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

Journal of Structural and Functional Genomics volume 14, pages 77–90 (2013)Cite this article

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

References

  1. Ward AB, Sali A, Wilson IA (2013) Science 339:913–915

    PubMed  Article  CAS  Google Scholar 

  2. Lipfert J, Doniach S (2007) Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annual Review of Biophysics and Biomolecular Structure, vol 36. Annual Review of Biophysics. Annual Reviews, Palo Alto, pp 307–327

  3. Subramaniam S, Milne JLS (2004) Annu Rev Biophys Biomol Struct 33:141–155

    PubMed  Article  CAS  Google Scholar 

  4. Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul Ü, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders APL, Dickman MJ, Doudna JA, Boekema EJ, Heck AJR, van der Oost J, Brouns SJJ (2011) Nat Struct Mol Biol 18:529–536

    PubMed  Article  CAS  Google Scholar 

  5. Lebowitz J, Lewis MS, Schuck P (2002) Protein Sci 11:2067–2079

    PubMed  Article  CAS  Google Scholar 

  6. Hyung S-J, Ruotolo BT (2012) Proteomics 12:1547–1564

    PubMed  Article  CAS  Google Scholar 

  7. Mendoza VL, Vachet RW (2009) Mass Spectrom Rev 28:785–815

    PubMed  Article  CAS  Google Scholar 

  8. Ruotolo BT, Benesch JLP, Sandercock AM, Hyung S-J, Robinson CV (2008) Nat Protocols 3:1139–1152

    Article  CAS  Google Scholar 

  9. Sharon M, Robinson CV (2007) The role of mass Spectrometry in structure elucidation of dynamic protein complexes. Annual Review of Biochemistry, vol 76. Annual Review of Biochemistry. Annual Reviews, Palo Alto, pp 167–193

  10. Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A (2012) Bioinformatics 28:3282–3289

    PubMed  Article  CAS  Google Scholar 

  11. Lasker K, Forster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W (2012) Proc Natl Acad Sci USA 109:1380–1387

    PubMed  Article  CAS  Google Scholar 

  12. Rappsilber J (2011) J Struct Biol 173:530–540

    PubMed  Article  CAS  Google Scholar 

  13. Sinz A (2006) Mass Spectrom Rev 25:663–682

    PubMed  Article  CAS  Google Scholar 

  14. Fabris D, Yu ET (2010) J Mass Spectrom 45:841–860

    PubMed  Article  CAS  Google Scholar 

  15. Singh P, Panchaud A, Goodlett DR (2010) Anal Chem 82:2636–2642

    PubMed  Article  CAS  Google Scholar 

  16. Miteva YV, Budayeva HG, Cristea IM (2012) Anal Chem 85:749–768

    PubMed  Article  Google Scholar 

  17. Soderberg CAG, Lambert W, Kjellstrom S, Wiegandt A, Wulff RP, Mansson C, Rutsdottir G, Emanuelsson C (2012) PLoS ONE 7:e38927. doi:10.1371/journal.pone.0038927

    PubMed  Article  Google Scholar 

  18. Mayne SLN, Patterton H-G (2011) Brief Bioinform 12:660–671

    PubMed  Article  CAS  Google Scholar 

  19. Young MM, Tang N, Hempel JC, Oshiro CM, Taylor EW, Kuntz ID, Gibson BW, Dollinger G (2000) Proc Natl Acad Sci USA 97:5802–5806

    PubMed  Article  CAS  Google Scholar 

  20. Paramelle D, Miralles G, Subra G, Martinez J (2013) Proteomics 13:438–456

    PubMed  Article  CAS  Google Scholar 

  21. Leitner A, Walzthoeni T, Kahraman A, Herzog F, Rinner O, Beck M, Aebersold R (2010) Mol Cell Proteomics 9:1634–1649

    PubMed  Article  CAS  Google Scholar 

  22. Schilling B, Row RH, Gibson BW, Guo X, Young MM (2003) J Am Soc Mass Spectrom 14:834–850

    PubMed  Article  CAS  Google Scholar 

  23. Pettelkau J, Schroder T, Ihling CH, Olausson BES, Kolbel K, Lange C, Sinz A (2012) Biochemistry 51:4932–4949

    PubMed  Article  CAS  Google Scholar 

  24. Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, Förster F, Aebersold R (2012) Mol Cell, Proteomics 11:M111.014126. doi:10.1074/mcp.M111.014126

  25. Novak P, Haskins WE, Ayson MJ, Jacobsen RB, Schoeniger JS, Leavell MD, Young MM, Kruppa GH (2005) Anal Chem 77:5101–5106

