Swatek, K. N. & Komander, D. Ubiquitin modifications. Cell Res. 26, 399–422 (2016).
Article CAS PubMed PubMed Central Google Scholar
Yau, R. & Rape, M. The increasing complexity of the ubiquitin code. Nat. Cell Biol. 18, 579–586 (2016).
Article CAS PubMed Google Scholar
Komander, D. & Rape, M. The ubiquitin code. Annu. Rev. Biochem. 81, 203–229 (2012).
Article CAS PubMed Google Scholar
Clague, M. J., Heride, C. & Urbé, S. The demographics of the ubiquitin system. Trends Cell Biol. 25, 417–426 (2015).
Article CAS PubMed Google Scholar
Hershko, A. & Ciechanover, A. The ubiquitin system. Annu. Rev. Biochem. 67, 425–479 (1998).
Article CAS PubMed Google Scholar
Deol, K. K., Lorenz, S. & Strieter, E. R. Enzymatic logic of ubiquitin chain assembly. Front. Physiol. 10, 835 (2019).
Article PubMed PubMed Central Google Scholar
Sun, M. & Zhang, X. Current methodologies in protein ubiquitination characterization: from ubiquitinated protein to ubiquitin chain architecture. Cell Biosci. 12, 126 (2022).
Article CAS PubMed PubMed Central Google Scholar
Faggiano, S. & Pastore, A. The challenge of producing ubiquitinated proteins for structural studies. Cells 3, 639–656 (2014).
Article PubMed PubMed Central Google Scholar
Chatterjee, C., McGinty, R. K., Pellois, J. P. & Muir, T. W. Auxiliary-mediated site-specific peptide ubiquitylation. Angew. Chem. Int. Ed. Engl. 46, 2814–2818 (2007).
Article CAS PubMed Google Scholar
Yang, R., Pasunooti, K. K., Li, F., Liu, X. W. & Liu, C. F. Dual native chemical ligation at lysine. J. Am. Chem. Soc. 131, 13592–13593 (2009).
Article CAS PubMed Google Scholar
Ajish Kumar, K. S., Haj-Yahya, M., Olschewski, D., Lashuel, H. A. & Brik, A. Highly efficient and chemoselective peptide ubiquitylation. Angew. Chem. Int. Ed. Engl. 48, 8090–8094 (2009).
Article CAS PubMed Google Scholar
Haj-Yahya, M., Ajish Kumar, K. S., Erlich, L. A. & Brik, A. Protecting group variations of delta-mercaptolysine useful in chemical ubiquitylation. Biopolymers 94, 504–510 (2010).
Article CAS PubMed Google Scholar
Virdee, S. et al. Traceless and site-specific ubiquitination of recombinant proteins. J. Am. Chem. Soc. 133, 10708–10711 (2011).
Article CAS PubMed PubMed Central Google Scholar
Weller, C. E., Huang, W. & Chatterjee, C. Facile synthesis of native and protease-resistant ubiquitylated peptides. Chembiochem 15, 1263–1267 (2014).
Article CAS PubMed PubMed Central Google Scholar
Weller, C. E. et al. Aromatic thiol-mediated cleavage of N-O bonds enables chemical ubiquitylation of folded proteins. Nat. Commun. 7, 12979 (2016).
Article CAS PubMed PubMed Central Google Scholar
Pan, M. et al. Quasi-racemic X-ray structures of K27-linked ubiquitin chains prepared by total chemical synthesis. J. Am. Chem. Soc. 138, 7429–7435 (2016).
Article CAS PubMed Google Scholar
Burlina, F. et al. Auxiliary-assisted chemical ubiquitylation of NEMO and linear extension by HOIP. Commun. Chem. 2, 111 (2019).
Sun, H. et al. Diverse fate of ubiquitin chain moieties: the proximal is degraded with the target, and the distal protects the proximal from removal and recycles. Proc. Natl. Acad. Sci. Usa. 116, 7805–7812 (2019).
Article CAS PubMed PubMed Central Google Scholar
Layfield, R. et al. Chemically synthesized ubiquitin extension proteins detect distinct catalytic capacities of deubiquitinating enzymes. Anal. Biochem. 274, 40–49 (1999).
Article CAS PubMed Google Scholar
Kumar, K. S., Spasser, L., Ohayon, S., Erlich, L. A. & Brik, A. Expeditious chemical synthesis of ubiquitinated peptides employing orthogonal protection and native chemical ligation. Bioconjug. Chem. 22, 137–143 (2011).
Article CAS PubMed Google Scholar
Cardella, D., Tsai, Y.-H. & Luk, L. Y. P. Towards the use of an amino acid cleavable linker for solid-phase chemical synthesis of peptides and proteins. Org. Biomol. Chem. 21, 966–969 (2023).
Article CAS PubMed Google Scholar
Virdee, S., Ye, Y., Nguyen, D. P., Komander, D. & Chin, J. W. Engineered diubiquitin synthesis reveals Lys29-isopeptide specificity of an OTU deubiquitinase. Nat. Chem. Biol. 6, 750–757 (2010).
Article CAS PubMed Google Scholar
Castañeda, C. et al. Nonenzymatic assembly of natural polyubiquitin chains of any linkage composition and isotopic labeling scheme. J. Am. Chem. Soc. 133, 17855–17868 (2011).
Article PubMed PubMed Central Google Scholar
Yin, L., Krantz, B., Russell, N. S., Deshpande, S. & Wilkinson, K. D. Nonhydrolyzable diubiquitin analogues are inhibitors of ubiquitin conjugation and deconjugation. Biochemistry 39, 10001–10010 (2000).
Article CAS PubMed Google Scholar
Lewis, Y. E., Abeywardana, T., Lin, Y. H., Galesic, A. & Pratt, M. R. Synthesis of a bis-thio-acetone (BTA) analogue of the lysine isopeptide bond and its application to investigate the effects of ubiquitination and SUMOylation on α-synuclein aggregation and toxicity. ACS Chem. Biol. 11, 931–942 (2016).
Article CAS PubMed PubMed Central Google Scholar
Yang, K. et al. Chemical protein ubiquitylation with preservation of the native cysteine residues. Chembiochem 17, 995–998 (2016).
Article CAS PubMed PubMed Central Google Scholar
Morgan, M. T. et al. Structural basis for histone H2B deubiquitination by the SAGA DUB module. Science 351, 725–728 (2016).
Article CAS PubMed PubMed Central Google Scholar
Chen, J., Ai, Y., Wang, J., Haracska, L. & Zhuang, Z. Chemically ubiquitylated PCNA as a probe for eukaryotic translesion DNA synthesis. Nat. Chem. Biol. 6, 270–272 (2010).
Article CAS PubMed Google Scholar
Chatterjee, C., McGinty, R. K., Fierz, B. & Muir, T. W. Disulfide-directed histone ubiquitylation reveals plasticity in hDot1L activation. Nat. Chem. Biol. 6, 267–269 (2010).
Article CAS PubMed Google Scholar
Meier, F. et al. Semisynthetic, site-specific ubiquitin modification of alpha-synuclein reveals differential effects on aggregation. J. Am. Chem. Soc. 134, 5468–5471 (2012).
Article CAS PubMed PubMed Central Google Scholar
Hemantha, H. P. et al. Nonenzymatic polyubiquitination of expressed proteins. J. Am. Chem. Soc. 136, 2665–2673 (2014).
Comments (0)