N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites

Journal of Computational Chemistry

Volumn 31, Issue 15, 2010, Pages 2759-2771

  Lee, Tzong Yi ^a   Hsu, Justin Bo Kai ^b   Lin, Feng Mao ^b   Chang, Wen Chi ^c   Hsu, Po Chiang ^b   Huang, Hsien Da ^b  

^a YUAN ZE UNIVERSITY   (Taiwan)

^b NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^c NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

Author keywords

accessible surface area; acetyltransferase; physicochemical properties; protein acetylation; support vector machine

Indexed keywords

ACCESSIBLE SURFACE AREAS; ACETYL TRANSFERASE; ACETYLATED PROTEINS; ACETYLTRANSFERASES; AMINO ACID SEQUENCE; APOPTOSIS; BIOLOGICAL PROCESS; COLOCALIZATION; COMPUTATIONAL APPROACH; COMPUTATIONAL MODEL; CYTOKINE SIGNALING; EXPERIMENTAL IDENTIFICATION; EXPERIMENTAL VALIDATIONS; INPUT/OUTPUT INTERFACE; N-ACETYLATION; PHYSICOCHEMICAL PROPERTY; POST-TRANSLATIONAL MODIFICATIONS; PREDICTION METHODS; PREDICTIVE ACCURACY; SOLVENT ACCESSIBILITY; SUB-CELLULAR; SUBSTRATE SPECIFICITY; TEST SETS; TRANSCRIPTIONAL REGULATION; TWO STAGE;

ACETYLATION; AMINO ACIDS; CELL DEATH; SUPPORT VECTOR MACHINES;

PROTEINS;

ACYLTRANSFERASE; AMINO ACID; PROTEIN; SOLVENT;

ACETYLATION; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; BIOCATALYSIS; CHEMICAL PHENOMENA; CHEMISTRY; ISOELECTRIC POINT; METABOLISM; PROTEIN PROCESSING; THERMODYNAMICS;

ACETYLATION; ACETYLTRANSFERASES; AMINO ACID SEQUENCE; AMINO ACIDS; BINDING SITES; BIOCATALYSIS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; ISOELECTRIC POINT; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; SOLVENTS; THERMODYNAMICS;

EID: 78149461454     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21569     Document Type: Article

References (51)

