GSHSite: Exploiting an iteratively statistical method to identify S-glutathionylation sites with substrate specificity

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Chen, Yi Ju ^a   Lu, Cheng Tsung ^b   Huang, Kai Yao ^b   Wu, Hsin Yi ^a   Chen, Yu Ju ^a   Lee, Tzong Yi ^b  

^a INSTITUTE OF CHEMISTRY   (Taiwan)

^b YUAN ZE UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; GLUTATHIONE; PROTEIN TYROSINE PHOSPHATASE 1B; THIOREDOXIN; PROTEIN;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; ENZYME SPECIFICITY; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; GLUTATHIONYLATION; MATHEMATICAL MODEL; MEASUREMENT ACCURACY; PREDICTION; PROTEIN MODIFICATION; PROTEIN MOTIF; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS; SUPPORT VECTOR MACHINE; ANIMAL; BIOLOGY; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR GENETICS; MOUSE; PROCEDURES; PROTEIN DATABASE; PROTEIN PROCESSING; SEQUENCE HOMOLOGY;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; CYSTEINE; DATABASES, PROTEIN; GLUTATHIONE; HUMANS; MICE; MOLECULAR SEQUENCE DATA; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY; SUPPORT VECTOR MACHINE; THIOREDOXINS;

EID: 84929493080     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0118752     Document Type: Article

References (51)

