[1]
Zhao, Y.; Jensen, O.N. Modification-specific proteomics: Strategies for characterization of post-translational modifications using enrichment techniques. Proteomics, 2009, 9, 4632-4641.
[2]
Choudhary, C.; Weinert, B.T.; Nishida, Y.; Verdin, E.; Mann, M. The growing landscape of lysine acetylation links metabolism and cell signalling. Nat. Rev. Mol. Cell Biol., 2014, 15(8), 536-550.
[3]
Müller, M.M.; Muir, T.W. Histones: at the crossroads of peptide and protein chemistry. Chem. Rev., 2014, 115(6), 2296-2349.
[4]
Zhang, Y.; Reinberg, D. Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev., 2001, 15, 2343-2360.
[5]
Greer, E.L.; Shi, Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat. Rev. Genet., 2012, 13(5), 343-357.
[6]
Chuikov, S.; Kurash, J.K.; Wilson, J.R.; Xiao, B.; Justin, N.; Ivanov, G.S.; McKinney, K.; Tempst, P.; Prives, C.; Gamblin, S.J. Regulation of p53 activity through lysine methylation. Nature, 2004, 432(7015), 353-360.
[7]
Hamamoto, R.; Saloura, V.; Nakamura, Y. Critical roles of non-histone protein lysine methylation in human tumorigenesis. Nat. Rev. Cancer, 2015, 15(2), 110-124.
[8]
Phillips, D.M. Acetyl groups as N-terminal aubstituents in calf-thymus histones. Biochem. J., 1961, 80(3), 40.
[9]
Manohar, M.; Mooney, A.M.; North, J.A.; Nakkula, R.J.; Picking, J.W.; Edon, A.; Fishel, R.; Poirier, M.G.; Ottesen, J.J. Acetylation of histone H3 at the nucleosome dyad alters DNA-histone binding. J. Biol. Chem., 2009, 284(35), 23312-23321.
[10]
Spange, S.; Wagner, T.; Heinzel, T.; Krämer, O.H. Acetylation of non-histone proteins modulates cellular signalling at multiple levels. Int. J. Biochem. Cell Biol., 2009, 41(1), 185-198.
[11]
Kothapalli, N.; Camporeale, G.; Kueh, A.; Chew, Y.C.; Oommen, A.M.; Griffin, J.B.; Zempleni, J. Biological functions of biotinylated histones. J. Nutr. Biochem., 2005, 16(7), 446-448.
[12]
Peng, C.; Lu, Z.; Xie, Z.; Cheng, Z.; Chen, Y.; Tan, M.; Luo, H.; Zhang, Y.; He, W.; Yang, K.; Zhao, Y. The first identification of lysine malonylation substrates and its regulatory enzyme. Mol. Cell. Proteomics, 2011, 10(12), M111. 012658.
[13]
Zhang, Z.; Tan, M.; Xie, Z.; Dai, L.; Chen, Y.; Zhao, Y. Identification of lysine succinylation as a new post-translational modification. Nat. Chem. Biol., 2011, 7(1), 58-63.
[14]
Tan, M.; Peng, C.; Anderson, K.A.; Chhoy, P.; Xie, Z.; Dai, L.; Park, J.; Chen, Y.; Huang, H.; Zhang, Y.; Ro, J.; Wagner, G.R.; Green, M.F.; Madsen, A.S.; Schmiesing, J.; Peterson, B.S.; Xu, G.; Ilkayeva, O.R.; Muehlbauer, M.J.; Braulke, T.; Muhlhausen, C.; Backos, D.S.; Olsen, C.A.; McGuire, P.J.; Pletcher, S.D.; Lombard, D.B.; Hirschey, M.D.; Zhao, Y. Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. Cell Metab., 2014, 19(4), 605-617.
[15]
Dai, L.; Peng, C.; Montellier, E.; Lu, Z.; Chen, Y.; Ishii, H.; Debernardi, A.; Buchou, T.; Rousseaux, S.; Jin, F. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat. Chem. Biol., 2014, 10(5), 365-370.
[16]
Jin, J.; He, B.; Zhang, X.; Lin, H.; Wang, Y. SIRT2 reverses 4-oxononanoyl lysine modification on histones. J. Am. Chem. Soc., 2016, 138(38), 12304-12307.
[17]
Xie, Z.; Zhang, D.; Chung, D.; Tang, Z.; Huang, H.; Dai, L.; Qi, S.; Li, J.; Colak, G.; Chen, Y.; Xia, C.; Peng, C.; Ruan, H.; Kirkey, M.; Wang, D.; Jensen, L.M.; Kwon, O.K.; Lee, S.; Pletcher, S.D.; Tan, M.; Lombard, D.B.; White, K.P.; Zhao, H.; Li, J.; Roeder, R.G.; Yang, X.; Zhao, Y. Metabolic regulation of gene expression by histone lysine β-hydroxybutyrylation. Mol. Cell, 2016, 62(2), 194-206.
