Skip to main content
SpringerLink
Log in

Targeted Cross-Linking Mass Spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae

  • Protocol
  • First Online:
Proteomics in Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2456))

Abstract

Protein cross-linking mass spectrometry (XL-MS) has been developed into a powerful and robust tool that is now well implemented and routinely used by an increasing number of laboratories. While bulk cross-linking of complexes provides useful information on whole complexes, it is limiting for the probing of specific protein “neighbourhoods,” or vicinity interactomes. For example, it is not unusual to find cross-linked peptide pairs that are disproportionately overrepresented compared to the surface areas of complexes, while very few or no cross-links are identified in other regions. When studying dynamic complexes along their pathways, some vicinity cross-links may be of too low abundance in the pool of heterogenous complexes of interest to be efficiently identified by standard XL-MS. In this chapter, we describe a targeted XL-MS approach from single-step affinity purified (ssAP) complexes that enables the investigation of specific protein “neighbourhoods” within molecular complexes in yeast, using a small cross-linker anchoring tag, the CH-tag. One advantage of this method over a general cross-linking strategy is the possibility to significantly enrich for localized anchored-cross-links within complexes, thus yielding a higher sensitivity to detect highly dynamic or low abundance protein interactions within a specific protein “neighbourhood” occurring along the pathway of a selected bait protein. Moreover, many variations of the method can be employed; the ssAP-tag and the CH-tag can either be fused to the same or different proteins in the complex, or the CH-tag can be fused to multiple protein components in the same cell line to explore dynamic vicinity interactions along a pathway.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Piersimoni L, Sinz A (2020) Cross-linking/mass spectrometry at the crossroads. Anal Bioanal Chem 412:5981–5987. https://doi.org/10.1007/s00216-020-02700-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Leitner A, Faini M, Stengel F, Aebersold R (2016) Crosslinking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines. Trends Biochem Sci 41:20–32. https://doi.org/10.1016/j.tibs.2015.10.008

    Article  CAS  PubMed  Google Scholar 

  3. Yu C, Huang L (2018) Cross-linking mass spectrometry (XL-MS): an emerging technology for interactomics and structural biology. Anal Chem 90:144–165. https://doi.org/10.1021/acs.analchem.7b04431

    Article  CAS  PubMed  Google Scholar 

  4. O’Reilly FJ, Rappsilber J (2018) Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology. Nat Struct Mol Biol 25:1000–1008. https://doi.org/10.1038/s41594-018-0147-0

    Article  CAS  PubMed  Google Scholar 

  5. Tang X, Wippel HH, Chavez JD, Bruce JE (2021) Crosslinking mass spectrometry: a link between structural biology and systems biology. Protein Sci 30:773–784. https://doi.org/10.1002/pro.4045

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Kim D, Setiaputra D, Jung T, Chung J, Leitner A, Yoon J, Aebersold R, Hebert H, Yip CK, Song J-J (2016) Molecular architecture of yeast chromatin assembly factor 1. Sci Rep 6:26702. https://doi.org/10.1038/srep26702

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Harrer N, Schindler CEM, Bruetzel LK, Forné I, Ludwigsen J, Imhof A, Zacharias M, Lipfert J, Mueller-Planitz F (2018) Structural architecture of the nucleosome remodeler ISWI determined from cross-linking, mass spectrometry, SAXS, and modeling. Structure 26:282–294.e6. https://doi.org/10.1016/j.str.2017.12.015

    Article  CAS  PubMed  Google Scholar 

  8. Kang JJ, Faubert D, Boulais J, Francis NJ (2020) DNA binding reorganizes the intrinsically disordered C-terminal region of PSC in drosophila PRC1. J Mol Biol 432:4856–4871. https://doi.org/10.1016/j.jmb.2020.07.002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Mashtalir N, Suzuki H, Farrell DP, Sankar A, Luo J, Filipovski M, D’Avino AR, St. Pierre R, Valencia AM, Onikubo T, Roeder RG, Han Y, He Y, Ranish JA, DiMaio F, Walz T, Kadoch C (2020) A structural model of the endogenous human BAF complex informs disease mechanisms. Cell 183:802–817.e24. https://doi.org/10.1016/j.cell.2020.09.051