1. Ghezzi P (2013) Protein glutathionylation in health and disease. Biochim Biophys Acta 1830: 3165-3172. doi: 10.1016/j.bbagen.2013.02.009 PMID: 23416063
2. Pastore A, Piemonte F (2012) S-Glutathionylation signaling in cell biology: Progress and prospects. Eur J Pharm Sci 46: 279-292. doi: 10.1016/j.ejps.2012.03.010 PMID: 22484331
3. Dalle-Donne I, Rossi R, Colombo G, Giustarini D, Milzani A (2009) Protein S-glutathionylation: a regulatory device from bacteria to humans. Trends Biochem Sci 34: 85-96. doi: 10.1016/j.tibs.2008.11.002 PMID: 19135374
4. Dalle-Donne I, Rossi R, Giustarini D, Colombo R, Milzani A (2007) S-glutathionylation in protein redox regulation. Free Radic Biol Med 43: 883-898. PMID: 17697933
5. Gallogly MM, Mieyal JJ (2007) Mechanisms of reversible protein glutathionylation in redox signaling and oxidative stress. Curr Opin Pharmacol 7: 381-391. PMID: 17662654
6. Dalle-Donne I, Milzani A, Gagliano N, Colombo R, Giustarini D, Rossi R (2008) Molecular mechanisms and potential clinical significance of S-glutathionylation. Antioxid Redox Signal 10: 445-473. PMID: 18092936
7. Mieyal JJ, Chock PB (2012) Posttranslational modification of cysteine in redox signaling and oxidative stress: Focus on S-glutathionylation. Antioxid Redox Signal 16: 471-475. doi: 10.1089/ars.2011.4454 PMID: 22136616
8. Grek CL, Zhang J, Manevich Y, Townsend DM, Tew KD (2013) Causes and consequences of cysteine S-glutathionylation. J Biol Chem 288: 26497-26504. doi: 10.1074/jbc.R113.461368 PMID: 23861399
9. Lind C, Gerdes R, Hamnell Y, Schuppe-Koistinen I, von Lowenhielm HB, Holmgren A, et al. (2002) Identification of S-glutathionylated cellular proteins during oxidative stress and constitutive metabolism by affinity purification and proteomic analysis. Arch Biochem Biophys 406: 229-240. PMID: 12361711
10. Newman SF, Sultana R, Perluigi M, Coccia R, Cai J, Pierce WM, et al. (2007) An increase in S-glutathionylated proteins in the Alzheimer's disease inferior parietal lobule, a proteomics approach. J Neurosci Res 85: 1506-1514. PMID: 17387692
11. Chiang BY, Chou CC, Hsieh FT, Gao S, Lin JC, Lin SH, et al. (2012) In vivo tagging and characterization of S-glutathionylated proteins by a chemoenzymatic method. Angew Chem Int Ed Engl 51: 5871-5875. doi: 10.1002/anie.201200321 PMID: 22555962
12. Dosztányi Z, Magyar C, Tusnády GE, Cserzö M, Fiser A, Simon I (2003) Servers for sequence-structure relationship analysis and prediction. Nucl Acids Res 31: 3359-3363. PMID: 12824327
13. Marino SM, Gladyshev VN (2012) Analysis and Functional Prediction of Reactive Cysteine Residues. J Biol Chem 287: 4419-4425. doi: 10.1074/jbc.R111.275578 PMID: 22157013
14. Sun M-a, Wang Y, Cheng H, Zhang Q, Ge W, Guo D (2012) RedoxDB - a curated database for experimentally verified protein oxidative modification. Bioinformatics 28: 2551-2552. PMID: 22833525
15. Mucchielli-Giorgi MH, Hazout S, Tufféry P (2002) Predicting the disulfide bonding state of cysteines using protein descriptors. Proteins 46: 243-249. PMID: 11835499
16. Sun C, Shi Z-Z, Zhou X, Chen L, Zhao X-M (2013) Prediction of S-Glutathionylation Sites Based on Protein Sequences. PLoS ONE 8: e55512. doi: 10.1371/journal.pone.0055512 PMID: 23418443
17. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94. PMID: 9149143
18. Su D, Gaffrey MJ, Guo J, Hatchell KE, Chu RK, Clauss TRW, et al. (2014) Proteomic identification and quantification of S-glutathionylation in mouse macrophages using resin-assisted enrichment and isobaric labeling. Free Radic Biol Med 67: 460-470. doi: 10.1016/j.freeradbiomed.2013.12.004 PMID: 24333276
19. Shien DM, Lee TY, Chang WC, Hsu JB, Horng JT, Hsu PC, et al. (2009) Incorporating structural characteristics for identification of protein methylation sites. J Comput Chem 30: 1532-1543. doi: 10.1002/jcc.21232 PMID: 19263424
20. Lee TY, Chen SA, Hung HY, Ou YY (2011) Incorporating distant sequence features and radial basis function networks to identify ubiquitin conjugation sites. PLoS One 6: e17331. doi: 10.1371/journal.pone.0017331 PMID: 21408064
21. Tatusova TA, Madden TL (1999) BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174: 247-250. PMID: 10339815
22. Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 89: 10915-10919. PMID: 1438297
23. Chang WC, Lee TY, Shien DM, Hsu JB, Horng JT, Hsu PC, et al. (2009) Incorporating support vector machine for identifying protein tyrosine sulfation sites. J Comput Chem.
24. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190. PMID: 15173120
25. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100. PMID: 2172928