[18]
Huang, H.; Zhang, D.; Wang, Y.; Perez-Neut, M.; Han, Z.; Zheng, Y.G.; Hao, Q.; Zhao, Y. Lysine benzoylation is a histone mark regulated by SIRT2. Nat. Commun., 2018, 9, Article number 3374.
[19]
Zhipeng, A. Wang; Li, M.; Li, H.; Liu, Z.; Li, Y.; Zheng, J.-S. Chemical (Semi-) synthesis and applications of lysine post-translationally modified proteins. Chin. J. Org. Chem., 2018, 38, 2400.
[20]
Liu, W.S.R.; Wang, Y.S.; Wan, W. Synthesis of proteins with defined posttranslational modifications using the genetic noncanonical amino acid incorporation approach. Mol. Biosyst., 2011, 7(1), 38-47.
[21]
Wang, Z-P.; Wang, Y-H.; Chu, G-C.; Shi, J.; Li, Y-M. The study of the chemical synthesis and preparation of histone with post-translational modifications. Curr. Org. Synth., 2015, 12(2), 150-162.
[22]
Wang, Z.; Ding, X.; Li, S.; Shi, J.; Li, Y. Engineered fluorescence tags for in vivo protein labelling. RSC Adv, 2014, 4(14), 7235-7245.
[23]
Tate, E.W. Recent advances in chemical proteomics: exploring the post-translational proteome. J. Chem. Biol., 2008, 1, 17-26.
[24]
Li, J-B.; Tang, S.; Zheng, J-S.; Tian, C-L.; Liu, L. Removable backbone modification method for the chemical synthesis of membrane proteins. Acc. Chem. Res., 2017, 50(5), 1143-1153.
[25]
Wang, Z.; Xu, W.; Liu, L.; Zhu, T.F. A synthetic molecular system capable of mirror-image genetic replication and transcription. Nat. Chem., 2016, 8(7), 698.
[26]
Dawson, P.E.; Kent, S.B.H. Synthesis of native proteins by chemical ligation. Annu. Rev. Biochem., 2000, 69(1), 923-960.
[27]
Muir, T.W.; Sondhi, D.; Cole, P.A. Expressed protein ligation: a general method for protein engineering. Proc. Natl. Acad. Sci. USA, 1998, 95(12), 6705-6710.
[28]
Zheng, J-S.; Tang, S.; Huang, Y-C.; Liu, L. Development of new thioester equivalents for protein chemical synthesis. Acc. Chem. Res., 2013, 46(11), 2475-2484.
[29]
Zheng, J-S.; He, Y.; Zuo, C.; Cai, X-Y.; Tang, S.; Wang, Z.A.; Zhang, L-H.; Tian, C-L.; Liu, L. Robust chemical synthesis of membrane proteins through a general method of removable backbone modification. J. Am. Chem. Soc., 2016, 138(10), 3553-3561.
[30]
Chen, X.; Tang, S.; Zheng, J-S.; Zhao, R.; Wang, Z-P.; Shao, W.; Chang, H-N.; Cheng, J-Y.; Zhao, H.; Liu, L. Chemical synthesis of a two-photon-activatable chemokine and photon-guided lymphocyte migration in vivo. Nat. Commun., 2015, 6, 1-9.
[31]
Fang, G.M.; Li, Y.M.; Shen, F.; Huang, Y.C.; Li, J.B.; Lin, Y.; Cui, H.K.; Liu, L. Protein chemical synthesis by ligation of peptide hydrazides. Angew. Chem. Int. Ed., 2011, 50(33), 7645-7649.
[32]
Pan, M.; Gao, S.; Zheng, Y.; Tan, X.; Lan, H.; Tan, X.; Sun, D.; Lu, L.; Wang, T.; Zheng, Q.; Liu, L. Quasi-racemic X-ray structures of K27-linked ubiquitin chains prepared by total chemical synthesis. J. Am. Chem. Soc., 2016, 138(23), 7429-7435.
[33]
Li, J.; Li, Y.; He, Q.; Li, Y.; Li, H.; Liu, L. One-pot native chemical ligation of peptide hydrazides enables total synthesis of modified histones. Org. Biomol. Chem., 2014, 12(29), 5435-5441.
[34]
Morgan, M.T.; Haj-Yahya, M.; Ringel, A.E.; Bandi, P.; Brik, A.; Wolberger, C. Structural basis for histone H2B deubiquitination by the SAGA DUB module. Science, 2016, 351(6274), 725-728.
[35]
Tang, S.; Liang, L.J.; Si, Y.Y.; Gao, S.; Wang, J.X.; Liang, J.; Mei, Z.; Zheng, J.S.; Liu, L. Practical chemical synthesis of atypical ubiquitin chains by using an isopeptide-linked ub isomer. Angew. Chem. Int. Ed., 2017, 56(43), 13333-13337.
[36]
Moyle, P.M.; Muir, T.W. Method for the synthesis of mono-ADP-ribose conjugated peptides. J. Am. Chem. Soc., 2010, 132(45), 15878-15880.
