A proteomics approach to study in vivo protein Nα-modifications

Journal of Proteomics

Volumn 73, Issue 2, 2009, Pages 240-251

  Zhang, Xumin ^a   Ye, Juanying ^a   Højrup, Peter ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Acetylation; CNBr activated Sepharose 4B; Formylation; Lys N; Propionylation; Protein N modifications

Indexed keywords

GLUTAMINE; PEPTIDE; S CARBAMOYLMETHYLCYSTEINE; SEPHAROSE; TRYPSIN; UNCLASSIFIED DRUG;

ACETYLATION; ALKYLATION; AMINO TERMINAL SEQUENCE; ARTICLE; CHEMICAL REACTION; CYCLIZATION; FORMYLATION; HELA CELL; HUMAN; HUMAN CELL; IN VIVO STUDY; PRIORITY JOURNAL; PROPIONYLATION; PROTEIN MODIFICATION; PROTEOMICS;

DATABASES, PROTEIN; HELA CELLS; HUMANS; PEPTIDE FRAGMENTS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; TANDEM MASS SPECTROMETRY; TRYPSIN;

EID: 70449519311     PISSN: 18743919     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jprot.2009.09.007     Document Type: Article

References (52)

1. Aebersold R., and Goodlett D.R. Mass spectrometry in proteomics. Chem Rev 101 (2001) 269-295
2. Olsen J.V., Macek B., Lange O., Makarov A., Horning S., and Mann M. Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods 4 (2007) 709-712
3. Krishna R.G., and Wold F. Post-translational modification of proteins. Adv Enzymol Relat Areas Mol Biol 67 (1993) 265-298
4. Delom F., and Chevet E. Phosphoprotein analysis: from proteins to proteomes. Proteome Sci 4 (2006) 15
5. Meinnel T., and Giglione C. Tools for analyzing and predicting N-terminal protein modifications. Proteomics 8 (2008) 626-649
6. Brown J.L. The N-terminal region of soluble proteins from procaryotes and eucaryotes. Biochim Biophys Acta 221 (1970) 480-488
7. Brown J.L., and Roberts W.K. Evidence that approximately eighty per cent of the soluble proteins from Ehrlich ascites cells are Nalpha-acetylated. J Biol Chem 251 (1976) 1009-1014
8. Polevoda B., and Sherman F. N alpha-terminal acetylation of eukaryotic proteins. J Biol Chem 275 (2000) 36479-36482
9. Mullen J.R., Kayne P.S., Moerschell R.P., Tsunasawa S., Gribskov M., Colavito-Shepanski M., et al. Identification and characterization of genes and mutants for an N-terminal acetyltransferase from yeast. Embo J 8 (1989) 2067-2075
10. Polevoda B., Norbeck J., Takakura H., Blomberg A., and Sherman F. Identification and specificities of N-terminal acetyltransferases from Saccharomyces cerevisiae. Embo J 18 (1999) 6155-6168
11. Berger E.M., Cox G., Weber L., and Kenney J.S. Actin acetylation in Drosophila tissue culture cells. Biochem Genet 19 (1981) 321-331
12. Tercero J.C., and Wickner R.B. MAK3 encodes an N-acetyltransferase whose modification of the L-A gag NH2 terminus is necessary for virus particle assembly. J Biol Chem 267 (1992) 20277-20281
13. Luka Z., Loukachevitch L.V., and Wagner C. Acetylation of N-terminal valine of glycine N-methyltransferase affects enzyme inhibition by folate. Biochim Biophys Acta 1784 (2008) 1342-1346
14. Arendt C.S., and Hochstrasser M. Eukaryotic 20 S proteasome catalytic subunit propeptides prevent active site inactivation by N-terminal acetylation and promote particle assembly. Embo J 18 (1999) 3575-3585
15. Siddig M.A., Kinsey J.A., Fincham J.R., and Keighren M. Frameshift mutations affecting the N-terminal sequence of Neurospora NADP-specific glutamate dehydrogenase. J Mol Biol 137 (1980) 125-135