26. Hsu JB, Bretana NA, Lee TY, Huang HD (2011) Incorporating evolutionary information and functional domains for identifying RNA splicing factors in humans. PLoS One 6: e27567. doi: 10.1371/journal.pone.0027567 PMID: 22110674
27. Xie D, Li A, Wang M, Fan Z, Feng H (2005) LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST. Nucleic Acids Res 33: W105-110. PMID: 15980436
28. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195-202. PMID: 10493868
29. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. PMID: 9254694
30. Pang CN, Hayen A, Wilkins MR (2007) Surface accessibility of protein post-translational modifications. J Proteome Res 6: 1833-1845. PMID: 17428077
31. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242. PMID: 10592235
32. Ahmad S, Gromiha MM, Sarai A (2003) RVP-net: online prediction of real valued accessible surface area of proteins from single sequences. Bioinformatics 19: 1849-1851. PMID: 14512359
33. Ahmad S, Gromiha MM, Sarai A (2003) Real value prediction of solvent accessibility from amino acid sequence. Proteins 50: 629-635. PMID: 12577269
34. Lee TY, Chen YJ, Lu CT, Ching WC, Teng YC, Huang HD (2012) dbSNO: a database of cysteine Snitrosylation. Bioinformatics 28: 2293-2295. doi: 10.1093/bioinformatics/bts436 PMID: 22782549
35. Bretana NA, Lu CT, Chiang CY, Su MG, Huang KY, Lee TY, et al. (2012) Identifying protein phosphorylation sites with kinase substrate specificity on human viruses. PLoS One 7: e40694. doi: 10.1371/journal.pone.0040694 PMID: 22844408
36. Lee TY, Lin ZQ, Hsieh SJ, Bretana NA, Lu CT (2011) Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences. Bioinformatics 27: 1780-1787. doi: 10.1093/bioinformatics/btr291 PMID: 21551145
37. Lee TY, Bretana NA, Lu CT (2011) PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity. BMC Bioinformatics 12: 261. doi: 10.1186/1471-2105-12-261 PMID: 21703007
38. Wong YH, Lee TY, Liang HK, Huang CM, Wang TY, Yang YH, et al. (2007) KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res 35: W588-594. PMID: 17517770
39. Huang HD, Lee TY, Tzeng SW, Wu LC, Horng JT, Tsou AP, et al. (2005) Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. J Comput Chem 26: 1032-1041. PMID: 15889432
40. Huang HD, Lee TY, Tzeng SW, Horng JT (2005) KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res 33: W226-229. PMID: 15980458
41. Chang C-C, Lin C-J (2011) LIBSVM: a library for support vector machines. ACM Transactions on Intelligent Systems and Technology 2: 1-27.
42. Lu CT, Chen SA, Bretana NA, Cheng TH, Lee TY (2011) Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites. J Comput Aided Mol Des 25: 987-995. doi: 10.1007/s10822-011-9477-2 PMID: 22038416
43. Vacic V, Iakoucheva LM, Radivojac P (2006) Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics 22: 1536-1537. PMID: 16632492
44. Wu C, Liu T, Chen W, Oka S-i, Fu C, Jain MR, et al. (2010) Redox Regulatory Mechanism of Transnitrosylation by Thioredoxin. Mol Cell Proteomics: (In press).
45. Chen Y-Y, Chu H-M, Pan K-T, Teng C-H, Wang D-L, Wang AHJ, et al. (2008) Cysteine S-Nitrosylation Protects Protein-tyrosine Phosphatase 1B against Oxidation-induced Permanent Inactivation. J Biol Chem 283: 35265-35272. doi: 10.1074/jbc.M805287200 PMID: 18840608
46. Lee T-Y, Chen Y-J, Lu C-T, Ching W-C, Teng Y-C, Huang H-D, et al. (2012) dbSNO: a database of cysteine S-nitrosylation. Bioinformatics 28: 2293-2295. doi: 10.1093/bioinformatics/bts436 PMID: 22782549
47. Wu C, Parrott AM, Liu T, Jain MR, Yang Y, Sadoshima J, et al. (2011) Distinction of thioredoxin transnitrosylation and denitrosylation target proteins by the ICAT quantitative approach. J Proteomics 74: 2498-2509. doi: 10.1016/j.jprot.2011.06.001 PMID: 21704743
48. Wu C, Liu T, Chen W, Oka S-i, Fu C, Jain MR, et al. (2010) Redox Regulatory Mechanism of Transnitrosylation by Thioredoxin. Mol Cell Proteomics 9: 2262-2275. doi: 10.1074/mcp.M110.000034 PMID: 20660346
49. Benhar M, Forrester MT, Hess DT, Stamler JS (2008) Regulated Protein Denitrosylation by Cytosolic and Mitochondrial Thioredoxins. Science 320: 1050-1054. doi: 10.1126/science.1158265 PMID: 18497292
50. Casagrande S, Bonetto V, Fratelli M, Gianazza E, Eberini I, Massignan T, et al. (2002) Glutathionylation of human thioredoxin: A possible crosstalk between the glutathione and thioredoxin systems. Proc Natl Acad Sci U S A 99: 9745-9749. PMID: 12119401
51. Silva GM, Netto LES, Discola KF, Piassa-Filho GM, Pimenta DC, Bárcena JA, et al. (2008) Role of glutaredoxin 2 and cytosolic thioredoxins in cysteinyl-based redox modification of the 20S proteasome. FEBS J 275: 2942-2955. doi: 10.1111/j.1742-4658.2008.06441.x PMID: 18435761