[37]
Kee, J-M.; Villani, B.; Carpenter, L.R.; Muir, T.W. Development of stable phosphohistidine analogues. J. Am. Chem. Soc., 2010, 132(41), 14327-14329.
[38]
Hsu, W.W.; Wu, B.; Liu, W.R. Sirtuins 1 and 2 are universal histone deacetylases. ACS Chem. Biol., 2016, 11, 792-799.
[39]
Wu, Y-W.; Goody, R.S. Probing protein function by chemical modification. J. Pept. Sci., 2010, 16, 514-523.
[40]
Eftekhari-Sis, B.; Zirak, M. Chemistry of α-oxoesters: a powerful tool for the synthesis of heterocycles. Chem. Rev., 2014, 115(1), 151-264.
[41]
Zheng, M.; Zheng, L.; Zhang, P.; Li, J.; Zhang, Y. Development of bioorthogonal reactions and their applications in bioconjugation. Molecules, 2015, 20, 3190-3205.
[42]
Best, M.D. Click chemistry and bioorthogonal reactions: unprecedented selectivity in the labeling of biological molecules. Biochemistry, 2009, 48, 6571-6584.
[43]
Chalker, J.M.; Bernardes, G.A.J.; Davis, B.G.A. “tag-and-modify” approach to site-selective protein modification. Acc. Chem. Res., 2011, 44(9), 730-741.
[44]
Dawson, P.E.; Muir, T.W.; Clark-Lewis, I.; Kent, S.B. Synthesis of proteins by native chemical ligation. Science, 1994, 266(5186), 776-779.
[45]
Zuo, C.; Tang, S.; Zheng, J.S. Chemical synthesis and biophysical applications of membrane proteins. J. Pept. Sci., 2015, 21(7), 540-549.
[46]
Guo, Q-Y.; Zhang, L-H.; Zuo, C.; Huang, D-L.; Wang, Z.A.; Zheng, J-S.; Tian, C-L. Channel activity of mirror-image M2 proton channel of influenza A virus is blocked by achiral or chiral inhibitors. Protein & Cell, 2018, 10(3), 211-216.
[47]
Wu, M.; Hayward, D.; Kalin, J.H.; Song, Y.; Schwabe, J.W.; Cole, P.A. Lysine-14 acetylation of histone H3 in chromatin confers resistance to the deacetylase and demethylase activities of an epigenetic silencing complex. eLife, 2018, 7, e37231.
[48]
Zheng, J-S.; Tang, S.; Qi, Y-K.; Wang, Z-P.; Liu, L. Chemical synthesis of proteins using peptide hydrazides as thioester surrogates. Nat. Protoc., 2013, 8(12), 2483-2495.
[49]
He, S.; Bauman, D.; Davis, J.S.; Loyola, A.; Nishioka, K.; Gronlund, J.L.; Reinberg, D.; Meng, F.Y.; Kelleher, N.; McCafferty, D.G. Facile synthesis of site-specifically acetylated and methylated histone proteins: Reagents for evaluation of the histone code hypothesis. Proc. Natl. Acad. Sci. USA, 2003, 100(21), 12033-12038.
[50]
Kawakami, T.; Akai, Y.; Fujimoto, H.; Kita, C.; Aoki, Y.; Konishi, T.; Waseda, M.; Takemura, L.; Aimoto, S. Sequential peptide ligation by combining the Cys-Pro Ester (CPE) and thioester methods and its application to the synthesis of histone H3 containing a trimethyl lysine residue. Bull. Chem. Soc. Jpn., 2013, 86(6), 690-697.
[51]
Jbara, M.; Guttmann-Raviv, N.; Maity, S.K.; Ayoub, N.; Brik, A. Total chemical synthesis of methylated analogues of histone 3 revealed KDM4D as a potential regulator of H3K79me3. Biorg. Med. Chem., 2017, 25(18), 4966-4970.
[52]
Kwon, Y.T.; Ciechanover, A. The ubiquitin code in the ubiquitin-proteasome system and autophagy. Trends Biochem. Sci., 2017, 42(11), 873-886.
[53]
Mali, S.M.; Singh, S.K.; Eid, E.; Brik, A. Ubiquitin signaling: Chemistry comes to the rescue. J. Am. Chem. Soc., 2017, 139(14), 4971-4986.
[54]
Kumar, K.A.; Spasser, L.; Ohayon, S.; Erlich, L.A.; Brik, A. Expeditious chemical synthesis of ubiquitinated peptides employing orthogonal protection and native chemical ligation. Bioconjugate. Chem., 2011, 22(2), 137-143.
[55]
Siman, P.; Karthikeyan, S.V.; Nikolov, M.; Fischle, W.; Brik, A. Convergent chemical synthesis of histone H2B Protein for the site-specific ubiquitination at Lys34. Angew. Chem. Int. Ed., 2013, 52(31), 8059-8063.
