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Semi-synthesis of disulfide-linked branched tri-ubiquitin mimics

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Abstract

Ubiquitin (Ub) chain isopeptide bond mimics are useful molecules for biochemical and biophysical studies. Herein, we report the semi-synthesis of the disulfide-linked K11/K48-branched tri-Ub (Ub311/48(S–S)), the first example of an isopeptide mimic for the branched Ub chains, which have recently emerged as an interesting category of Ub modifications. Our strategy comprised the E1-dependent synthesis of the Ub conjugate of aminoethanethiol, followed by disulfide formation with Ub(K11C, K48C). The structure of the synthetic isopeptide bond mimics was verified by the crystal structure of Ub311/48(S–S). Deubiquitination and pulldown assays indicated that the synthetic Ub311/48(S–S) could be hydrolyzed by linkage-specific deubiquitinases (K11-specific Cezanne and K48-specific OTUB1), and recognized by proteasomal ubiquitin receptor S5a.

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References

  1. Hershko A, Ciechanover A. Annu Rev Biochem, 1998, 67: 425–479

    Article  CAS  PubMed  Google Scholar 

  2. Kulathu Y, Komander D. Nat Rev Mol Cell Biol, 2012, 13: 508–523

    Article  CAS  PubMed  Google Scholar 

  3. Emmerich CH, Ordureau A, Strickson S, Arthur JSC, Pedrioli PGA, Komander D, Cohen P. Proc Natl Acad Sci USA, 2013, 110: 15247–15252

    Article  PubMed  Google Scholar 

  4. Swatek KN, Komander D. Cell Res, 2016, 26: 399–422

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Kim HT, Kim KP, Lledias F, Kisselev AF, Scaglione KM, Skowyra D, Gygi SP, Goldberg AL. J Biol Chem, 2007, 282: 17375–17386

    Article  CAS  PubMed  Google Scholar 

  6. Meyer HJ, Rape M. Cell, 2014, 157: 910–921

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Ohtake F, Saeki Y, Ishido S, Kanno J, Tanaka K. Mol Cell, 2016, 64: 251–266

    Article  CAS  PubMed  Google Scholar 

  8. Liu C, Liu W, Ye Y, Li W. Nat Commun, 2017, 8: 14274–14289

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP. Nat Biotech, 2003, 21: 921–926

    Article  CAS  Google Scholar 

  10. Hemantha HP, Brik A. Bioorg Med Chem, 2013, 21: 3411–3420

    Article  CAS  PubMed  Google Scholar 

  11. Dixon EK, Castañeda CA, Kashyap TR, Wang Y, Fushman D. Bioorg Med Chem, 2013, 21: 3421–3429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Virdee S, Ye Y, Nguyen DP, Komander D, Chin JW. Nat Chem Biol, 2010, 6: 750–757

    Article  CAS  PubMed  Google Scholar 

  13. El Oualid F, Merkx R, Ekkebus R, Hameed DS, Smit JJ, de Jong A, Hilkmann H, Sixma TK, Ovaa H. Angew Chem Int Ed, 2010, 49: 10149–10153

    Article  CAS  Google Scholar 

  14. Kumar KSA, Spasser L, Erlich LA, Bavikar SN, Brik A. Angew Chem Int Ed, 2010, 49: 9126–9131

    Article  CAS  Google Scholar 

  15. Kumar KSA, Bavikar SN, Spasser L, Moyal T, Ohayon S, Brik A. Angew Chem Int Ed, 2011, 50: 6137–6141

    Article  CAS  Google Scholar 

  16. Pan M, Gao S, Zheng Y, Tan X, Lan H, Tan X, Sun D, Lu L, Wang T, Zheng Q, Huang Y, Wang J, Liu L. J Am Chem Soc, 2016, 138: 7429–7435

    Article  CAS  PubMed  Google Scholar 

  17. Gao S, Pan M, Zheng Y, Huang Y, Zheng Q, Sun D, Lu L, Tan X, Tan X, Lan H, Wang J, Wang T, Wang J, Liu L. J Am Chem Soc, 2016, 138: 14497–14502