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex: cell. https://www.cell.com/fulltext/S0092-8674(13)01010-6. Accessed 3 Jun 2021

  11. Nguyen VQ, Ranjan A, Stengel F, Wei D, Aebersold R, Wu C, Leschziner AE (2013) Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1. Cell 154:1220–1231. https://doi.org/10.1016/j.cell.2013.08.018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kloet SL, Baymaz HI, Makowski M, Groenewold V, Jansen PWTC, Berendsen M, Niazi H, Kops GJ, Vermeulen M (2015) Towards elucidating the stability, dynamics and architecture of the nucleosome remodeling and deacetylase complex by using quantitative interaction proteomics. FEBS J 282:1774–1785. https://doi.org/10.1111/febs.12972

    Article  CAS  PubMed  Google Scholar 

  13. Fasci D, van Ingen H, Scheltema RA, Heck AJR (2018) Histone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei. Mol Cell Proteomics 17:2018–2033. https://doi.org/10.1074/mcp.RA118.000924

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Chen ZA, Jawhari A, Fischer L, Buchen C, Tahir S, Kamenski T, Rasmussen M, Lariviere L, Bukowski-Wills J-C, Nilges M, Cramer P, Rappsilber J (2010) Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J 29:717–726. https://doi.org/10.1038/emboj.2009.401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Blattner C, Jennebach S, Herzog F, Mayer A, Cheung ACM, Witte G, Lorenzen K, Hopfner K-P, Heck AJR, Aebersold R, Cramer P (2011) Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes Dev 25:2093–2105. https://doi.org/10.1101/gad.17363311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Jennebach S, Herzog F, Aebersold R, Cramer P (2012) Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage. Nucleic Acids Res 40:5591–5601. https://doi.org/10.1093/nar/gks220

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Luo J, Fishburn J, Hahn S, Ranish J (2012) An integrated chemical cross-linking and mass spectrometry approach to study protein complex architecture and function. Mol Cell Proteomics MCP 11:M111.008318. https://doi.org/10.1074/mcp.M111.008318

    Article  CAS  PubMed  Google Scholar 

  18. Murakami K, Elmlund H, Kalisman N, Bushnell DA, Adams CM, Azubel M, Elmlund D, Levi-Kalisman Y, Liu X, Gibbons BJ, Levitt M, Kornberg RD (2013) Architecture of an RNA polymerase II transcription pre-initiation complex. Science 342:1238724. https://doi.org/10.1126/science.1238724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Mühlbacher W, Sainsbury S, Hemann M, Hantsche M, Neyer S, Herzog F, Cramer P (2014) Conserved architecture of the core RNA polymerase II initiation complex. Nat Commun 5:4310. https://doi.org/10.1038/ncomms5310

    Article  CAS  PubMed  Google Scholar 

  20. Martinez-Rucobo FW, Kohler R, van de Waterbeemd M, Heck AJR, Hemann M, Herzog F, Stark H, Cramer P (2015) Molecular basis of transcription-coupled pre-mRNA capping. Mol Cell 58:1079–1089. https://doi.org/10.1016/j.molcel.2015.04.004

    Article  CAS  PubMed  Google Scholar 

  21. Robinson PJJ, Bushnell DA, Trnka MJ, Burlingame AL, Kornberg RD (2012) Structure of the mediator head module bound to the carboxy-terminal domain of RNA polymerase II. Proc Natl Acad Sci U S A 109:17931–17935. https://doi.org/10.1073/pnas.1215241109

    Article  PubMed  PubMed Central  Google Scholar 

  22. Plaschka C, Larivière L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P (2015) Architecture of the RNA polymerase II-mediator core initiation complex. Nature 518:376–380. https://doi.org/10.1038/nature14229