[56]
Li, J.; He, Q.; Liu, Y.; Liu, S.; Tang, S.; Li, C.; Sun, D.; Li, X.; Zhou, M.; Zhu, P. Chemical synthesis of K34-ubiquitylated H2B for nucleosome reconstitution and single-particle cryo-electron microscopy structural analysis. ChemBioChem, 2017, 18, 176-180.
[57]
McGinty, R.K.; Kim, J.; Chatterjee, C.; Roeder, R.G.; Muir, T.W. Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation. Nature, 2008, 453(7196), 812-816.
[58]
McGinty, R.K.; Kohn, M.; Chatterjee, C.; Chiang, K.P.; Pratt, M.R.; Muir, T.W. Structure-activity analysis of semisynthetic nucleosomes: mechanistic insights into the stimulation of Dot1L by ubiquitylated histone H2B. ACS Chem. Biol., 2009, 4(11), 958-968.
[59]
Chatterjee, C.; McGinty, R.K.; Fierz, B.; Muir, T.W. Disulfide-directed histone ubiquitylation reveals plasticity in hDot1L activation. Nat. Chem. Biol., 2010, 6(4), 267-269.
[60]
Wojcik, F.; Dann, G.P.; Beh, L.Y.; Debelouchina, G.T.; Hofmann, R.; Muir, T.W. Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants. Nat. Commun., 2018, 9(1), 1394.
[61]
Liang, J.; Zhang, L.; Tan, X.L.; Qi, Y.K.; Feng, S.; Deng, H.; Yan, Y.; Zheng, J.S.; Liu, L.; Tian, C.L. Chemical synthesis of diubiquitin-based photoaffinity probes for selectively profiling ubiquitin-binding proteins. Angew. Chem. Int. Ed., 2017, 129(10), 2788-2792.
[62]
Bondalapati, S.; Eid, E.; Mali, S.M.; Wolberger, C.; Brik, A. Total chemical synthesis of SUMO-2-Lys63-linked diubiquitin hybrid chains assisted by removable solubilizing tags. Chem. Sci., 2017, 8, 4027-4034.
[63]
Liang, L-J.; Si, Y.; Tang, S.; Huang, D.; Wang, Z.A.; Tian, C.; Zheng, J-S. Biochemical properties of K11, 48-branched ubiquitin chains. Chin. Chem. Lett., 2018, 29, 1155-1159.
[64]
Si, Y-Y.; Liang, L-J.; Tang, S.; Qi, Y-K.; Huang, Y.; Zheng, J-S. One-pot ligation strategy for atypical ubiquitin chains synthesis by using the trifluoroacetamidomethyl-protected isopeptide-linked Ub (Tfacm-isoUb) unit. Tetrahedron Lett., 2018, 59(3), 268-271.
[65]
Qi, Y-K.; He, Q-Q.; Ai, H-S.; Li, J-B.; Zheng, J-S. Convergent total synthesis of histone H2B protein with site-specific ubiquitination at Lys120. Synlett, 2017, 28(15), 1907-1912.
[66]
Li, J.; He, Q.; Liu, Y.; Liu, S.; Tang, S.; Li, C.; Sun, D.; Li, X.; Zhou, M.; Zhu, P. Chemical synthesis of K34-ubiquitylated H2B for nucleosome reconstitution and single-particle cryo-electron microscopy structural analysis. ChemBioChem, 2017, 18(2), 176-180.
[67]
Luo, J.; Li, M.; Tang, Y.; Laszkowska, M.; Roeder, R.G.; Gu, W. Acetylation of p53 augments its site-specific DNA binding both in vitro and in vivo. Proc. Natl. Acad. Sci. USA, 2004, 101(8), 2259-2264.
[68]
Li, M.; Luo, J.; Brooks, C.L.; Gu, W. Acetylation of p53 inhibits its ubiquitination by Mdm2. J. Biol. Chem., 2002, 277(52), 50607-50611.
[69]
Tang, Y.; Zhao, W.; Chen, Y.; Zhao, Y.; Gu, W. Acetylation is indispensable for p53 activation. Cell, 2008, 133(4), 612-626.
[70]
Martino, F.; Kueng, S.; Robinson, P.; Tsai-Pflugfelder, M.; van Leeuwen, F.; Ziegler, M.; Cubizolles, F.; Cockell, M.M.; Rhodes, D.; Gasser, S.M. Reconstitution of yeast silent chromatin: Multiple contact sites and O-AADPR binding load SIR complexes onto nucleosomes in vitro. Mol. Cell, 2009, 33(3), 323-334.
[71]
Nguyen, D.P.; Garcia Alai, M.M.; Kapadnis, P.B.; Neumann, H.; Chin, J.W. Genetically encoding N(epsilon)-methyl-L-lysine in recombinant histones. J. Am. Chem. Soc., 2009, 131(40), 14194-14195.
[72]
Yin, J.; Liu, F.; Li, X.H.; Walsh, C.T. Labeling proteins with small molecules by site-specific posttranslational modification. J. Am. Chem. Soc., 2004, 126(25), 7754-7755.
