Repurposing a plant peptide cyclase for targeted lysine acylation.
Journal
Nature chemistry
ISSN: 1755-4349
Titre abrégé: Nat Chem
Pays: England
ID NLM: 101499734
Informations de publication
Date de publication:
24 May 2024
24 May 2024
Historique:
received:
10
10
2022
accepted:
25
03
2024
medline:
25
5
2024
pubmed:
25
5
2024
entrez:
24
5
2024
Statut:
aheadofprint
Résumé
Transpeptidases are powerful tools for protein engineering but are largely restricted to acting at protein backbone termini. Alternative enzymatic approaches for internal protein labelling require bulky recognition motifs or non-proteinogenic reaction partners, potentially restricting which proteins can be modified or the types of modification that can be installed. Here we report a strategy for labelling lysine side chain ε-amines by repurposing an engineered asparaginyl ligase, which naturally catalyses peptide head-to-tail cyclization, for versatile isopeptide ligations that are compatible with peptidic substrates. We find that internal lysines with an adjacent leucine residue mimic the conventional N-terminal glycine-leucine substrate. This dipeptide motif enables efficient intra- or intermolecular ligation through internal lysine side chains, minimally leaving an asparagine C-terminally linked to the lysine side chain via an isopeptide bond. The versatility of this approach is demonstrated by the chemoenzymatic synthesis of peptides with non-native C terminus-to-side chain topology and the conjugation of chemically modified peptides to recombinant proteins.
Identifiants
pubmed: 38789555
doi: 10.1038/s41557-024-01520-1
pii: 10.1038/s41557-024-01520-1
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024. The Author(s).
Références
Stephanopoulos, N. & Francis, M. B. Choosing an effective protein bioconjugation strategy. Nat. Chem. Biol. 7, 876–884 (2011).
pubmed: 22086289
doi: 10.1038/nchembio.720
Boutureira, O. & Bernardes, G. J. Advances in chemical protein modification. Chem. Rev. 115, 2174–2195 (2015).
pubmed: 25700113
doi: 10.1021/cr500399p
Zhang, Y., Park, K. Y., Suazo, K. F. & Distefano, M. D. Recent progress in enzymatic protein labelling techniques and their applications. Chem. Soc. Rev. 47, 9106–9136 (2018).
pubmed: 30259933
pmcid: 6289631
doi: 10.1039/C8CS00537K
Shah, N. H. & Muir, T. W. Inteins: Nature’s gift to protein chemists. Chem. Sci. 5, 446–461 (2014).
pubmed: 24634716
doi: 10.1039/C3SC52951G
Morgan, H. E., Turnbull, W. B. & Webb, M. E. Challenges in the use of sortase and other peptide ligases for site-specific protein modification. Chem. Soc. Rev. 51, 4121–4145 (2022).
pubmed: 35510539
pmcid: 9126251
doi: 10.1039/D0CS01148G
Weeks, A. M. & Wells, J. A. Subtiligase-catalyzed peptide ligation. Chem. Rev. 120, 3127–3160 (2020).
pubmed: 31663725
doi: 10.1021/acs.chemrev.9b00372
Lotze, J., Reinhardt, U., Seitz, O. & Beck-Sickinger, A. G. Peptide-tags for site-specific protein labelling in vitro and in vivo. Mol. Biosyst. 12, 1731–1745 (2016).
pubmed: 26960991
doi: 10.1039/C6MB00023A
Zakeri, B. et al. Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proc. Natl Acad. Sci. USA 109, E690–E697 (2012).
pubmed: 22366317
pmcid: 3311370
doi: 10.1073/pnas.1115485109
Keeble, A. H. et al. DogCatcher allows loop-friendly protein-protein ligation. Cell Chem. Biol. 29, 339–350 (2022).
pubmed: 34324879
pmcid: 8878318
doi: 10.1016/j.chembiol.2021.07.005
Hofmann, R., Akimoto, G., Wucherpfennig, T. G., Zeymer, C. & Bode, J. W. Lysine acylation using conjugating enzymes for site-specific modification and ubiquitination of recombinant proteins. Nat. Chem. 12, 1008–1015 (2020).
pubmed: 32929246
doi: 10.1038/s41557-020-0528-y
Akimoto, G., Fernandes, A. P. & Bode, J. W. Site-specific protein ubiquitylation using an engineered, chimeric E1 activating enzyme and E2 SUMO conjugating enzyme Ubc9. ACS Cent. Sci. 8, 275–281 (2022).
pubmed: 35237717
pmcid: 8883482
doi: 10.1021/acscentsci.1c01490
Richter, D., Lakis, E. & Piel, J. Site-specific bioorthogonal protein labelling by tetrazine ligation using endogenous beta-amino acid dienophiles. Nat. Chem. https://doi.org/10.1038/s41557-023-01252-8 (2023).
doi: 10.1038/s41557-023-01252-8
pubmed: 37400596
pmcid: 10533398
Harris, K. S. et al. Efficient backbone cyclization of linear peptides by a recombinant asparaginyl endopeptidase. Nat. Commun. 6, 10199 (2015).