    Article  CAS  PubMed  Google Scholar 

  18. Tang S, Liang LJ, Si YY, Gao S, Wang JX, Liang J, Mei Z, Zheng JS, Liu L. Angew Chem Int Ed, 2017, 56: 13333–13337

    Article  CAS  Google Scholar 

  19. Meledin R, Mali SM, Singh SK, Brik A. Org Biomol Chem, 2016, 14: 4817–4823

    Article  CAS  PubMed  Google Scholar 

  20. Huang Y, Liu L. Sci China Chem, 2015, 58: 1779–1781

    Article  CAS  Google Scholar 

  21. Lee CL, Li X. Sci China Chem, 2016, 59: 1061–1064

    Article  CAS  Google Scholar 

  22. Huang YC, Fang GM, Liu L. Natl Sci Rev, 2016, 3: 107–116

    Article  CAS  Google Scholar 

  23. Li H, Dong S. Sci China Chem, 2017, 60: 201–213

    Article  CAS  Google Scholar 

  24. He Q, Li J, Qi Y, Wang Z, Huang Y, Liu L. Sci China Chem, 2017, 60: 621–627

    Article  CAS  Google Scholar 

  25. Lewis YE, Abeywardana T, Lin YH, Galesic A, Pratt MR. ACS Chem Biol, 2016, 11: 931–942

    Article  CAS  PubMed  Google Scholar 

  26. Chatterjee C, McGinty RK, Fierz B, Muir TW. Nat Chem Biol, 2010, 6: 267–269

    Article  CAS  PubMed  Google Scholar 

  27. Chen J, Ai Y, Wang J, Haracska L, Zhuang Z. Nat Chem Biol, 2010, 6: 270–272

    Article  CAS  PubMed  Google Scholar 

  28. Hemantha HP, Bavikar SN, Herman-Bachinsky Y, Haj-Yahya N, Bondalapati S, Ciechanover A, Brik A. J Am Chem Soc, 2014, 136: 2665–2673

    Article  CAS  PubMed  Google Scholar 

  29. Holt MT, David Y, Pollock S, Tang Z, Jeon J, Kim J, Roeder RG, Muir TW. Proc Natl Acad Sci USA, 2015, 112: 10365–10370

    Article  CAS  PubMed  Google Scholar 

  30. Debelouchina GT, Gerecht K, Muir TW. Nat Chem Biol, 2017, 13: 105–110

    Article  CAS  PubMed  Google Scholar 

  31. Shanmugham A, Fish A, Luna-Vargas MPA, Faesen AC, El Oualid F, Sixma TK, Ovaa H. J Am Chem Soc, 2010, 132: 8834–8835

    Article  CAS  PubMed  Google Scholar 

  32. Singh SK, Sahu I, Mali SM, Hemantha HP, Kleifeld O, Glickman MH, Brik A. J Am Chem Soc, 2016, 138: 16004–16015

    Article  CAS  PubMed  Google Scholar 

  33. Mali SM, Singh SK, Eid E, Brik A. J Am Chem Soc, 2017, 139: 4971–4986

    Article  CAS  Google Scholar 

  34. Wang XA, Kurra Y, Huang Y, Lee YJ, Liu WR. ChemBioChem, 2014, 15: 37–41

    Article  CAS  PubMed  Google Scholar 

  35. Dong KC, Helgason E, Yu C, Phu L, Arnott DP, Bosanac I, Compaan DM, Huang OW, Fedorova AV, Kirkpatrick DS, Hymowitz SG, Dueber EC. Structure, 2011, 19: 1053–1063

    Article  CAS  PubMed  Google Scholar 

  36. Bremm A, Freund SMV, Komander D. Nat Struct Mol Biol, 2010, 17: 939–947

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Mevissen TET, Kulathu Y, Mulder MPC, Geurink PP, Maslen SL, Gersch M, Elliott PR, Burke JE, van Tol BDM, Akutsu M, El Oualid F, Kawasaki M, Freund SMV, Ovaa H, Komander D. Nature, 2016, 538: 402–405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Wang T, Yin L, Cooper EM, Lai MY, Dickey S, Pickart CM, Fushman D, Wilkinson KD, Cohen RE, Wolberger C. J Mol Biol, 2009, 386: 1011–1023

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Edelmann MJ, Iphöfer A, Akutsu M, Altun M, di Gleria K, Kramer HB, Fiebiger E, Dhe-Paganon S, Kessler BM. Biochem J, 2009, 418: 379–390

    Article  CAS  PubMed  Google Scholar 

  40. Mevissen TET, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SMV, Ovaa H, Komander D. Cell, 2013, 154: 169–184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Mevissen TET, Komander D. Annu Rev Biochem, 2017, 86: 159–192

    Article  CAS  PubMed  Google Scholar 

  42. Zhang N, Wang Q, Ehlinger A, Randles L, Lary JW, Kang Y, Haririnia A, Storaska AJ, Cole JL, Fushman D, Walters KJ. Mol Cell, 2009, 35: 280–290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported by the National Key R&D Program of China (2017YFA0505200), the National Natural Science Foundation of China (91753205, 21532004, 21761142008), and the Program of Introducing Talents of Discipline to Universities of China (B16028).

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Correspondence to Lei Liu.

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Si, Y., Liang, L., Tang, S. et al. Semi-synthesis of disulfide-linked branched tri-ubiquitin mimics. Sci. China Chem. 61, 412–417 (2018). https://doi.org/10.1007/s11426-017-9189-6

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  • DOI: https://doi.org/10.1007/s11426-017-9189-6

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