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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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