    Article  CAS  PubMed  Google Scholar 

  23. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD (2015) Molecular architecture of the yeast mediator complex. eLife 4:e08719. https://doi.org/10.7554/eLife.08719

    Article  PubMed  PubMed Central  Google Scholar 

  24. Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J (2015) Architecture of the human and yeast general transcription and DNA repair factor TFIIH. Mol Cell 59:794–806. https://doi.org/10.1016/j.molcel.2015.07.016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Murakami K, Tsai K-L, Kalisman N, Bushnell DA, Asturias FJ, Kornberg RD (2015) Structure of an RNA polymerase II preinitiation complex. Proc Natl Acad Sci U S A 112:13543–13548. https://doi.org/10.1073/pnas.1518255112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Sadian Y, Tafur L, Kosinski J, Jakobi AJ, Wetzel R, Buczak K, Hagen WJ, Beck M, Sachse C, Müller CW (2017) Structural insights into transcription initiation by yeast RNA polymerase I. EMBO J 36:2698–2709. https://doi.org/10.15252/embj.201796958

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Wu C-C, Herzog F, Jennebach S, Lin Y-C, Pai C-Y, Aebersold R, Cramer P, Chen H-T (2012) RNA polymerase III subunit architecture and implications for open promoter complex formation. Proc Natl Acad Sci U S A 109:19232–19237. https://doi.org/10.1073/pnas.1211665109

    Article  PubMed  PubMed Central  Google Scholar 

  28. Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP (2016) Structure and function of the nuclear pore complex cytoplasmic mRNA export platform. Cell 167:1215–1228.e25. https://doi.org/10.1016/j.cell.2016.10.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Zhong X, Wu X, Schweppe DK, Chavez JD, Mathay M, Eng JK, Keller A, Bruce JE (2020) In vivo cross-linking MS reveals conservation in OmpA linkage to different classes of β-lactamase enzymes. J Am Soc Mass Spectrom 31:190–195. https://doi.org/10.1021/jasms.9b00021

    Article  CAS  PubMed  Google Scholar 

  30. Wittig S, Ganzella M, Barth M, Kostmann S, Riedel D, Pérez-Lara Á, Jahn R, Schmidt C (2021) Cross-linking mass spectrometry uncovers protein interactions and functional assemblies in synaptic vesicle membranes. Nat Commun 12:858. https://doi.org/10.1038/s41467-021-21102-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP (2018) Integrative structure and functional anatomy of a nuclear pore complex. Nature 555:475–482. https://doi.org/10.1038/nature26003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT (2014) Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol Cell Proteomics MCP 13:2927–2943. https://doi.org/10.1074/mcp.M114.041673

    Article  CAS  PubMed  Google Scholar 

  33. Thierbach K, von Appen A, Thoms M, Beck M, Flemming D, Hurt E (2013) Protein interfaces of the conserved Nup84 complex from Chaetomium thermophilum shown by crosslinking mass spectrometry and electron microscopy. Structure 21:1672–1682. https://doi.org/10.1016/j.str.2013.07.004

    Article  CAS  PubMed  Google Scholar 

  34. Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Chait BT, Almo SC, Rout MP, Sali A (2014) Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. Mol Cell Proteomics MCP 13:2911–2926. https://doi.org/10.1074/mcp.M114.040915

    Article  CAS  PubMed  Google Scholar 

  35. von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull M-T, Banterle N, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, Bork P, Antonin W, Glavy JS, Bui KH, Beck M (2015) In situ structural analysis of the human nuclear pore complex. Nature 526:140–143. https://doi.org/10.1038/nature15381

    Article  CAS  Google Scholar 

  36. Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N (2014) Molecular architecture of the 40S·eIF1·eIF3 translation initiation complex. Cell 158:1123–1135. https://doi.org/10.1016/j.cell.2014.07.044