[73]
Scheffner, M.; Nuber, U.; Huibregtse, J.M. Protein ubiquitination involving an E1-E2-E3 enzyme ubiquitin thioester cascade. Nature, 1995, 373(6509), 81.
[74]
Park, S.; Krist, D.T.; Statsyuk, A.V. Protein ubiquitination and formation of polyubiquitin chains without ATP, E1 and E2 enzymes. Chem. Sci, 2015, 6(3), 1770-1779.
[75]
Wang, X.A.; Kurra, Y.; Huang, Y.; Lee, Y.J.; Liu, W.R. E1-Catalyzed ubiquitin C-terminal amidation for the facile synthesis of deubiquitinase substrates. ChemBioChem, 2014, 15(1), 37-41.
[76]
Faggiano, S.; Menon, R.P.; Kelly, G.P.; McCormick, J.; Todi, S.V.; Scaglione, K.M.; Paulson, H.L.; Pastore, A. Enzymatic production of mono-ubiquitinated proteins for structural studies: The example of the Josephin domain of ataxin-3. FEBS Open Bio, 2013, 3(1), 453-458.
[77]
Komander, D.; Rape, M. The ubiquitin code. Annu. Rev. Biochem., 2012, 81, 203-229.
[78]
Foley, T.L.; Burkart, M.D. Site-specific protein modification: advances and applications. Curr. Opin. Chem. Biol., 2007, 11(1), 12-19.
[79]
Dempsey, D.R.; Jiang, H.; Kalin, J.H.; Chen, Z.; Cole, P.A. Site-specific protein labeling with NHS-esters and the analysis of ubiquitin ligase mechanisms. J. Am. Chem. Soc., 2018, 140(30), 9374-9378.
[80]
Wang, Z-P.A.; Tian, C-L.; Zheng, J-S. The recent developments and applications of traceless-staudinger reaction in the chemical biology study. RSC Adv, 2015, 5, 107192-107199.
[81]
Lang, K.; Chin, J.W. Bioorthogonal reactions for labeling proteins. ACS Chem. Biol., 2014, 9(1), 16-20.
[82]
Baslé, E.; Joubert, N.; Pucheault, M. Protein chemical modification on endogenous amino acids. Chem. Biol., 2010, 17(3), 213-227.
[83]
Davis, B.G. Mimicking posttranslational modifications of proteins. Science, 2004, 303(5657), 480-482.
[84]
Li, Y.; Yang, M.; Huang, Y.; Song, X.; Liu, L.; Chen, P.R. Genetically encoded alkenyl–pyrrolysine analogues for thiol–ene reaction mediated site-specific protein labeling. Chem. Sci., 2012, 3, 2766-2770.
[85]
Simon, M.D.; Chu, F.; Racki, L.R.; Cecile, C.; Burlingame, A.L.; Panning, B.; Narlikar, G.J.; Shokat, K.M. The site-specific installation of methyl-lysine analogs into recombinant histones. Cell, 2007, 128(5), 1003-1012.
[86]
van Kasteren, S.I.; Kramer, H.B.; Jensen, H.H.; Campbell, S.J.; Kirkpatrick, J.; Oldham, N.J.; Anthony, D.C.; Davis, B.G. Expanding the diversity of chemical protein modification allows post-translational mimicry. Nature, 2007, 446(7139), 1105-1109.
[87]
Li, F.P.; Allahverdi, A.; Yang, R.L.; Lua, G.B.J.; Zhang, X.H.; Cao, Y.; Korolev, N.; Nordenskiold, L.; Liu, C.F. A direct method for site-specific protein acetylation. Angew. Chem. Int. Ed., 2011, 50(41), 9611-9614.
[88]
Bhat, S.; Hwang, Y.; Gibson, M.D.; Morgan, M.T.; Taverna, S.D.; Zhao, Y.; Wolberger, C.; Poirier, M.G.; Cole, P.A. Hydrazide mimics for protein lysine acylation to assess nucleosome dynamics and deubiquitinase action. J. Am. Chem. Soc., 2018, 140(30), 9478-9485.
[89]
Willey, J.M.; van der Donk, W.A. Lantibiotics: Peptides of diverse structure and function. Annu. Rev. Microbiol., 2007, 61, 477-501.
[90]
Bar-Or, R.; Rael, L.T.; Bar-Or, D. Dehydroalanine derived from cysteine is a common post-translational modification in human serum albumin. Rapid Commun. Mass Spectrom., 2008, 22(5), 711-716.
[91]
Hashimoto, K.; Sakai, M.; Okuno, T.; Shirahama, H. beta-phenylseleno-alanine as a dehydroalanine precursor-efficient synthesis of alternariolide (AM-toxin I) (May, pg 1139, 1996). Chem. Commun., 1996, (15), 1849-1849.
[92]
Seebeck, F.P.; Szostak, J.W. Ribosomal synthesis of dehydroalanine-containing peptides. J. Am. Chem. Soc., 2006, 128(22), 7150-7151.