1. Polevoda, B.,;, Sherman, F., J Biol Chem 2000, 275, 36479.
2. Polevoda, B.,;, Sherman, F., Genome Biol 2002, 3, reviews 0006.1 - 0006.6.
3. Polevoda, B.,;, Sherman, F., J Mol Biol 2003, 325, 595.
4. Yang, X. J., Bioessays 2004, 26, 1076.
5. Yang, X. J.,;, Gregoire, S., EMBO Rep 2007, 8, 556.
6. Glozak, M. A.,;, Sengupta, N.,;, Zhang, X.,;, Seto, E., Gene 2005, 363, 15.
7. Nightingale, K. P.,;, O'Neill, L. P.,;, Turner, B. M., Curr Opin Genet Dev 2006, 16, 125.
8. Ramanathan, B.,;, Smerdon, M. J., J Biol Chem 1989, 264, 11026.
9. Murr, R.,;, Loizou, J. I.,;, Yang, Y. G.,;, Cuenin, C.,;, Li, H.,;, Wang, Z. Q.,;, Herceg, Z., Nat Cell Biol 2006, 8, 91.
10. Groth, A.,;, Rocha, W.,;, Verreault, A.,;, Almouzni, G., Cell 2007, 128, 721.
11. Cohen, H. Y.,;, Lavu, S.,;, Bitterman, K. J.,;, Hekking, B.,;, Imahiyerobo, T. A.,;, Miller, C.,;, Frye, R.,;, Ploegh, H.,;, Kessler, B. M.,;, Sinclair, D. A., Mol Cell 2004, 13, 627.
12. Luo, J.,;, Su, F.,;, Chen, D.,;, Shiloh, A.,;, Gu, W., Nature 2000, 408, 377.
13. Subramanian, C.,;, Opipari, A. W., Jr.,;, Bian, X.,;, Castle, V. P.,;, Kwok, R. P., Proc Natl Acad Sci USA 2005, 102, 4842.
14. Tang, Y.,;, Luo, J.,;, Zhang, W.,;, Gu, W., Mol Cell 2006, 24, 827.
15. Bannister, A. J.,;, Miska, E. A.,;, Gorlich, D.,;, Kouzarides, T., Curr Biol 2000, 10, 467.
16. Kouzarides, T., EMBO J 2000, 19, 1176.
17. Medzihradszky, K. F., Methods Enzymol 2005, 402, 209.
18. Welsch, D. J.,;, Nelsestuen, G. L., Biochemistry 1988, 27, 4939.
19. Umlauf, D.,;, Goto, Y.,;, Feil, R., Methods Mol Biol 2004, 287, 99.
20. Kiemer, L.,;, Bendtsen, J. D.,;, Blom, N., Bioinformatics 2005, 21, 1269.
21. Liu, Y.,;, Lin, Y., Genomics Proteomics Bioinformatics 2004, 2, 253.
22. Li, A.,;, Xue, Y.,;, Jin, C.,;, Wang, M.,;, Yao, X., Biochem Biophys Res Commun 2006, 350, 818.
23. Basu, A.,;, Rose, K. L.,;, Zhang, J.,;, Beavis, R. C.,;, Ueberheide, B.,;, Garcia, B. A.,;, Chait, B.,;, Zhao, Y.,;, Hunt, D. F.,;, Segal, E.,;, Allis, C. D.,;, Hake, S. B., Proc Natl Acad Sci USA 2009, 106, 13785.
24. Li, S.,;, Li, H.,;, Li, M.,;, Shyr, Y.,;, Xie, L.,;, Li, Y., Protein Pept Lett 2009, 16, 977.
25. Lee, T. Y.,;, Huang, H. D.,;, Hung, J. H.,;, Huang, H. Y.,;, Yang, Y. S.,;, Wang, T. H., Nucleic Acids Res 2006, 34 (Database issue), D622.
26. Bairoch, A.,;, Apweiler, R., Nucleic Acids Res 1998, 26, 38.
27. Boeckmann, B.,;, Bairoch, A.,;, Apweiler, R.,;, Blatter, M. C.,;, Estreicher, A.,;, Gasteiger, E.,;, Martin, M. J.,;, Michoud, K.,;, O'Donovan, C.,;, Phan, I.,;, Pilbout, S.,;, Schneider, M., Nucleic Acids Res 2003, 31, 365.
28. Xue, Y.,;, Chen, H.,;, Jin, C.,;, Sun, Z.,;, Yao, X., BMC Bioinformatics 2006, 7, 458.
29. Tatusova, T. A.,;, Madden, T. L., FEMS Microbiol Lett 1999, 174, 247.
30. Shien, D. M.,;, Lee, T. Y.,;, Chang, W. C.,;, Hsu, J. B.,;, Horng, J. T.,;, Hsu, P. C.,;, Wang, T. Y.,;, Huang, H. D., J Comput Chem 2009, 30, 1532.
31. Chang, W. C.,;, Lee, T. Y.,;, Shien, D. M.,;, Hsu, J. B.,;, Horng, J. T.,;, Hsu, P. C.,;, Wang, T. Y.,;, Huang, H. D.,;, Pan, R. L., J Comput Chem 2009, 30, 2526 - 2537.
32. Hutchens, J. O., In Handbook of Biochemistry, 2nd ed.;, Sober, H. A., Ed.; Chemical Rubber Co: Cleveland, Ohio, 1970; pp. B60 - B61.
33. Oobatake, M.,;, Ooi, T., J Theor Biol 1977, 67, 567.
34. Dawson, D. M.,;, Brock, D. J. H.,;, Mayo, O., Eds.; The Biochemical Genetics of Man, Academic Press: New York, 1972; pp. 1 - 38.
35. Dayhoff, M. O.,;, Hunt, L. T.,;, Hurst-Calderone, S., In Atlas of Protein Sequence and Structure, Vol 5, Suppl 3;, Dayhoff, M. O., Ed.; National Biomedical Research Foundation: Washington, DC, 1978; p 363.
36. Charton, M., J Theor Biol 1981, 91, 115.
37. Cid, H.,;, Bunster, M.,;, Canales, M.,;, Gazitua, F., Protein Eng 1992, 5, 373.
38. Jones, D. D., J Theor Biol 1975, 50, 167.
39. Pontius, J.,;, Richelle, J.,;, Wodak, S. J., J Mol Biol 1996, 264, 121.
40. Radzicka, A.,;, Wolfenden, R., Biochemistry 1988, 27, 1664.
41. Fauchere, J. L.,;, Charton, M.,;, Kier, L. B.,;, Verloop, A.,;, Pliska, V., Int J Pept Protein Res 1988, 32, 269.
42. Zimmerman, J. M.,;, Eliezer, N.,;, Simha, R., J Theor Biol 1968, 21, 170.
43. Kawashima, S.,;, Pokarowski, P.,;, Pokarowska, M.,;, Kolinski, A.,;, Katayama, T.,;, Kanehisa, M., Nucleic Acids Res 2008, 36 (Database issue), D202 - 205.
44. Ahmad, S.,;, Gromiha, M. M.,;, Sarai, A., Bioinformatics 2003, 19, 1849.
45. Ahmad, S.,;, Gromiha, M. M.,;, Sarai, A., Proteins 2003, 50, 629.
46. Chang, C.-C.,;, Lin, C.-J., Software available at.
47. Chou, K. C.,;, Shen, H. B., Anal Biochem 2007, 370, 1.
48. Chou, K. C.,;, Zhang, C. T., Crit Rev Biochem Mol Biol 1995, 30, 275.
49. Crooks, G. E.,;, Hon, G.,;, Chandonia, J. M.,;, Brenner, S. E., Genome Res 2004, 14, 1188.
50. Schneider, T. D.,;, Stephens, R. M., Nucleic Acids Res 1990, 18, 6097.
51. Wochnik, G. M.,;, Ruegg, J.,;, Abel, G. A.,;, Schmidt, U.,;, Holsboer, F.,;, Rein, T., J Biol Chem 2005, 280, 4609.