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Lauber MA, Reilly JP (2011) Structural analysis of a prokaryotic ribosome using a novel amidinating cross-linker and mass spectrometry. J Proteome Res 10(8):3604–3616. https://pubs.acs.org/doi/10.1021/pr200260n. Accessed 3 Jun 2021

    Article  CAS  PubMed  Google Scholar 

  38. Lauber MA, Rappsilber J, Reilly JP (2012) Dynamics of ribosomal protein S1 on a bacterial ribosome with cross-linking and mass spectrometry. Mol Cell Proteomics 11:1965–1976. https://doi.org/10.1074/mcp.M112.019562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Greber BJ, Boehringer D, Leibundgut M, Bieri P, Leitner A, Schmitz N, Aebersold R, Ban N (2014) The complete structure of the large subunit of the mammalian mitochondrial ribosome. Nature 515:283–286. https://doi.org/10.1038/nature13895

    Article  CAS  PubMed  Google Scholar 

  40. Greber BJ, Bieri P, Leibundgut M, Leitner A, Aebersold R, Boehringer D, Ban N (2015) Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome. Science 348:303–308. https://doi.org/10.1126/science.aaa3872

    Article  CAS  PubMed  Google Scholar 

  41. Kiosze-Becker K, Ori A, Gerovac M, Heuer A, Nürenberg-Goloub E, Rashid UJ, Becker T, Beckmann R, Beck M, Tampé R (2016) Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry. Nat Commun 7:13248. https://doi.org/10.1038/ncomms13248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Tüting C, Iacobucci C, Ihling CH, Kastritis PL, Sinz A (2020) Structural analysis of 70S ribosomes by cross-linking/mass spectrometry reveals conformational plasticity. Sci Rep 10:12618. https://doi.org/10.1038/s41598-020-69313-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Götze M, Iacobucci C, Ihling CH, Sinz A (2019) A simple cross-linking/mass spectrometry workflow for studying system-wide protein interactions. Anal Chem 91:10236–10244. https://doi.org/10.1021/acs.analchem.9b02372

    Article  CAS  PubMed  Google Scholar 

  44. de Oliveira LC, Volpon L, Rahardjo AK, Osborne MJ, Culjkovic-Kraljacic B, Trahan C, Oeffinger M, Kwok BH, Borden KLB (2019) Structural studies of the eIF4E–VPg complex reveal a direct competition for capped RNA: implications for translation. Proc Natl Acad Sci U S A 116:24056–24065. https://doi.org/10.1073/pnas.1904752116

    Article  CAS  Google Scholar 

  45. Sharon M, Taverner T, Ambroggio XI, Deshaies RJ, Robinson CV (2006) Structural organization of the 19S proteasome lid: insights from MS of intact complexes. PLoS Biol 4:e267. https://doi.org/10.1371/journal.pbio.0040267

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Bohn S, Beck F, Sakata E, Walzthoeni T, Beck M, Aebersold R, Förster F, Baumeister W, Nickell S (2010) Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution. Proc Natl Acad Sci U S A 107:20992–20997. https://doi.org/10.1073/pnas.1015530107

    Article  PubMed  PubMed Central  Google Scholar 

  47. Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W (2012) Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci U S A 109:1380–1387. https://doi.org/10.1073/pnas.1120559109

    Article  PubMed  PubMed Central  Google Scholar 

  48. Kao A, Randall A, Yang Y, Patel VR, Kandur W, Guan S, Rychnovsky SD, Baldi P, Huang L (2012) Mapping the structural topology of the yeast 19S proteasomal regulatory particle using chemical cross-linking and probabilistic modeling. Mol Cell Proteomics 11:1566–1577. https://doi.org/10.1074/mcp.M112.018374

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. 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) Identification of cross-linked peptides from complex samples. Nat Methods 9:904–906. https://doi.org/10.1038/nmeth.2099