[93]
Okeley, N.M.; Zhu, Y.T.; van der Donk, W.A. Facile chemoselective synthesis of dehydroalanine-containing peptides. Org. Lett., 2000, 2(23), 3603-3606.
[94]
Bernardes, G.J.; Chalker, J.M.; Errey, J.C.; Davis, B.G. Facile conversion of cysteine and alkyl cysteines to dehydroalanine on protein surfaces: versatile and switchable access to functionalized proteins. J. Am. Chem. Soc., 2008, 130(15), 5052-5053.
[95]
Chalker, J.M.; Gunnoo, S.B.; Boutureira, O.; Gerstberger, S.C.; Fernández-González, M.; Bernardes, G.J.; Griffin, L.; Hailu, H.; Schofield, C.J.; Davis, B.G. Methods for converting cysteine to dehydroalanine on peptides and proteins. Chem. Sci., 2011, 2(9), 1666-1676.
[96]
Wang, Z.U.; Wang, Y-S.; Pai, P-J.; Russell, W.K.; Russell, D.H.; Liu, W.R. A facile method to synthesize histones with posttranslational modification mimics. Biochemistry, 2012, 51(26), 5232-5234.
[97]
Yang, A.; Ha, S.; Ahn, J.; Kim, R.; Kim, S.; Lee, Y.; Kim, J.; Söll, D.; Lee, H-Y.; Park, H-S. A chemical biology route to site-specific authentic protein modifications. Science, 2016, 354(6312), 623-626.
[98]
Wright, T.H.; Bower, B.J.; Chalker, J.M.; Bernardes, G.J.; Wiewiora, R.; Ng, W-L.; Raj, R.; Faulkner, S.; Vallée, M.R.J.; Phanumartwiwath, A.; Davis, B.G. Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity. Science, 2016, 354(6312), aag1465.
[99]
Wang, L.; Brock, A.; Herberich, B.; Schultz, P.G. Expanding the genetic code of Escherichia coli. Science, 2001, 292(5516), 498-500.
[100]
Ambrogelly, A.; Gundllapalli, S.; Herring, S.; Polycarpo, C.; Frauer, C.; Söll, D. Pyrrolysine is not hardwired for cotranslational insertion at UAG codons. Proc. Natl. Acad. Sci. USA, 2007, 104(9), 3141-3146.
[101]
Namy, O.; Zhou, Y.; Gundllapalli, S.; Polycarpo, C.R.; Denise, A.; Rousset, J-P.; Söll, D.; Ambrogelly, A. Adding pyrrolysine to the Escherichia coli genetic code. FEBS Lett., 2007, 581(27), 5282-5288.
[102]
Hancock, S.M.; Uprety, R.; Deiters, A.; Chin, J.W. Expanding the genetic code of yeast for incorporation of diverse unnatural amino acids via a pyrrolysyl-tRNA synthetase/tRNA pair. J. Am. Chem. Soc., 2010, 132(42), 14819-14824.
[103]
Mukai, T.; Kobayashi, T.; Hino, N.; Yanagisawa, T.; Sakamoto, K.; Yokoyama, S. Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases. Biochem. Biophys. Res. Commun., 2008, 371(4), 818-822.
[104]
Greiss, S.; Chin, J.W. Expanding the genetic code of an animal. J. Am. Chem. Soc., 2011, 133(36), 14196-14199.
[105]
Neumann, H.; Peak-Chew, S.Y.; Chin, J.W. Genetically encoding Nε-acetyllysine in recombinant proteins. Nat. Chem. Biol., 2008, 4(4), 232-234.
[106]
Neumann, H.; Hancock, S.M.; Buning, R.; Routh, A.; Chapman, L.; Somers, J.; Owen-Hughes, T.; van Noort, J.; Rhodes, D.; Chin, J.W. A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation. Mol. Cell, 2009, 36(1), 153-163.
[107]
Kim, C.H.; Kang, M.; Kim, H.J.; Chatterjee, A.; Schultz, P.G. Site-specific incorporation of epsilon-N-crotonyllysine into histones. Angew. Chem. Int. Ed., 2012, 51(29), 7246-7249.
[108]
Gattner, M.J.; Vrabel, M.; Carell, T. Synthesis of epsilon-N-propionyl-, epsilon-N-butyryl-, and epsilon-N-crotonyl-lysine containing histone H3 using the pyrrolysine system. Chem. Commun. (Camb.), 2013, 49(4), 379-381.
[109]
Lee, Y-J.; Wu, B.; Raymond, J.E.; Zeng, Y.; Fang, X.; Wooley, K.L.; Liu, W.R. A genetically encoded acrylamide functionality. ACS Chem. Biol., 2013, 8(8), 1664-1670.
[110]
Xiao, H.; Xuan, W.; Shao, S.; Liu, T.; Schultz, P.G. Genetic incorporation of ε-N-2-hydroxyisobutyryl-lysine into recombinant histones. ACS Chem. Biol., 2015, 10(7), 1599-1603.