16. de Haan E.C., Wauben M.H., Wagenaar-Hilbers J.P., Grosfeld-Stulemeyer M.C., Rijkers D.T., Moret E.E., et al. Stabilization of peptide guinea pig myelin basic protein 72-85 by N-terminal acetylation-implications for immunological studies. Mol Immunol 40 (2004) 943-948
17. Pesaresi P., Gardner N.A., Masiero S., Dietzmann A., Eichacker L., Wickner R., Salamini F., and Leister D. Cytoplasmic N-terminal protein acetylation is required for efficient photosynthesis in Arabidopsis. Plant Cell 15 (2003) 1817-1832
18. Maytum R., Geeves M.A., and Konrad M. Actomyosin regulatory properties of yeast tropomyosin are dependent upon N-terminal modification. Biochemistry 39 (2000) 11913-11920
19. Setty S.R., Strochlic T.I., Tong A.H., Boone C., and Burd C.G. Golgi targeting of ARF-like GTPase Arl3p requires its Nalpha-acetylation and the integral membrane protein Sys1p. Nat Cell Biol 6 (2004) 414-419
20. Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., et al. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol 21 (2003) 566-569
21. McDonald L., and Beynon R.J. Positional proteomics: preparation of amino-terminal peptides as a strategy for proteome simplification and characterization. Nat Protoc 1 (2006) 1790-1798
22. McDonald L., Robertson D.H., Hurst J.L., and Beynon R.J. Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides. Nat Methods 2 (2005) 955-957
23. Yamaguchi M., Nakazawa T., Kuyama H., Obama T., Ando E., Okamura T.A., et al. High-throughput method for N-terminal sequencing of proteins by MALDI mass spectrometry. Anal Chem 77 (2005) 645-651
24. Zhou C., Zhang Y., Qin P., Liu X., Zhao L., Yang S., et al. A method for rapidly confirming protein N-terminal sequences by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun Mass Spectrom 20 (2006) 2878-2884
25. Yamaguchi M., Obama T., Kuyama H., Nakayama D., Ando E., Okamura T.A., et al. Specific isolation of N-terminal fragments from proteins and their high-fidelity de novo sequencing. Rapid Commun Mass Spectrom 21 (2007) 3329-3336
26. Kuyama H., Sonomura K., Nishimura O., and Tsunasawa S. A method for N-terminal de novo sequence analysis of proteins by matrix-assisted laser desorption/ionization mass spectrometry. Anal Biochem 380 (2008) 291-296
27. Gorman J.J., and Shiell B.J. Isolation of carboxyl-termini and blocked amino-termini of viral proteins by high-performance cation-exchange chromatography. J Chromatogr 646 (1993) 193-205
28. Dormeyer W., Mohammed S., Breukelen B., Krijgsveld J., and Heck A.J. Targeted analysis of protein termini. J Proteome Res 6 (2007) 4634-4645
29. Staes A., Van Damme P., Helsens K., Demol H., Vandekerckhove J., and Gevaert K. Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics 8 (2008) 1362-1370
30. Mikami T., and Takao T. Selective isolation of N-blocked peptides by isocyanate-coupled resin. Anal Chem 79 (2007) 7910-7915
31. Akiyama T.H., Sasagawa T., Suzuki M., and Titani K. A method for selective isolation of the amino-terminal peptide from alpha-amino-blocked proteins. Anal Biochem 222 (1994) 210-216
32. Kim S.C., Chen Y., Mirza S., Xu Y., Lee J., Liu P., et al. A clean, more efficient method for in-solution digestion of protein mixtures without detergent or urea. J Proteome Res 5 (2006) 3446-3452
33. Gobom J., Nordhoff E., Mirgorodskaya E., Ekman R., and Roepstorff P. Sample purification and preparation technique based on nano-scale reversed-phase columns for the sensitive analysis of complex peptide mixtures by matrix-assisted laser desorption/ionization mass spectrometry. J Mass Spectrom 34 (1999) 105-116
