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Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze

Abstract

Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature. These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes.

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Abbreviations

AP-MS:

Affinity purification-mass spectrometry

BS3 :

Bis[sulfosuccinimidyl]suberate

CID:

Collision-induced dissociation

CP:

PLRV coat protein

DSS:

Disuccinimidyl suberate

FDR:

False discovery rate

IGBP1:

Immunoglobulin binding protein 1

IMS:

Ion mobility spectrometry

LC:

Liquid chromatography

MIX:

Mixed-isotope cross-linking

MS:

Mass spectrometry

MS1 :

Precursor scan in a mass spectrometry experiment

MS2 :

Tandem mass spectrometry (MS/MS) scan in a mass spectrometry experiment that yields a fragmentation spectrum of a precursor selected in MS1

MS3 :

Third-order tandem mass spectrometry (MS/MS/MS) scan that yields a fragmentation spectrum of an MS2-derived fragment ion

NHS:

N-hydroxysuccinimide

NMR:

Nuclear magnetic resonance spectroscopy

PLRV:

Potato leaf roll virus

PP2A:

Protein phosphatase 2A

PP2AA:

The A subunit of protein phosphatase 2A

ReACT:

Real-time analysis for cross-linked peptide technology

RTP:

PLRV read-through protein

SCX:

Strong cation exchange chromatography

SDS-PAGE:

Sodium dodecylsulfate polyacrylamide gel electrophoresis

SEC:

Size exclusion exchange chromatography

XL–MS:

Chemical cross-linking-mass spectrometry

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Acknowledgments

This research was funded by the National Institute of General Medical Sciences PSI:Biology project (NIGMS grant GM094623). Portions of this work were performed in the Environmental Molecular Science Laboratory, a U.S. Department of Energy/BER national scientific user facility at Pacific Northwest National Laboratory in Richland, WA. The authors would like to thank Nathan Johnson for assistance in preparing the figures, and Penny Colton, Michael Daily, and Gyorgy Babnigg for reviewing the manuscript in advance of publication.

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Correspondence to Eric D. Merkley.

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Merkley, E.D., Cort, J.R. & Adkins, J.N. Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze. J Struct Funct Genomics 14, 77–90 (2013). https://doi.org/10.1007/s10969-013-9160-z

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  • DOI: https://doi.org/10.1007/s10969-013-9160-z

Keywords

  • Chemical cross-linking
  • Mass spectrometry
  • Structural biology
  • Protein complexes
  • Computational modeling
  • Integrative structural biology