pubmed: 26680698
doi: 10.1038/ncomms10199
Yang, R. et al. Engineering a catalytically efficient recombinant protein ligase. J. Am. Chem. Soc. 139, 5351–5358 (2017).
pubmed: 28199119
doi: 10.1021/jacs.6b12637
Du, J. et al. A bifunctional asparaginyl endopeptidase efficiently catalyzes both cleavage and cyclization of cyclic trypsin inhibitors. Nat. Commun. 11, 1575 (2020).
pubmed: 32221295
pmcid: 7101308
doi: 10.1038/s41467-020-15418-2
Harmand, T. J. et al. Asparaginyl ligase-catalyzed one-step cell surface modification of red blood cells. ACS Chem. Biol. 16, 1201–1207 (2021).
pubmed: 34129316
doi: 10.1021/acschembio.1c00216
Rehm, F. B. H. et al. Site-specific sequential protein labeling catalyzed by a single recombinant ligase. J. Am. Chem. Soc. 141, 17388–17393 (2019).
pubmed: 31573802
pmcid: 7372569
doi: 10.1021/jacs.9b09166
Rehm, F. B. H. et al. Papain-like cysteine proteases prepare plant cyclic peptide precursors for cyclization. Proc. Natl Acad. Sci. USA 116, 7831–7836 (2019).
pubmed: 30944220
pmcid: 6475389
doi: 10.1073/pnas.1901807116
Rehm, F. B. H., Tyler, T. J., de Veer, S. J., Craik, D. J. & Durek, T. Enzymatic C-to-C protein ligation. Angew. Chem. Int. Ed. 61, e202116672 (2022).
doi: 10.1002/anie.202116672
Rehm, F. B. H. et al. Asparaginyl ligases: new enzymes for the protein engineer’s toolbox. ChemBioChem 22, 2079–2086 (2021).
pubmed: 33687132
doi: 10.1002/cbic.202100071
Rehm, F. B. H. et al. Enzymatic C-terminal protein engineering with amines. J. Am. Chem. Soc. 143, 19498–19504 (2021).
pubmed: 34761936
doi: 10.1021/jacs.1c08976
Rehm, F. B. H., Tyler, T. J., Yap, K., Durek, T. & Craik, D. J. Improved asparaginyl-ligase-catalyzed transpeptidation via selective nucleophile quenching. Angew. Chem. Int. Ed. 60, 4004–4008 (2021).
doi: 10.1002/anie.202013584
Yap, K. et al. Yeast-based bioproduction of disulfide-rich peptides and their cyclization via asparaginyl endopeptidases. Nat. Protoc. 16, 1740–1760 (2021).
pubmed: 33597770
doi: 10.1038/s41596-020-00483-0
Yap, K. et al. An environmentally sustainable biomimetic production of cyclic disulfide-rich peptides. Green Chem. 22, 5002–5016 (2020).
doi: 10.1039/D0GC01366H
Ngo, K. H. et al. Cyclization of a G4-specific peptide enhances its stability and G-quadruplex binding affinity. Chem. Commun. 56, 1082–1084 (2020).
doi: 10.1039/C9CC06748E
Bi, X. et al. Enzymatic engineering of live bacterial cell surfaces using butelase 1. Angew. Chem. Int. Ed. 56, 7822–7825 (2017).
doi: 10.1002/anie.201703317
Bi, X. et al. Tagging transferrin receptor with a disulfide FRET probe to gauge the redox state in endosomal compartments. Anal. Chem. 92, 12460–12466 (2020).
pubmed: 32686399
doi: 10.1021/acs.analchem.0c02264
Hemu, X., Qiu, Y., Nguyen, G. K. & Tam, J. P. Total synthesis of circular bacteriocins by butelase 1. J. Am. Chem. Soc. 138, 6968–6971 (2016).
pubmed: 27206099
doi: 10.1021/jacs.6b04310
Fottner, M. et al. Site-specific protein labeling and generation of defined ubiquitin-protein conjugates using an asparaginyl endopeptidase. J. Am. Chem. Soc. 144, 13118–13126 (2022).
pubmed: 35850488
pmcid: 9335880
doi: 10.1021/jacs.2c02191
de Veer, S. J., Kan, M. W. & Craik, D. J. Cyclotides: from structure to function. Chem. Rev. 119, 12375–12421 (2019).
pubmed: 31829013
doi: 10.1021/acs.chemrev.9b00402
Hemu, X. et al. Structural determinants for peptide-bond formation by asparaginyl ligases. Proc. Natl Acad. Sci. USA 116, 11737–11746 (2019).
pubmed: 31123145
pmcid: 6576118
doi: 10.1073/pnas.1818568116
Zhang, D. et al. pH-controlled protein orthogonal ligation using asparaginyl peptide ligases. J. Am. Chem. Soc. 143, 8704–8712 (2021).
pubmed: 34096285
doi: 10.1021/jacs.1c02638
Tang, T. M. S. et al. Use of an asparaginyl endopeptidase for chemo-enzymatic peptide and protein labeling. Chem. Sci. 11, 5881–5888 (2020).