    Article  CAS  PubMed  Google Scholar 

  50. Pflieger D, Jünger MA, Müller M, Rinner O, Lee H, Gehrig PM, Gstaiger M, Aebersold R (2008) Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation. Mol Cell Proteomics 7:326–346. https://doi.org/10.1074/mcp.M700282-MCP200

    Article  CAS  PubMed  Google Scholar 

  51. Xu H, Hsu P-H, Zhang L, Tsai M-D, Freitas MA (2010) Database search algorithm for identification of intact cross-links in proteins and peptides using tandem mass spectrometry. J Proteome Res 9:3384–3393. https://doi.org/10.1021/pr100369y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Buncherd H, Roseboom W, de Koning LJ, de Koster CG, de Jong L (2014) A gas phase cleavage reaction of cross-linked peptides for protein complex topology studies by peptide fragment fingerprinting from large sequence database. J Proteome 108:65–77. https://doi.org/10.1016/j.jprot.2014.05.003

    Article  CAS  Google Scholar 

  53. Liu F, Rijkers DTS, Post H, Heck AJR (2015) Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry. Nat Methods 12:1179–1184. https://doi.org/10.1038/nmeth.3603

    Article  CAS  PubMed  Google Scholar 

  54. Liu F, Lössl P, Scheltema R, Viner R, Heck AJR (2017) Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. Nat Commun 8:15473. https://doi.org/10.1038/ncomms15473

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Tan D, Li Q, Zhang M-J, Liu C, Ma C, Zhang P, Ding Y-H, Fan S-B, Tao L, Yang B, Li X, Ma S, Liu J, Feng B, Liu X, Wang H-W, He S-M, Gao N, Ye K, Dong M-Q, Lei X (2016) Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states. Elife 5:e12509. https://doi.org/10.7554/eLife.12509

    Article  PubMed  PubMed Central  Google Scholar 

  56. Zhang H, Tang X, Munske GR, Tolic N, Anderson GA, Bruce JE (2009) Identification of protein-protein interactions and topologies in living cells with chemical cross-linking and mass spectrometry. Mol Cell Proteomics 8:409–420. https://doi.org/10.1074/mcp.M800232-MCP200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Navare AT, Chavez JD, Zheng C, Weisbrod CR, Eng JK, Siehnel R, Singh PK, Manoil C, Bruce JE (2015) probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry. Structure 23:762–773. https://doi.org/10.1016/j.str.2015.01.022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Wu X, Chavez JD, Schweppe DK, Zheng C, Weisbrod CR, Eng JK, Murali A, Lee SA, Ramage E, Gallagher LA, Kulasekara HD, Edrozo ME, Kamischke CN, Brittnacher MJ, Miller SI, Singh PK, Manoil C, Bruce JE (2016) In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075. Nat Commun 7:13414. https://doi.org/10.1038/ncomms13414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Zhong X, Navare AT, Chavez JD, Eng JK, Schweppe DK, Bruce JE (2017) Large-scale and targeted quantitative cross-linking MS using isotope-labeled protein interaction reporter (PIR) cross-linkers. J Proteome Res 16:720–727. https://doi.org/10.1021/acs.jproteome.6b00752

    Article  CAS  PubMed  Google Scholar 

  60. Chavez JD, Weisbrod CR, Zheng C, Eng JK, Bruce JE (2013) Protein interactions, post-translational modifications and topologies in human cells. Mol Cell Proteomics 12:1451–1467. https://doi.org/10.1074/mcp.M112.024497

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Schweppe DK, Chavez JD, Lee CF, Caudal A, Kruse SE, Stuppard R, Marcinek DJ, Shadel GS, Tian R, Bruce JE (2017) Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry. Proc Natl Acad Sci U S A 114:1732–1737. https://doi.org/10.1073/pnas.1617220114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. de Jong L, de Koning EA, Roseboom W, Buncherd H, Wanner MJ, Dapic I, Jansen PJ, van Maarseveen JH, Corthals GL, Lewis PJ, Hamoen LW, de Koster CG (2017) In-culture cross-linking of bacterial cells reveals large-scale dynamic protein-protein interactions at the peptide level. J Proteome Res 16:2457–2471. https://doi.org/10.1021/acs.jproteome.7b00068