    PubMed  Article  CAS  Google Scholar 

  26. Fritzsche R, Ihling CH, Gotze M, Sinz A (2012) Rapid Commun Mass Spectrom 26:653–658

    PubMed  Article  CAS  Google Scholar 

  27. Lauber MA, Reilly JP (2011) J Proteome Res 10:3604–3616

    PubMed  Article  CAS  Google Scholar 

  28. Clifford-Nunn B, Showalter HDH, Andrews PC (2012) J Am Soc Mass Spectrom 23:201–212

    PubMed  Article  CAS  Google Scholar 

  29. Lu Y, Tanasova M, Borhan B, Reid GE (2008) Anal Chem 80:9279–9287

    PubMed  Article  CAS  Google Scholar 

  30. Herzog F, Kahraman A, Boehringer D, Mak R, Bracher A, Walzthoeni T, Leitner A, Beck M, Hartl F-U, Ban N, Malmström L, Aebersold R (2012) Science 337:1348–1352

    PubMed  Article  CAS  Google Scholar 

  31. Zheng CX, Yang L, Hoopmann MR, Eng JK, Tang XT, Weisbrod CR, Bruce JE (2011) Mol Cell Proteomics 10: M110.006841. doi:10.1074/mcp.M110.006841

  32. Chavez JD, Cilia M, Weisbrod CR, Ju HJ, Eng JK, Gray SM, Bruce JE (2012) J Proteome Res 11:2968–2981

    PubMed  Article  CAS  Google Scholar 

  33. Petrotchenko EV, Serpa JJ, Borchers CH (2011) Mol Cell Proteomics 10: M110.001420. doi:10.1074/mcp.M110.001420

  34. Sinz A, Kalkhof S, Ihling C (2005) J Am Soc Mass Spectrom 16:1921–1931

    PubMed  Article  CAS  Google Scholar 

  35. Luo J, Fishburn J, Hahn S, Ranish J (2012) Mol Cell Proteomics 11: M111.008318. doi:10.1074/mcp.M111.008318

  36. Chowdhury SM, Du XX, Tolic N, Wu S, Moore RJ, Mayer MU, Smith RD, Adkins JN (2009) Anal Chem 81:5524–5532

    PubMed  Article  CAS  Google Scholar 

  37. Weisbrod CR, Chavez JD, Eng JK, Yang L, Zheng C, Bruce JE (2013) J Proteome Res 12:1569–1579

    Article  CAS  Google Scholar 

  38. Walzthoeni T, Claassen M, Leitner A, Herzog F, Bohn S, Forster F, Beck M, Aebersold R (2012) Nat Meth 9:901–903

    Article  CAS  Google Scholar 

  39. Marcotte EM (2007) Nat Biotech 25:755–757

    Article  CAS  Google Scholar 

  40. Rinner O, Seebacher J, Walzthoeni T, Mueller L, Beck M, Schmidt A, Mueller M, Aebersold R (2008) Nat Meth 5:315–318

    Article  CAS  Google Scholar 

  41. Yang B, Wu Y-J, Zhu M, Fan S-B, Lin J, Zhang K, Li S, Chi H, Li Y-X, Chen H-F, Luo S-K, Ding Y-H, Wang L-H, Hao Z, Xiu L-Y, Chen S, Ye K, He S-M, Dong M-Q (2012) Nat Meth 9:904–906

    Article  CAS  Google Scholar 

  42. Anderson GA, Tolic N, Tang XT, Zheng CX, Bruce JE (2007) J Proteome Res 6:3412–3421

    PubMed  Article  CAS  Google Scholar 

  43. Gotze M, Pettelkau J, Schaks S, Bosse K, Ihling CH, Krauth F, Fritzsche R, Kuhn U, Sinz A (2012) J Am Soc Mass Spectrom 23:76–87

    PubMed  Article  Google Scholar 

  44. Li W, O’Neill HA, Wysocki VH (2012) Bioinformatics 28:2548–2550

    PubMed  Article  CAS  Google Scholar 

  45. Storey JD, Tibshirani R (2003) Proc Natl Acad Sci USA 100:9440–9445

    PubMed  Article  CAS  Google Scholar 

  46. Nesvizhskii AI (2010) J Proteomics 73:2092–2123

    PubMed  Article  CAS  Google Scholar 

  47. Hoopmann MR, Weisbrod CR, Bruce JE (2010) J Proteome Res 9:6323–6333

    PubMed  Article  CAS  Google Scholar 

  48. Merkley ED, Baker ES, Crowell KL, Orton DJ, Taverner T, Ansong C, Ibrahim YM, Burnet MC, Cort JR, Anderson GA, Smith RD, Adkins JN (2013) J Am Soc Mass Spectrom 24:444–449

    PubMed  Article  CAS  Google Scholar 

  49. Lee YJ, Lackner LL, Nunnari JM, Phinney BS (2007) J Proteome Res 6:3908–3917

    PubMed  Article  CAS  Google Scholar 

  50. Lee L, Kaplan IB, Ripoll DR, Liang D, Palukaitis P, Gray SM (2005) J Virol 79:1207–1214

    PubMed  Article  CAS  Google Scholar 

  51. Tang XT, Munske GR, Siems WF, Bruce JE (2005) Anal Chem 77:311–318

    PubMed  Article  CAS  Google Scholar 

  52. Chowdhury SM, Munske GR, Tang XT, Bruce JE (2006) Anal Chem 78:8183–8193

    PubMed  Article  CAS  Google Scholar 

  53. Zhang HZ, Tang XT, Munske GR, Tolic N, Anderson GA, Bruce JE (2009) Mol Cell Proteomics 8:409–420

    PubMed  Article  CAS  Google Scholar 

  54. Eng JK, McCormack AL, Yates JR (1994) J Am Soc Mass Spectrom 5:976–989

    Article  CAS  Google Scholar 

  55. Perkins DN, Pappin DJC, Creasy DM, Cottrell JS (1999) Electrophoresis 20:3551–3567

    PubMed  Article  CAS  Google Scholar 

  56. Kelley LA, Sternberg MJE (2009) Nat Protocols 4:363–371

    Article  CAS  Google Scholar 

  57. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) Nucleic Acids Res 33:W363–W367

