Prediction of Nitrosocysteine Sites Using Position and Composition Variant Features

Author(s): Yaser Daanial Khan , Aroosa Batool , Nouman Rasool , Sher Afzal Khan* , Kuo-Chen Chou .

Journal Name: Letters in Organic Chemistry

Volume 16 , Issue 4 , 2019

Become EABM
Become Reviewer

Graphical Abstract:


Abstract:

S-nitrosylation is one of the most prominent posttranslational modification among proteins. It involves the addition of nitrogen oxide group to cysteine thiols forming S-nitrosocysteine. Evidence suggests that S-nitrosylation plays a foremost role in numerous human diseases and disorders. The incorporation of techniques for robust identification of S-nitrosylated proteins is highly anticipated in biological research and drug discovery. The proposed system endeavors a novel strategy based on a statistical and computational intelligent methods for the identification of S-nitrosocystiene sites within a given primary protein sequence. For this purpose, 5-step rule was approached comprising of benchmark dataset creation, mathematical modelling, prediction, evaluation and web-server development. For position relative feature extraction, statistical moments were used and a multilayer neural network was trained adapting Gradient Descent and Adaptive Learning algorithms. The results were comparatively analyzed with existing techniques using benchmark datasets. It is inferred through conclusive experimentation that the proposed scheme is very propitious, accurate and exceptionally effective for the prediction of S-nitrosocystiene in protein sequences.

Keywords: Nitrosocystiene, prediction model, neural network, statistical moments, 5-step rule, ribosome.