pubmed: 32874509
pmcid: 7441500
doi: 10.1039/D0SC02023K
Nguyen, G. K., Cao, Y., Wang, W., Liu, C. F. & Tam, J. P. Site-specific N-terminal labeling of peptides and proteins using butelase 1 and thiodepsipeptide. Angew. Chem. Int. Ed. 54, 15694–15698 (2015).
doi: 10.1002/anie.201506810
Xia, Y. et al. A cascade enzymatic reaction scheme for irreversible transpeptidative protein ligation. J. Am. Chem. Soc. 145, 6838–6844 (2023).
pubmed: 36924109
doi: 10.1021/jacs.2c13628
Chen, I., Dorr, B. M. & Liu, D. R. A general strategy for the evolution of bond-forming enzymes using yeast display. Proc. Natl Acad. Sci. USA 108, 11399–11404 (2011).
pubmed: 21697512
pmcid: 3136257
doi: 10.1073/pnas.1101046108
Popp, M. W., Antos, J. M., Grotenbreg, G. M., Spooner, E. & Ploegh, H. L. Sortagging: a versatile method for protein labeling. Nat. Chem. Biol. 3, 707–708 (2007).
pubmed: 17891153
doi: 10.1038/nchembio.2007.31
Haskell-Luevano, C. et al. Discovery of prototype peptidomimetic agonists at the human melanocortin receptors MC1R and MC4R. J. Med. Chem. 40, 2133–2139 (1997).
pubmed: 9216831
doi: 10.1021/jm960840h
Hruby, V. J. et al. α-Melanotropin: the minimal active sequence in the frog skin bioassay. J. Med. Chem. 30, 2126–2130 (1987).
pubmed: 2822931
doi: 10.1021/jm00394a033
Mandal, K. et al. Design, total chemical synthesis and X-ray structure of a protein having a novel linear-loop polypeptide chain topology. Angew. Chem. Int. Ed. 51, 1481–1486 (2012).
doi: 10.1002/anie.201107846
Xie, J. et al. Neurotoxic and cytotoxic peptides underlie the painful stings of the tree nettle Urtica ferox. J. Biol. Chem. 298, 102218 (2022).
pubmed: 35780839
pmcid: 9352542
doi: 10.1016/j.jbc.2022.102218
Sokalingam, S., Raghunathan, G., Soundrarajan, N. & Lee, S. G. A study on the effect of surface lysine to arginine mutagenesis on protein stability and structure using green fluorescent protein. PLoS ONE 7, e40410 (2012).
pubmed: 22792305
pmcid: 3392243
doi: 10.1371/journal.pone.0040410
Pishesha, N. et al. Induction of antigen-specific tolerance by nanobody-antigen adducts that target class-II major histocompatibility complexes. Nat. Biomed. Eng. 5, 1389–1401 (2021).
pubmed: 34127819
doi: 10.1038/s41551-021-00738-5
Pishesha, N. et al. A class II MHC-targeted vaccine elicits immunity against SARS-CoV-2 and its variants. Proc. Natl Acad. Sci. USA 118, e2116147118 (2021).
pubmed: 34654739
pmcid: 8612213
doi: 10.1073/pnas.2116147118
Ling, J. et al. A nanobody that recognizes a 14-residue peptide epitope in the E2 ubiquitin-conjugating enzyme UBC6e modulates its activity. Mol. Immunol. 114, 513–523 (2019).
pubmed: 31518855
pmcid: 6774866
doi: 10.1016/j.molimm.2019.08.008
Linsky, T. W. et al. De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2. Science 370, 1208–1214 (2020).
pubmed: 33154107
pmcid: 7920261
doi: 10.1126/science.abe0075
Philippe, G. et al. Development of cell-penetrating peptide-based drug leads to inhibit MDMX:p53 and MDM2:p53 interactions. Biopolymers 106, 853–863 (2016).
pubmed: 27287767
doi: 10.1002/bip.22893
Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779–815 (1993).
pubmed: 8254673
doi: 10.1006/jmbi.1993.1626
Hu, S. et al. Structural basis for proenzyme maturation, substrate recognition and ligation by a hyperactive peptide asparaginyl ligase. Plant Cell 34, 4936–4949 (2022).
pubmed: 36099055
pmcid: 9709980
doi: 10.1093/plcell/koac281
Elsasser, B. et al. Distinct roles of catalytic cysteine and histidine in the protease and ligase mechanisms of human legumain as revealed by DFT-based QM/MM simulations. ACS Catal. 7, 5585–5593 (2017).
pubmed: 28932620
pmcid: 5600538
doi: 10.1021/acscatal.7b01505
Phillips, J. C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020).
pubmed: 32752662
pmcid: 7395834
doi: 10.1063/5.0014475
Wuethrich, I. et al. Site-specific chemoenzymatic labeling of aerolysin enables the identification of new aerolysin receptors. PLoS ONE 9, e109883 (2014).
pubmed: 25275512
pmcid: 4183550
doi: 10.1371/journal.pone.0109883