[111]
Dumas, A.; Lercher, L.; Spicer, C.D.; Davis, B.G. Designing logical codon reassignment–Expanding the chemistry in biology. Chem. Sci., 2015, 6(1), 50-69.
[112]
Rogerson, D.T.; Sachdeva, A.; Wang, K.; Haq, T.; Kazlauskaite, A.; Hancock, S.M.; Huguenin-Dezot, N.; Muqit, M.M.K.; Fry, A.M.; Bayliss, R.; Chin, J.W. Efficient genetic encoding of phosphoserine and its nonhydrolyzable analog. Nat. Chem. Biol., 2015, 11, 496-506.
[113]
Bertozzi, C.R. A decade of bioorthogonal chemistry. Acc. Chem. Res., 2011, 44(9), 651-653.
[114]
Zhang, G.; Zheng, S.; Liu, H.; Chen, P.R. Illuminating biological processes through site-specific protein labeling. Chem. Soc. Rev., 2015, 44, 3405-3417.
[115]
Chin, J.W.; Santoro, S.W.; Martin, A.B.; King, D.S.; Wang, L.; Schultz, P.G. Addition of p-Azido-l-phenylalanine to the Genetic Code of Escherichia coli. J. Am. Chem. Soc., 2002, 124(31), 9026-9027.
[116]
Li, J.; Chen, P.R. Development and application of bond cleavage reactions in bioorthogonal chemistry. Nat. Chem. Biol., 2016, 12(3), 129-137.
[117]
Ai, H.W.; Lee, J.W.; Schultz, P.G. A method to site-specifically introduce methyllysine into proteins in E. coli. Chem. Commun. (Camb.), 2010, 46(30), 5506-5508.
[118]
Wang, Y-S.; Wu, B.; Wang, Z.; Huang, Y.; Wan, W.; Russell, W.K.; Pai, P-J.; Moe, Y.N.; Russell, D.H.; Liu, W.R. A genetically encoded photocaged Nε-methyl-l-lysine. Mol. Biosyst., 2010, 6(9), 1557-1560.
[119]
Gautier, A.; Deiters, A.; Chin, J.W. Light-activated kinases enable temporal dissection of signaling networks in living cells. J. Am. Chem. Soc., 2011, 133(7), 2124-2127.
[120]
Hemphill, J.; Chou, C.; Chin, J.W.; Deiters, A. Genetically encoded light-activated transcription for spatiotemporal control of gene expression and gene silencing in mammalian cells. J. Am. Chem. Soc., 2013, 135, 13433-13439.
[121]
Nguyen, D.P.; Alai, M.M.G.; Virdee, S.; Chin, J.W. Genetically directing ɛ-N, N-dimethyl-l-lysine in recombinant histones. Chem. Biol., 2010, 17(10), 1072-1076.
[122]
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., 2010, 6(10), 750-757.
[123]
Zhang, G.; Li, J.; Xie, R.; Fan, X.; Liu, Y.; Zheng, S.; Ge, Y.; Chen, P.R. Bioorthogonal chemical activation of kinases in living systems. ACS Cent. Sci., 2016, 2, 325-331.
[124]
Spicer, C.D.; Davis, B.G. Selective chemical protein modification. Nat. Commun., 2014, 5, 1-14.
[125]
Li, X.; Fekner, T.; Ottesen, J.J.; Chan, M.K. A pyrrolysine analogue for site-specific protein ubiquitination. Angew. Chem. Int. Ed., 2009, 121(48), 9348-9351.
[126]
Nguyen, D.P.; Elliott, T.; Holt, M.; Muir, T.W.; Chin, J.W. Genetically encoded 1, 2-aminothiols facilitate rapid and site-specific protein labeling via a bio-orthogonal cyanobenzothiazole condensation. J. Am. Chem. Soc., 2011, 133(30), 11418-11421.
[127]
Virdee, S.; Kapadnis, P.B.; Elliott, T.; Lang, K.; Madrzak, J.; Nguyen, D.P.; Riechmann, L.; Chin, J.W. Traceless and site-specific ubiquitination of recombinant proteins. J. Am. Chem. Soc., 2011, 133(28), 10708-10711.
[128]
Amamoto, Y.; Aoi, Y.; Nagashima, N.; Suto, H.; Yoshidome, D.; Arimura, Y.; Osakabe, A.; Kato, D.; Kurumizaka, H.; Kawashima, S.A. Synthetic posttranslational modifications: Chemical catalyst-driven regioselective histone acylation of native chromatin. J. Am. Chem. Soc., 2017, 139(22), 7568-7576.
[129]
Chatterjee, C.; McGinty, R.K.; Pellois, J.P.; Muir, T.W. Auxiliary-mediated site-specific peptide ubiquitylation. Angew. Chem. Int. Ed., 2007, 119(16), 2872-2876.
[130]
Weller, C.E.; Huang, W.; Chatterjee, C. Facile synthesis of native and protease-resistant ubiquitylated peptides. ChemBioChem, 2014, 15(9), 1263-1267.
