes with sensitive CX-MS analysis, with particular application to the yeast RNA processing exosome complexes.

Keywords: Affinity proteomics; Chemical cross-linking and mass spectrometry; Integrative structural modeling; Native macromolecular assembly; RNA degradation; RNA exosome complex; Structural proteomics.

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References

1. Alber F, Forster F, Korkin D, Topf M, Sali A (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 77:443–477 - DOI - PubMed
1. Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y (2016) Revealing higher order protein structure using mass spectrometry. J Am Soc Mass Spectrom 27(6):952–965 - DOI - PubMed - PMC
1. Rappsilber J (2011) The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J Struct Biol 173(3):530–540 - DOI - PubMed - PMC
1. Cohen SL, Chait BT (2001) Mass spectrometry as a tool for protein crystallography. Annu Rev Biophys Biomol Struct 30:67–85 - DOI - PubMed
1. Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, Forster F, Aebersold R (2012) Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol Cell Proteomics 11(3):M111 014126 - DOI - PubMed - PMC

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[1] Alber F, Forster F, Korkin D, Topf M, Sali A (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 77:443–477 - DOI - PubMed

[2] Alber F, Forster F, Korkin D, Topf M, Sali A (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 77:443–477 - DOI - PubMed

[3] Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y (2016) Revealing higher order protein structure using mass spectrometry. J Am Soc Mass Spectrom 27(6):952–965 - DOI - PubMed - PMC

[4] Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y (2016) Revealing higher order protein structure using mass spectrometry. J Am Soc Mass Spectrom 27(6):952–965 - DOI - PubMed - PMC

[5] Rappsilber J (2011) The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J Struct Biol 173(3):530–540 - DOI - PubMed - PMC

[6] Rappsilber J (2011) The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J Struct Biol 173(3):530–540 - DOI - PubMed - PMC

[7] Cohen SL, Chait BT (2001) Mass spectrometry as a tool for protein crystallography. Annu Rev Biophys Biomol Struct 30:67–85 - DOI - PubMed

[8] Cohen SL, Chait BT (2001) Mass spectrometry as a tool for protein crystallography. Annu Rev Biophys Biomol Struct 30:67–85 - DOI - PubMed

[9] Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, Forster F, Aebersold R (2012) Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol Cell Proteomics 11(3):M111 014126 - DOI - PubMed - PMC

[10] Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, Forster F, Aebersold R (2012) Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol Cell Proteomics 11(3):M111 014126 - DOI - PubMed - PMC

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Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes

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Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes

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