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Trahan C, Oeffinger M (2016) Targeted cross-linking-mass spectrometry determines vicinal interactomes within heterogeneous RNP complexes. Nucleic Acids Res 44:1354–1369. https://doi.org/10.1093/nar/gkv1366

    Article  CAS  PubMed  Google Scholar 

  64. Oeffinger M, Wei KE, Rogers R, DeGrasse JA, Chait BT, Aitchison JD, Rout MP (2007) Comprehensive analysis of diverse ribonucleoprotein complexes. Nat Methods 4:951–956. https://doi.org/10.1038/nmeth1101

    Article  CAS  PubMed  Google Scholar 

  65. Trahan C, Oeffinger M (2021) Single-step affinity purification (ssAP) and mass spectrometry of macromolecular complexes in the Yeast S. cerevisiae. Methods Mol Biol 1361:265–287

    Article  Google Scholar 

  66. Miseta A, Csutora P (2000) Relationship between the occurrence of cysteine in proteins and the complexity of organisms. Mol Biol Evol 17:1232–1239. https://doi.org/10.1093/oxfordjournals.molbev.a026406

    Article  CAS  PubMed  Google Scholar 

  67. Krishna MMG, Englander SW (2005) The N-terminal to C-terminal motif in protein folding and function. Proc Natl Acad Sci U S A 102:1053–1058. https://doi.org/10.1073/pnas.0409114102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Laughery MF, Hunter T, Brown A, Hoopes J, Ostbye T, Shumaker T, Wyrick JJ (2015) New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae. Yeast 32:711–720. https://doi.org/10.1002/yea.3098

    Article  CAS  PubMed  Google Scholar 

  69. Hofmann T, Fischer AW, Meiler J, Kalkhof S (2015) Protein structure prediction guided by crosslinking restraints—A systematic evaluation of the impact of the crosslinking spacer length. Methods 89:79–90. https://doi.org/10.1016/j.ymeth.2015.05.014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, Förster 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:M111.014126. https://doi.org/10.1074/mcp.M111.014126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Kessner D, Chambers M, Burke R, Agus D, Mallick P (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24:2534–2536. https://doi.org/10.1093/bioinformatics/btn323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Chi H, Liu C, Yang H, Zeng W-F, Wu L, Zhou W-J, Wang R-M, Niu X-N, Ding Y-H, Zhang Y, Wang Z-W, Chen Z-L, Sun R-X, Liu T, Tan G-M, Dong M-Q, Xu P, Zhang P-H, He S-M (2018) Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine. Nat Biotechnol 36:1059–1061. https://doi.org/10.1038/nbt.4236

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We thank Denis Faubert for mass spectrometry support during the initial development of the method as well as the pFind Studio team, especially Shengbo Fan and Pengzhi Mao, for adapting pLink and pLink2, respectively. C.T is supported by funding awarded to M.O. from the Canadian Institutes for Health Research (PJT153313).

Author information

Authors and Affiliations

  1. Institut de recherches cliniques de Montréal, Montréal, QC, Canada

    Christian Trahan & Marlene Oeffinger

  2. Département de biochimie, Faculté de médecine, Université de Montréal, Montréal, QC, Canada

    Marlene Oeffinger

  3. Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada

    Marlene Oeffinger

Authors
  1. Christian Trahan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marlene Oeffinger
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Marlene Oeffinger .

Editor information

Editors and Affiliations

  1. Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada

    Jennifer Geddes-McAlister

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Trahan, C., Oeffinger, M. (2022). Targeted Cross-Linking Mass Spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae. In: Geddes-McAlister, J. (eds) Proteomics in Systems Biology. Methods in Molecular Biology, vol 2456. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2124-0_13

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2124-0_13

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2123-3

  • Online ISBN: 978-1-0716-2124-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation