Prediction of protein amidation sites by feature selection and analysis

Molecular Genetics and Genomics

Volumn 288, Issue 9, 2013, Pages 391-400

  Cui, Weiren ^b   Niu, Shen ^b,c   Zheng, Lulu ^c,d   Hu, Lele ^a   Huang, Tao ^b,c   Gu, Lei ^e   Feng, Kaiyan ^c   Zhang, Ning ^f   Cai, Yudong ^a   Li, Yixue ^b,c  

^a SHANGHAI UNIVERSITY   (China)

^b Chinese Academy of Sciences   (China)

^c SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^d HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^e GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^f TIANJIN UNIVERSITY   (China)

Author keywords

Amidation; Incremental feature selection; Maximum relevance minimum redundancy; Nearest neighbor algorithm

Indexed keywords

ALGORITHM; AMIDATION; ARTICLE; K NEAREST NEIGHBOR; PREDICTION; PRIORITY JOURNAL; PROTEIN AMIDATION SITE; PROTEIN PROCESSING; PROTEIN STRUCTURE;

ALGORITHMS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

INVERTEBRATA; VERTEBRATA;

EID: 84884291415     PISSN: 16174615     EISSN: 16174623     Source Type: Journal    
DOI: 10.1007/s00438-013-0760-x     Document Type: Article

References (44)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402 [pii: gka562]
2. Apweiler R, Martin MJ, O'Donovan C, Magrane M, Alam-Faruque Y, Antunes R, Barrell D, Bely B, Bingley M, Binns D, Bower L, Browne P, Chan WM, Dimmer E, Eberhardt R, Fedotov A, Foulger R, Garavelli J, Huntley R, Jacobsen J, Kleen M, Laiho K, Leinonen R, Legge D, Lin Q, Liu WD, Luo J, Orchard S, Patient S, Poggioli D, Pruess M, Corbett M, di Martino G, Donnelly M, van Rensburg P, Bairoch A, Bougueleret L, Xenarios I, Altairac S, Auchincloss A, Argoud-Puy G, Axelsen K, Baratin D, Blatter MC, Boeckmann B, Bolleman J, Bollondi L, Boutet E, Quintaje SB, Breuza L, Bridge A, deCastro E, Ciapina L, Coral D, Coudert E, Cusin I, Delbard G, Doche M, Dornevil D, Roggli PD, Duvaud S, Estreicher A, Famiglietti L, Feuermann M, Gehant S, Farriol-Mathis N, Ferro S, Gasteiger E, Gateau A, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Hulo N, James J, Jimenez S, Jungo F, Kappler T, Keller G, Lachaize C, Lane-Guermonprez L, Langendijk-Genevaux P, Lara V, Lemercier P, Lieberherr D, Lima TD, Mangold V, Martin X, Masson P, Moinat M, Morgat A, Mottaz A, Paesano S, Pedruzzi I, Pilbout S, Pillet V, Poux S, Pozzato M, Redaschi N, Rivoire C, Roechert B, Schneider M, Sigrist C, Sonesson K, Staehli S, Stanley E, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey AL, Yip LN, Zuletta L, Wu C, Arighi C, Arminski L, Barker W, Chen CM, Chen YX, Hu ZZ, Huang HZ, Mazumder R, McGarvey P, Natale DA, Nchoutmboube J, Petrova N, Subramanian N, Suzek BE, Ugochukwu U, Vasudevan S, Vinayaka CR, Yeh LS, Zhang J, Consortium U (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38:D142-D148. doi: 10.1093/Nar/Gkp846
3. Atchley WR, Zhao J, Fernandes AD, Druke T (2005) Solving the protein sequence metric problem. Proc Natl Acad Sci USA 102(18):6395-6400. doi: 10.1073/pnas.0408677102
4. Bousquet-Moore D, Prohaska JR, Nillni EA, Czyzyk T, Wetsel WC, Mains RE, Eipper BA (2010) Interactions of peptide amidation and copper: novel biomarkers and mechanisms of neural dysfunction. Neurobiol Dis 37(1):130-140. doi: 10.1016/j.nbd.2009.09.016
5. Cai Y, He J, Li X, Lu L, Yang X, Feng K, Lu W, Kong X (2009) A novel computational approach to predict transcription factor DNA binding preference. J Proteome Res 8(2):999-1003. doi: 10.1021/pr800717y
6. Cheng J, Randall AZ, Sweredoski MJ, Baldi P (2005) SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 33:W72-W76. doi: 10.1093/Nar/Gki396
7. Chufan EE, De M, Eipper BA, Mains RE, Amzel LM (2009) Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme. Structure 17(7):965-973. doi: 10.1016/j.str.2009.05.008
8. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14(6):1188-1190. doi: 10.1101/gr.849004
9. De M, Bell J, Blackburn NJ, Mains RE, Eipper BA (2006) Role for an essential tyrosine in peptide amidation. J Biol Chem 281(30):20873-20882
10. Dennison SR, Phoenix DA (2011) Influence of C-terminal amidation on the efficacy of Modelin-5. Biochemistry 50:1514-1523
11. Dennison SR, Harris F, Bhatt T, Singh J, Phoenix DA (2009) The effect of C-terminal amidation on the efficacy and selectivity of antimicrobial and anticancer peptides. Mol Cell Biochem 332(1-2):43-50. doi: 10.1007/s11010-009- 0172-8
12. Driscoll WJ, Mueller SA, Eipper BA, Mueller GP (1999) Differential regulation of peptide α-amidation by dexamethasone and disulfiram. Mol Pharmacol 55:1067-1076
13. Eipper BA, Milgram SL, Husten EJ, Yun HY, Mains RE (1993) Peptidylglycine alpha-amidating monooxygenase: a multifunctional protein with catalytic, processing, and routing domains. Protein Sci 2(4):489-497
14. Eipper BA, Stoffers DA, Mains RE (1992) The biosynthesis of neuropeptides: peptide alpha-amidation. Annu Rev Neurosci 15:57-85. doi: 10.1146/annurev.ne.15.030192.000421
15. Goldschmidt L, Teng PK, Riek R, Eisenberg D (2010) Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proc Natl Acad Sci USA 107(8):3487-3492. doi: 10.1073/pnas.0915166107
16. Huang T, Cui W, Hu L, Feng K, Li YX, Cai YD (2009) Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles. PLoS ONE 4(12):e8126. doi: 10.1371/journal.pone.0008126
17. Huang T, Shi XH, Wang P, He Z, Feng KY, Hu L, Kong X, Li YX, Cai YD, Chou KC (2010) Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS ONE 5(6):e10972. doi: 10.1371/journal.pone.0010972
18. Huang T, Tu K, Shyr Y, Wei CC, Xie L, Li YX (2008) The prediction of interferon treatment effects based on time series microarray gene expression profiles. J Transl Med 6:44. doi: 10.1186/1479-5876-6-44
19. 2 and Pro-Tyr-NH2 hydrochloride salts. Chem Pharm Bull (Tokyo) 50(5):571-577
20. Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, Suzek BE, Martin MJ, McGarvey P, Gasteiger E (2009) Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics 10:136. doi: 10.1186/1471-2105-10-136
21. Jordan IK, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV, Kondrashov AS, Sunyaev S (2005) A universal trend of amino acid gain and loss in protein evolution. Nature 433(7026):633-638. doi: 10.1038/Nature03306
22. Kang TS, Vivekanandan S, Jois SDS, Kini RM (2005) Effect of C-terminal amidation on folding and disulfide-pairing of α-conotoxin ImI. Angew Chem Int Ed 44:6333-6337
23. Katopodis AG, Ping DS, Smith CE, May SW (1991) Functional and structural characterization of peptidylamidoglycolate lyase, the enzyme catalyzing the second step in peptide amidation. Biochemistry 30(25):6189-6194
24. Kawashima S, Kanehisa M (2000) AAindex: amino acid index database. Nucleic Acids Res 28(1):374. doi: gkd029
25. Kolhekar AS, Roberts MS, Jiang N, Johnson RC, Mains RE, Eipper BA, Taghert PH (1997) Neuropeptide amidation in Drosophila: separate genes encode the two enzymes catalyzing amidation. J Neurosci 17(4):1363-1376
26. Kuyama H, Nakajima C, Nakazawa T, Nishimura O, Tsunasawa S (2009) A new approach for detecting C-terminal amidation of proteins and peptides by mass spectrometry in conjunction with chemical derivatization. Proteomics 9(16):4063-4070. doi: 10.1002/pmic.200900267
27. Liu J, Tan H, Rost B (2002) Loopy proteins appear conserved in evolution. J Mol Biol 322(1):53-64 [pii: S0022283602007362]
28. Liu MC, Yasuda S, Idell S (2007) Sulfation of nitrotyrosine: biochemistry and functional implications. IUBMB Life 59(10):622-627. doi: 10.1080/15216540701589320
29. Ma BY, Elkayam T, Wolfson H, Nussinov R (2003) Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. P Natl Acad Sci USA 100(10):5772-5777. doi: 10.1073/pnas.1030237100
30. Mueller GP, Driscoll WJ (2008) alpha-Amidated peptides: approaches for analysis. Methods Mol Biol 446:67-84. doi: 10.1007/978-1-60327-084-7-5
31. Peng H, Long F, Ding C (2005) Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell 27(8):1226-1238. doi: 10.1109/TPAMI.2005.159
32. Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z (2006) Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 7:208. doi: 10.1186/1471-2105-7-208
33. Plewczynski D, Tkacz A, Wyrwicz LS, Rychlewski L (2005) AutoMotif server: prediction of single residue post-translational modifications in proteins. Bioinformatics 21(10):2525-2527
34. Popelier PL, Aicken FM (2003) Atomic properties of selected biomolecules: quantum topological atom types of carbon occurring in natural amino acids and derived molecules. J Am Chem Soc 125(5):1284-1292. doi: 10.1021/ja0284198
35. Priggea ST, Mainsb RE, Eipperb BA, Amzel LM (2000) New insights into copper monooxygenases and peptide amidation: structure, mechanism and function. CMLS Cell Mol Life Sci 57:1236-1259
36. Qian Z, Cai YD, Li Y (2006) A novel computational method to predict transcription factor DNA binding preference. Biochem Biophys Res Commun 348(3):1034-1037
37. Rocchi P, Boudouresque F, Zamora AJ, Muracciole X, Lechevallier E, Martin PM, Ouafik L (2001) Expression of adrenomedullin and peptide amidation activity in human prostate cancer and in human prostate cancer cell lines. Cancer Res 61(3):1196-1206
38. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18(20):6097-6100
39. Shimosawa T, Kanozawa K, Nagasawa R, Mitarai T, Isoda K, Takahashi K, Ando K, Tozawa Y, Nagase M, Sasaki N, Fujita M, Takano K, Iiri T, Fujita T (2000) Adrenomedullin amidation enzyme activities in hypertensive patients. Hypertens Res 23(2):167-171
40. Tompa P (2002) Intrinsically unstructured proteins. Trends Biochem Sci 27(10):527-533 [pii: S0968000402021692]
41. Trouillas P, Berges J, Houee-Levin C (2011) Toward understanding the protein oxidation processes: (OH)-O-center dot addition on tyrosine, phenylalanine, or methionine? Int J Quantum Chem 111(6):1143-1151. doi: 10.1002/Qua.22556
42. Wilkins MR, Gasteiger E, Gooley AA, Herbert BR, Molloy MP, Binz PA, Ou K, Sanchez JC, Bairoch A, Williams KL, Hochstrasser DF (1999) High-throughput mass spectrometric discovery of protein post-translational modifications. J Mol Biol 289(3):645-657. doi: 10.1006/jmbi.1999.2794
43. Wright PE, Dyson HJ (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 293(2):321-331. doi: 10.1006/jmbi.1999.3110
44. Yamaguchi H, Sasaki K, Satomi Y, Shimbara T, Kageyama H, Mondal MS, Toshinai K, Date Y, Gonzalez LJ, Shioda S, Takao T, Nakazato M, Minamino N (2007) Peptidomic identification and biological validation of neuroendocrine regulatory peptide-1 and -2. J Biol Chem 282(36):26354-26360. doi: 10.1074/jbc.M701665200