Prediction of Nε-acetylation on internal lysines implemented in Bayesian Discriminant Method

Biochemical and Biophysical Research Communications

Volumn 350, Issue 4, 2006, Pages 818-824

  Li, Ao ^a   Xue, Yu ^b   Jin, Changjiang ^b   Wang, Minghui ^c   Yao, Xuebiao ^b,d  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^c BEIJING UNIVERSITY OF TECHNOLOGY   (China)

^d MOREHOUSE SCHOOL OF MEDICINE   (United States)

Author keywords

Bayesian Discriminant Method; Computational analyses; Internal; Lysine; N Acetylation; PAIL; Post translation modification

Indexed keywords

LYSINE; PROTEIN; ACYLTRANSFERASE;

ACETYLATION; ALGORITHM; ARTICLE; BAYES THEOREM; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; VALIDATION PROCESS; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DISCRIMINANT ANALYSIS; METHODOLOGY; PROTEIN BINDING; SEQUENCE ANALYSIS;

ACETYLATION; ACETYLTRANSFERASES; BAYES THEOREM; BINDING SITES; COMPUTER SIMULATION; DISCRIMINANT ANALYSIS; LYSINE; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; SEQUENCE ANALYSIS, PROTEIN;

EID: 33750051342     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.08.199     Document Type: Article

References (31)