    PubMed  Article  CAS  Google Scholar 

  58. Guo X, Bandyopadhyay P, Schilling B, Young MM, Fujii N, Aynechi T, Guy RK, Kuntz ID, Gibson BW (2008) Anal Chem 80:951–960

    PubMed  Article  CAS  Google Scholar 

  59. Kahraman A, Malmström L, Aebersold R (2011) Bioinformatics 27:2163–2164

    PubMed  Article  CAS  Google Scholar 

  60. Taverner T, Hall NE, O’Hair RAJ, Simpson RJ (2002) J Biol Chem 277:46487–46492

    PubMed  Article  CAS  Google Scholar 

  61. Guo X, Schilling B, Young M, Medzihradsky M, Kuntz ID, Guy RK, Gibson BW (2002) Using homobifunctional crosslinking reagents with normal and N-15 labeled proteins for the determination of protein tertiary structure and protein–protein interactions. Annual Conference of the American Society of Mass Spectrometry, Orlando, FL, USA

  62. Bohrer BC, Mererbloom SI, Koeniger SL, Hilderbrand AE, Clemmer DE (2008) Biomolecule Analysis by Ion Mobility Spectrometry. Annual Review of Analytical Chemistry, vol 1. Annual Review of Analytical Chemistry. Annual Reviews, Palo Alto, pp 293–327

  63. Back JW, de Jong L, Muijsers AO, de Koster CG (2003) J Mol Biol 331:303–313

    PubMed  Article  CAS  Google Scholar 

  64. Janssens V, Goris J (2001) Biochem J 353:417–439

    PubMed  Article  CAS  Google Scholar 

  65. Gingras A-C, Gstaiger M, Raught B, Aebersold R (2007) Nat Rev Mol Cell Biol 8:645–654

    PubMed  Article  CAS  Google Scholar 

  66. Gingras AC, Raught B (2012) FEBS Lett 586:2723–2731

    PubMed  Article  CAS  Google Scholar 

  67. Xu Y, Chen Y, Zhang P, Jeffrey PD, Shi Y (2008) Mol Cell 31:873–885

    PubMed  Article  CAS  Google Scholar 

  68. Xu Z, Cetin B, Anger M, Cho US, Helmhart W, Nasmyth K, Xu W (2009) Mol Cell 35:426–441

    PubMed  Article  CAS  Google Scholar 

  69. Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YEA, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popovic Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P (2011) Rosetta3: an object-oriented software suite for the simulation and design of macromolecules. In: Johnson ML, Brand L (eds) Methods in Enzymology, vol 487: computer methods, Pt C. methods in enzymology. Elsevier Academic Press Inc, San Diego, pp 545–574

    Google Scholar 

  70. Das R, Baker D (2008) Ann Rev Biochem 77:363–382

    PubMed  Article  CAS  Google Scholar 

  71. Kaufmann KW, Lemmon GH, DeLuca SL, Sheehan JH, Meiler J (2010) Biochemistry 49:2987–2998

    PubMed  Article  CAS  Google Scholar 

  72. Schulz DM, Ihling C, Clore GM, Sinz A (2004) Biochemistry 43:4703–4715

    PubMed  Article  CAS  Google Scholar 

  73. Zhang HZ, Tang XT, Munske GR, Zakharova N, Yang L, Zheng CX, Wolff MA, Tolic N, Anderson GA, Shi L, Marshall MJ, Fredrickson JK, Bruce JE (2008) J Proteome Res 7:1712–1720

    PubMed  Article  CAS  Google Scholar 

  74. Mealman TD, Bagai I, Singh P, Goodlett DR, Rensing C, Zhou H, Wysocki VH, McEvoy MM (2011) Biochemistry 50:2559–2566

    PubMed  Article  CAS  Google Scholar 

  75. Mädler S, Seitz M, Robinson J, Zenobi R (2010) J Am Soc Mass Spectrom 21:1775–1783

    PubMed  Article  Google Scholar 

  76. Kindy JM, Taraszka JA, Regnier FE, Clemmer DE (2002) Anal Chem 74:950–958

    Google Scholar 

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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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Authors and Affiliations

  1. MS K8-98, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA

    Eric D. Merkley, John R. Cort & Joshua N. Adkins

Authors
  1. Eric D. Merkley
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  2. John R. Cort
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  3. Joshua N. Adkins
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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