[131]
Weller, C.E.; Dhall, A.; Ding, F.; Linares, E.; Whedon, S.D.; Senger, N.A.; Tyson, E.L.; Bagert, J.D.; Li, X.; Augusto, O.; Chatterjee, C. Aromatic thiol-mediated cleavage of N–O bonds enables chemical ubiquitylation of folded proteins. Nat. Commun., 2016, 7, 12979.
[132]
Wang, Z.A.; Liu, W.R. Proteins with site-specific lysine methylation. Chem. Eur. J., 2017, 23(49), 11732-11737.
[133]
Wang, Z.A.; Zeng, Y.; Kurra, Y.; Wang, X.; Tharp, J.M.; Vatansever, E.C.; Hsu, W.W.; Dai, S.; Fang, X.; Liu, W.R. A Genetically Encoded Allysine for the Synthesis of Proteins with Site-Specific Lysine Dimethylation. Angew. Chem. Int. Ed., 2017, 56(1), 212-216.
[134]
Wang, Z.A.; Kurra, Y.; Wang, X.; Zeng, Y.; Lee, Y-J.; Sharma, V.; Lin, H.; Dai, S.Y.; Liu, W.R. A versatile approach for site-specific lysine acylation in proteins. Angew. Chem. Int. Ed., 2017, 56(6), 1643-1647.
[135]
Ngo, J.T.; Schuman, E.M.; Tirrell, D.A. Mutant methionyl-tRNA synthetase from bacteria enables site-selective N-terminal labeling of proteins expressed in mammalian cells. Proc. Natl. Acad. Sci. USA, 2013, 110(13), 4992-4997.
[136]
Mahdavi, A.; Segall-Shapiro, T.H.; Kou, S.; Jindal, G.A.; Hoff, K.G.; Liu, S.; Chitsaz, M.; Ismagilov, R.F.; Silberg, J.J.; Tirrell, D.A. A genetically encoded AND gate for cell-targeted metabolic labeling of proteins. J. Am. Chem. Soc., 2013, 135(8), 2979-2982.
[137]
Yang, R.; Bi, X.; Li, F.; Cao, Y.; Liu, C-F. Native chemical ubiquitination using a genetically incorporated azidonorleucine. Chem. Commun., 2014, 50(59), 7971-7974.
[138]
Gong, Y.; Pan, L. Recent advances in bioorthogonal reactions for site-specific protein labeling and engineering. Tetrahedron Lett., 2015, 56, 2123-2132.
[139]
Bowman, G.D.; Poirier, M.G. Post-translational modifications of histones that influence nucleosome dynamics. Chem. Rev., 2015, 115(6), 2274.
[140]
Sueoka, T.; Koyama, K.; Hayashi, G.; Okamoto, A. Chemistry-driven epigenetic investigation of histone and DNA modifications. Chem. Rec., 2018, 18(12), 1727-1744.
[141]
Fareghi-Alamdari, R.; Mansouri, F.; Golestanzadeh, M.; Zekri, N. Recent developments in the synthesis of antioxidant derivatives using recoverable and/or nano-catalysts. Curr. Org. Chem., 2018, 22(14), 1373-1419.
[142]
Eftekhari-Sis, B.; Zirak, M. α-Imino esters in organic synthesis: Recent advances. Chem. Rev., 2017, 117(12), 8326-8419.
[143]
Ngo, J.T.; Tirrell, D.A. Noncanonical amino acids in the interrogation of cellular protein synthesis. Acc. Chem. Res., 2011, 44(9), 677-685.
[144]
Lang, K.; Chin, J.W. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem. Rev., 2014, 114(9), 4764-4806.
[145]
Delgado-Andrade, C. Carboxymethyl-lysine: thirty years of investigation in the field of AGE formation. Food Funct., 2016, 7(1), 46-57.
[146]
Park, M.H. The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A). J. Biochem., 2006, 139(2), 161-169.
[147]
Lang, K.; Davis, L.; Torres-Kolbus, J.; Chou, C.J.; Deiters, A.; Chin, J.W. Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction. Nat. Chem., 2012, 4(4), 298-304.
[148]
Mohammadi, O.; Golestanzadeh, M.; Abdouss, M. Recent advances in organic reactions catalyzed by graphene oxide and sulfonated graphene as heterogeneous nanocatalysts: A review. New J. Chem., 2017, 41(20), 11471-11497.
[149]
Murar, C.E.; Thuaud, F.; Bode, J.W. KAHA ligations that form aspartyl aldehyde residues as synthetic handles for protein modification and purification. J. Am. Chem. Soc., 2014, 136(52), 18140-18148.
[150]
Hao, Z.; Hong, S.; Chen, X.; Chen, P.R. Introducing bioorthogonal functionalities into proteins in living cells. Acc. Chem. Res., 2011, 44(9), 742-751.
[151]
Krall, N.; da Cruz, F.P.; Boutureira, O.; Bernardes, G.J.L. Site-selective protein-modification chemistry for basic biology and drug development. Nat. Chem., 2016, 8(2), 102-112.
Download PDF Flyer