34. de Jonge H.R., Hogema B., and Tilly B.C. Protein N-myristoylation: critical role in apoptosis and salt tolerance. Sci STKE (2000) 2000:PE1
35. Farazi T.A., Waksman G., and Gordon J.I. The biology and enzymology of protein N-myristoylation. J Biol Chem 276 (2001) 39501-39504
36. Martin M.L., and Busconi L. Membrane localization of a rice calcium-dependent protein kinase (CDPK) is mediated by myristoylation and palmitoylation. Plant J 24 (2000) 429-435
37. Linder M.E., and Deschenes R.J. Palmitoylation: policing protein stability and traffic. Nat Rev Mol Cell Biol 8 (2007) 74-84
38. Washburn M.P., Wolters D., and Yates III J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19 (2001) 242-247
39. Geoghegan K.F., Hoth L.R., Tan D.H., Borzilleri K.A., Withka J.M., and Boyd J.G. Cyclization of N-terminal S-carbamoylmethylcysteine causing loss of 17 Da from peptides and extra peaks in peptide maps. J Proteome Res 1 (2002) 181-187
40. Zhang X., Rogowska-Wrzesinska A., and Roepstorff P. On-target sample preparation of 4-sulfophenyl isothiocyanate-derivatized peptides using AnchorChip Targets. J Mass Spectrom 43 (2008) 346-359
41. Stark G.R. Reactions of cyanate with functional groups of proteins. 3. Reactions with amino and carboxyl groups. Biochemistry 4 (1965) 1030-1036
42. Stark G.R. Reactions of cyanate with functional groups of proteins. IV. Inertness of aliphatic hydroxyl groups. Formation of carbamyl- and acylhydantoins. Biochemistry 4 (1965) 2363-2367
43. McCarthy J., Hopwood F., Oxley D., Laver M., Castagna A., Righetti P.G., et al. Carbamylation of proteins in 2-D electrophoresis-myth or reality?. J Proteome Res 2 (2003) 239-242
44. Rabenstein D.L., Hari S.P., and Kaerner A. Determination of acid dissociation constants of peptide side-chain functional groups by two-dimensional NMR. Anal Chem 69 (1997) 4310-4316
45. Lee Y.H., Kim M.S., Choie W.S., Min H.K., and Lee S.W. Highly informative proteome analysis by combining improved N-terminal sulfonation for de novo peptide sequencing and online capillary reverse-phase liquid chromatography/tandem mass spectrometry. Proteomics 4 (2004) 1684-1694
46. Rao K.C., Carruth R.T., and Miyagi M. Proteolytic 18O labeling by peptidyl-Lys metalloendopeptidase for comparative proteomics. J Proteome Res 4 (2005) 507-514
47. Rao K.C., Palamalai V., Dunlevy J.R., and Miyagi M. Peptidyl-Lys metalloendopeptidase-catalyzed 1 fs labeling for comparative proteomics: application to cytokine/lipolysaccharide-treated human retinal pigment epithelium cell line. Mol Cell Proteomics 4 (2005) 1550-1557
48. Taouatas N., Drugan M.M., Heck A.J., and Mohammed S. Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase. Nat Methods 5 (2008) 405-407
49. Polevoda B, Sherman F. The diversity of acetylated proteins. Genome Biol 2002;3:reviews0006.
50. Polevoda B., and Sherman F. N-terminal acetyltransferases and sequence requirements for N-terminal acetylation of eukaryotic proteins. J Mol Biol 325 (2003) 595-622
51. Shen P.T., Hsu J.L., and Chen S.H. Dimethyl isotope-coded affinity selection for the analysis of free and blocked N-termini of proteins using LC-MS/MS. Anal Chem 79 (2007) 9520-9530
52. Chen Y., Sprung R., Tang Y., Ball H., Sangras B., Kim S.C., et al. Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics 6 (2007) 812-819