Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 42, 2013, Pages 16778-16783

  Islam, Kabirul ^a   Chen, Yuling ^b   Wu, Hong ^b   Bothwell, Ian R ^a   Blum, Gil J ^a   Zeng, Hong ^c   Dong, Aiping ^c   Zheng, Weihong ^a   Min, Jinrong ^c,d   Deng, Haiteng ^b   Luo, Minkui ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b TSINGHUA UNIVERSITY   (China)

^c UNIVERSITY OF TORONTO   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

Bump hole; Epigenetic; Posttranslation; Proteomics

Indexed keywords

CCAAT BINDING FACTOR; DNA (CYTOSINE 5) METHYLTRANSFERASE; ELACRIDAR; EPTAPIRONE; NUCLEAR PROTEIN; NUCLEOLIN; PROTEIN METHYLTRANSFERASE; PROTEIN METHYLTRANSFERASE COFACTOR; PROTEOME; RNA HELICASE; S ADENOSYLMETHIONINE; SULFONIUM DERIVATIVE; UNCLASSIFIED DRUG; VINFLUNINE;

ALKYLATION; ARTICLE; CELL LYSATE; CELLULAR DISTRIBUTION; CHEMICAL STRUCTURE; CHROMATIN ASSEMBLY AND DISASSEMBLY; COMPARATIVE STUDY; CONTROLLED STUDY; GAIN OF FUNCTION MUTATION; HUMAN; HUMAN CELL; HUMAN TISSUE; LIQUID CHROMATOGRAPHY; MOLECULAR GENETICS; ORTHOGONAL ROTATION; PRIORITY JOURNAL; PROTEIN METHYLATION; PROTEIN MODIFICATION; PROTEIN PROCESSING; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY; VALIDATION STUDY;

BUMP-HOLE; EPIGENETIC; POSTTRANSLATION; PROTEOMICS;

HEK293 CELLS; HISTOCOMPATIBILITY ANTIGENS; HISTONE-LYSINE N-METHYLTRANSFERASE; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; METHYLATION; NEOPLASM PROTEINS; NEOPLASMS; PROTEIN-ARGININE N-METHYLTRANSFERASES; S-ADENOSYLMETHIONINE; SUBSTRATE SPECIFICITY;

EID: 84885710981     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1216365110     Document Type: Article

References (36)