1. Glozak M.A., Sengupta N., Zhang X., and Seto E. Acetylation and deacetylation of non-histone proteins. Gene 363 (2005) 15-23
2. Kouzarides T. Acetylation: a regulatory modification to rival phosphorylation?. EMBO J. 19 (2000) 1176-1179
3. Polevoda B., and Sherman F. Nalpha-terminal acetylation of eukaryotic proteins. J. Biol. Chem. 275 (2000) 36479-36482
4. Polevoda B., and Sherman F. The diversity of acetylated proteins. Genome Biol. 3 (2002) reviews0006
5. Yang X.J. The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases. Nucleic Acids Res. 32 (2004) 959-976
6. Bannister A.J., Miska E.A., Gorlich D., and Kouzarides T. Acetylation of importin-alpha nuclear import factors by CBP/p300. Curr. Biol. 10 (2000) 467-470
7. Brunet A., Sweeney L.B., Sturgill J.F., Chua K.F., Greer P.L., Lin Y., Tran H., Ross S.E., Mostoslavsky R., Cohen H.Y., Hu L.S., Cheng H.L., Jedrychowski M.P., Gygi S.P., Sinclair D.A., Alt F.W., and Greenberg M.E. Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science 303 (2004) 2011-2015
8. Cohen H.Y., Lavu S., Bitterman K.J., Hekking B., Imahiyerobo T.A., Miller C., Frye R., Ploegh H., Kessler B.M., and Sinclair D.A. Acetylation of the C terminus of Ku70 by CBP and PCAF controls Bax-mediated apoptosis. Mol. Cell 13 (2004) 627-638
9. Faiola F., Liu X., Lo S., Pan S., Zhang K., Lymar E., Farina A., and Martinez E. Dual regulation of c-Myc by p300 via acetylation-dependent control of Myc protein turnover and coactivation of Myc-induced transcription. Mol. Cell. Biol. 25 (2005) 10220-10234
10. Murr R., Loizou J.I., Yang Y.G., Cuenin C., Li H., Wang Z.Q., and Herceg Z. Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks. Nat. Cell Biol. 8 (2006) 91-99
11. Subramanian C., Opipari Jr. A.W., Bian X., Castle V.P., and Kwok R.P. Ku70 acetylation mediates neuroblastoma cell death induced by histone deacetylase inhibitors. Proc. Natl. Acad. Sci. USA 102 (2005) 4842-4847
12. Yuan Z.L., Guan Y.J., Chatterjee D., and Chin Y.E. Stat3 dimerization regulated by reversible acetylation of a single lysine residue. Science 307 (2005) 269-273
13. Yang X.J. Lysine acetylation and the bromodomain: a new partnership for signaling. Bioessays 26 (2004) 1076-1087
14. Marsh V.L., Peak-Chew S.Y., and Bell S.D. Sir2 and the acetyltransferase, Pat, regulate the archaeal chromatin protein, Alba. J. Biol. Chem. 280 (2005) 21122-21128
15. Starai V.J., Gardner J.G., and Escalante-Semerena J.C. Residue Leu-641 of acetyl-CoA synthetase is critical for the acetylation of residue Lys-609 by the protein acetyltransferase enzyme of Salmonella enterica. J. Biol. Chem. 280 (2005) 26200-26205
16. Cereseto A., Manganaro L., Gutierrez M.I., Terreni M., Fittipaldi A., Lusic M., Marcello A., and Giacca M. Acetylation of HIV-1 integrase by p300 regulates viral integration. EMBO J. 24 (2005) 3070-3081
17. Verdin E., Dequiedt F., and Kasler H.G. Class II histone deacetylases: versatile regulators. Trends Genet. 19 (2003) 286-293
18. Li D., Yea S., Dolios G., Martignetti J.A., Narla G., Wang R., Walsh M.J., and Friedman S.L. Regulation of Kruppel-like factor 6 tumor suppressor activity by acetylation. Cancer Res. 65 (2005) 9216-9225
19. Bae S.C., and Lee Y.H. Phosphorylation, acetylation and ubiquitination: the molecular basis of RUNX regulation. Gene (2005)
20. Barnes P.J., Adcock I.M., and Ito K. Histone acetylation and deacetylation: importance in inflammatory lung diseases. Eur. Respir J. 25 (2005) 552-563
21. Iwabata H., Yoshida M., and Komatsu Y. Proteomic analysis of organ-specific post-translational lysine-acetylation and -methylation in mice by use of anti-acetyllysine and -methyllysine mouse monoclonal antibodies. Proteomics 5 (2005) 4653-4664
22. Kelly W.K., and Marks P.A. Drug insight: Histone deacetylase inhibitors-development of the new targeted anticancer agent suberoylanilide hydroxamic acid. Nat. Clin. Pract. Oncol. 2 (2005) 150-157
23. Tabe Y., Konopleva M., Contractor R., Munsell M., Schober W.D., Jin L., Tsutsumi-Ishii Y., Nagaoka I., Igari J., and Andreeff M. Upregulation of MDR1 and induction of doxorubicin resistance by histone deacetylase inhibitor depsipeptide (FK228) and ATRA in acute promyelocytic leukemia cells. Blood (2005)
24. Dormeyer W., Ott M., and Schnolzer M. Probing lysine acetylation in proteins: strategies, limitations, and pitfalls of in vitro acetyltransferase assays. Mol. Cell. Proteomics 4 (2005) 1226-1239
25. Kiemer L., Bendtsen J.D., and Blom N. NetAcet: prediction of N-terminal acetylation sites. Bioinformatics 21 (2005) 1269-1270
26. Liu Y., and Lin Y. A novel method for N-terminal acetylation prediction. Genomics Proteomics Bioinformatics 2 (2004) 253-255
27. Xue Y., Li A., Wang L., Xu W., Feng H., and Yao X. PPSP: prediction of PK-Specific phosphorylation site with Bayesian Decision Theory. BMC Bioinformatics 7 (2006) 163
28. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
29. Xue Y., Zhou F., Zhu M., Ahmed K., Chen G., and Yao X. GPS: a comprehensive www server for phosphorylation sites prediction. Nucleic Acids Res. 33 (2005) W184-W187
30. Zhou F.F., Xue Y., Chen G.L., and Yao X. GPS: a novel group-based phosphorylation predicting and scoring method. Biochem. Biophys. Res. Commun. 325 (2004) 1443-1448
31. Xie D., Li A., Wang M., Fan Z., and Feng H. LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST. Nucleic Acids Res. 33 (2005) W105-W110