1. Martin C, Zhang Y (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6(11): 838-849.
2. Zhang X, Wen H, Shi X (2012) Lysine methylation: Beyond histones. Acta Biochim Biophys Sin (Shanghai) 44(1): 14-27.
3. Erce MA, Pang CN, Hart-Smith G, Wilkins MR (2012) The methylproteome and the intracellular methylation network. Proteomics 12(4-5): 564-586.
4. Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 14(11): 1025-1040.
5. Bhaumik SR, Smith E, Shilatifard A (2007) Covalent modifications of histones during development and disease pathogenesis. Nat Struct Mol Biol 14(11): 1008-1016.
6. Fontecave M, Atta M, Mulliez E (2004) S-adenosylmethionine: Nothing goes to waste. Trends Biochem Sci 29(5): 243-249.
7. Dillon SC, Zhang X, Trievel RC, Cheng X (2005) The SET-domain protein superfamily: Protein lysine methyltransferases. Genome Biol 6(8): 227.
8. Fritsch L, et al. (2010) A subset of the histone H3 lysine 9 methyltransferases Suv39h1, G9a, GLP, and SETDB1 participate in a multimeric complex. Mol Cell 37(1): 46-56.
9. Rathert P, Dhayalan A, Ma HM, Jeltsch A (2008) Specificity of protein lysine methyltransferases and methods for detection of lysine methylation of non-histone proteins. Mol Biosyst 4(12): 1186-1190.
10. Luo M (2012) Current chemical biology approaches to interrogate protein methyltransferases. ACS Chem Biol 7(3): 443-463.
11. Demko ZP, Sharpless KB (2002) A click chemistry approach to tetrazoles by Huisgen 1,3-dipolar cycloaddition: Synthesis of 5-sulfonyl tetrazoles from azides and sulfonyl cyanides. Angew Chem Int Ed Engl 41(12): 2110-2113.
12. Tornøe CW, Christensen C, Meldal M (2002) Peptidotriazoles on solid phase: [1,2,3]- triazoles by regiospecific copper(i)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J Org Chem 67(9): 3057-3064.
13. Islam K, et al. (2012) Bioorthogonal profiling of protein methylation using azido derivative of S-adenosyl-L-methionine. J Am Chem Soc 134(13): 5909-5915.
14. Bishop AC, Buzko O, Shokat KM (2001) Magic bullets for protein kinases. Trends Cell Biol 11(4): 167-172.
15. Rathert P, et al. (2008) Protein lysine methyltransferase G9a acts on non-histone targets. Nat Chem Biol 4(6): 344-346.
16. Huang J, et al. (2010) G9a and Glp methylate lysine 373 in the tumor suppressor p53. J Biol Chem 285(13): 9636-9641.
17. Lee JS, et al. (2010) Negative regulation of hypoxic responses via induced Reptin methylation. Mol Cell 39(1): 71-85.
18. Pless O, et al. (2008) G9a-mediated lysine methylation alters the function of CCAAT/enhancer-binding protein-beta. J Biol Chem 283(39): 26357-26363.
19. Ling BM, et al. (2012) Lysine methyltransferase G9a methylates the transcription factor MyoD and regulates skeletal muscle differentiation. Proc Natl Acad Sci USA 109(3): 841-846.
20. Chang Y, et al. (2011) MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a. Nat Commun 2: 533.
21. Chin HG, et al. (2007) Automethylation of G9a and its implication in wider substrate specificity and HP1 binding. Nucleic Acids Res 35(21): 7313-7323.
22. Shinkai Y, Tachibana M (2011) H3K9 methyltransferase G9a and the related molecule GLP. Genes Dev 25(8): 781-788.
23. Binda O, et al. (2011) A chemical method for labeling lysine methyltransferase substrates. ChemBioChem 12(2): 330-334.
24. Peters W, et al. (2010) Enzymatic site-specific functionalization of protein methyltransferase substrates with alkynes for click labeling. Angew Chem Int Ed Engl 49(30): 5170-5173.
25. Islam K, Zheng W, Yu H, Deng H, Luo M (2011) Expanding cofactor repertoire of protein lysine methyltransferase for substrate labeling. ACS Chem Biol 6(7): 679-684.
26. Wang R, Zheng W, Yu H, Deng H, Luo M (2011) Labeling substrates of protein arginine methyltransferase with engineered enzymes and matched S-adenosyl-L-methionine analogues. J Am Chem Soc 133(20): 7648-7651.
27. Chakraborty D, Islam K, LuoM(2012) Facile synthesis and altered ionization efficiency of diverse Ne-alkyllysine-containing peptides. Chem Commun (Camb) 48(10): 1514-1516.
28. Wu H, et al. (2010) Structural biology of human H3K9 methyltransferases. PLoS ONE 5(1):e8570.
29. Cheng XD, Collins RE, Zhang X (2005) Structural and sequence motifs of protein (histone) methylation enzymes. Annu Rev Biophys Biomol Struct 34: 267-294.
30. Kouzarides T (2007) SnapShot: Histone-modifying enzymes. Cell 128(4): 802-803.
31. Charron G, et al. (2009) Robust fluorescent detection of protein fatty-acylation with chemical reporters. J Am Chem Soc 131(13): 4967-4975.
32. Yang YY, Grammel M, Raghavan AS, Charron G, Hang HC (2010) Comparative analysis of cleavable azobenzene-based affinity tags for bioorthogonal chemical proteomics. Chem Biol 17(11): 1212-1222.
33. Dalhoff C, Lukinavicius G, Klimasauskas S, Weinhold E (2006) Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases. Nat Chem Biol 2(1): 31-32.
34. Horowitz S, Yesselman JD, Al-Hashimi HM, Trievel RC (2011) Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9. J Biol Chem 286(21): 18658-18663.
35. Couture JF, Hauk G, Thompson MJ, Blackburn GM, Trievel RC (2006) Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases. J Biol Chem 281(28): 19280-19287.
36. Estève PO, et al. (2005) Functional analysis of the N- and C-terminus of mammalian G9a histone H3 methyltransferase. Nucleic Acids Res 33(10): 3211-3223.