[1]
Branden, C.I. Introduction to protein structure; Garland Science, 1999.
[2]
Nott, A.; Watson, P.M.; Robinson, J.D.; Crepaldi, L.; Riccio, A. Nature, 2008, 455, 411-415.
[3]
Gould, N.; Doulias, P-T.; Tenopoulou, M.; Raju, K.; Ischiropoulos, H. J. Biol. Chem., 2013, 288(37), 26473-26479.
[4]
Lee, T-Y.; Chen, Y-J.; Lu, T-C.; Huang, H-D.; Chen, Y-J. PLoS One, 2011, 6, e21849.
[5]
Xu, L.; Eu, J.P.; Meissner, G.; Stamler, J.S. Science, 1998, 279, 234-237.
[6]
Singel, D.J.; Stamler, J.S. Annu. Rev. Physiol., 2005, 67, 99-145.
[7]
Ozawa, K.; Whalen, E.J.; Nelson, C.D.; Mu, Y.; Hess, D.T.; Lefkowitz, R.J.; Stamler, J.S. Mol. Cell, 2008, 31, 395-405.
[8]
Benhar, M.; Forrester, M.T.; Hess, D.T.; Stamler, J.S. Science, 2008, 320, 1050-1054.
[9]
Nakamura, T.; Prikhodko, O.A.; Pirie, E.; Nagar, S.; Akhtar, M.W.; Oh, C-K.; McKercher, S.R.; Ambasudhan, R.; Okamoto, S-i.; Lipton, S.A. Neurobiol. Dis., 2015, 84, 99-108.
[10]
Foster, M.W.; McMahon, T.J.; Stamler, J.S. Trends Mol. Med., 2003, 9, 160-168.
[11]
Foster, M.W.; Hess, D.T.; Stamler, J.S. Trends Mol. Med., 2009, 15, 391-404.
[12]
Raju, K.; Doulias, P-T.; Tenopoulou, M.; Greene, J.L.; Ischiropoulos, H. Biochim. Biophys. Acta, 2012, 1820, 684-688.
[13]
Seth, D.; Stamler, J.S. Curr. Opin. Chem. Biol., 2011, 15, 129-136.
[14]
Jaffrey, S.R.; Snyder, S.H. Sci. STKE, 2001, 2001, pl1-pl1.
[15]
Hao, G.; Derakhshan, B.; Shi, L.; Campagne, F.; Gross, S.S. Proc. Natl. Acad. Sci. USA, 2006, 103, 1012-1017.
[16]
Forrester, M.T.; Thompson, J.W.; Foster, M.W.; Nogueira, L.; Moseley, M.A.; Stamler, J.S. Nat. Biotechnol., 2009, 27, 557-559.
[17]
Jones, D.T. J. Mol. Biol., 1999, 292, 195-202.
[18]
Xue, Y.; Liu, Z.; Gao, X.; Jin, C.; Wen, L.; Yao, X.; Ren, J. PLoS One, 2010, 5, e11290.
[19]
Xue, Y.; Ren, J.; Gao, X.; Jin, C.; Wen, L.; Yao, X. Mol. Cell. Proteomics, 2008, 7, 1598-1608.
[20]
Li, Y-X.; Shao, Y-H.; Jing, L.; Deng, N-Y. Protein Pept. Lett., 2011, 18, 573-587.
[21]
Zhang, J.; Zhao, X.; Sun, P.; Ma, Z. Int. J. Mol. Sci., 2014, 15, 11204-11219.
[22]
Kumar, R.; Srivastava, A.; Kumari, B.; Kumar, M. J. Theor. Biol., 2015, 365, 96-103.
[23]
Xu, Y.; Ding, J.; Wu, L-Y.; Chou, K-C. PLoS One, 2013, 8, e55844.
[24]
Xu, Y.; Shao, X-J.; Wu, L-Y.; Deng, N-Y.; Chou, K-C. PeerJ, 2013, 1, e171.
[25]
Jia, C.; Lin, X.; Wang, Z. Int. J. Mol. Sci., 2014, 15, 10410-10423.
[26]
Jia, C-Z.; Liu, T.; Wang, Z-P. Mol. Biosyst., 2013, 9, 2909-2913.
[27]
Xu, Y.; Chou, K-C. Curr. Top. Med. Chem., 2016, 16, 591-603.
[28]
Chou, K-C. J. Theor. Biol., 2011, 273, 236-247.
[29]
Jiao, Y.; Du, P. Quant. Biol., 2016, 4, 320-330.
[30]
Chen, X.-X.; Tang, H.; Li, W.-C.; Wu, H.; Chen, W.; Ding, H.; Lin, H. BioMed Res. Int, 2016, 2016
[31]
Feng, P.-M.; Ding, H.; Chen, W.; Lin, H. Comput. Math. Methods Med., 2013, 2013
[32]
Feng, P.-M.; Lin, H.; Chen, W. Comput. Math. Methods Med., 2013, 2013
[33]
Lai, H-Y.; Chen, X-X.; Chen, W.; Tang, H.; Lin, H. Oncotarget, 2017, 8, 28169.
[34]
Lin, H.; Ding, C.; Song, Q.; Yang, P.; Ding, H.; Deng, K-J.; Chen, W. J. Biomol. Struct. Dyn., 2012, 29, 1147-1153.
[35]
Lin, H.; Liang, Z.-Y.; Tang, H.; Chen, W. IEEE/ACM Trans. Comput. Biol. Bioinform., 2017.
[36]
Tang, H.; Zhang, C.; Chen, R.; Huang, P.; Duan, C.; Zou, P. Lett. Org. Chem., 2017, 14, 621-624.
[37]
Yang, H.; Tang, H.; Chen, X.-X.; Zhang, C.-J.; Zhu, P.-P.; Ding, H.; Chen, W.; Lin, H. BioMed Res. Int., 2016, 2016
[38]
Zhao, Y-W.; Lai, H-Y.; Tang, H.; Chen, W.; Lin, H. Sci. Rep., 2016, 6, 34817.
[39]
Akmal, M.A.; Rasool, N.; Khan, Y.D. PLoS One, 2017, 12, e0181966.
[40]
Khan, Y.D.; Ahmed, F.; Khan, S.A. Neural Comput. Appl., 2014, 24, 1519-1529.
[41]
Khan, Y.D.; Khan, N.S.; Farooq, S.; Abid, A.; Khan, S.A.; Ahmad, F.; Mahmood, M.K. Sci. World J, 2014, 2014
[42]
Khan, Y.D.; Ahmad, F.; Anwar, M.W. World Appl. Sci. J., 2012, 16, 678-685.
[43]
Khan, Y.D.; Khan, S.A.; Ahmad, F.; Islam, S. Sci. World J., 2014, 2014
[44]
Butt, A.H.; Khan, S.A.; Jamil, H.; Rasool, N.; Khan, Y.D. BioMed. Res. Int., 2016, 2016
[45]
Butt, A.H.; Rasool, N.; Khan, Y.D. J. Membr. Biol., 2017, 250, 55-76.
[46]
Chou, K-C.; Shen, H-B. Nat. Sci., 2009, 1, 63.
[47]
Chen, W.; Feng, P.; Yang, H.; Ding, H.; Lin, H.; Chou, K-C. Oncotarget, 2017, 8, 4208.
[48]
Cheng, X.; Xiao, X.; Chou, K-C. Genomics, 2017, 110, 50-58.
[49]
Cheng, X.; Xiao, X.; Chou, K-C. Mol. Biosyst., 2017, 13, 1722-1727.
[50]
Cheng, X.; Xiao, X.; Chou, K-C. Gene, 2017, 628, 315-321.
[51]
Cheng, X.; Zhao, S-G.; Lin, W-Z.; Xiao, X.; Chou, K-C. Bioinformatics, 2017, 33, 3524-3531.
[52]
Cheng, X.; Zhao, S-G.; Xiao, X.; Chou, K-C. Bioinformatics, 2016, 33, 341-346.
[53]
Feng, P.; Ding, H.; Yang, H.; Chen, W.; Lin, H.; Chou, K-C. Mol. Ther. Nucleic Acids, 2017, 7, 155-163.
[54]
Liu, B.; Wang, S.; Long, R.; Chou, K-C. Bioinformatics, 2016, 33, 35-41.
[55]
Liu, B.; Yang, F.; Chou, K-C. Mol. Ther. Nucleic Acids, 2017, 7, 267-277.
[56]
Liu, L-M.; Xu, Y.; Chou, K-C. Med. Chem., 2017, 13, 552-559.
[57]
Qiu, W.R.; Sun, B.Q.; Xiao, X.; Xu, D.; Chou, K.C. Mol. Inform., 2017, 36, 5-6.
[58]
Qiu, W-R.; Jiang, S-Y.; Xu, Z-C.; Xiao, X.; Chou, K-C. Oncotarget, 2017, 8, 41178.
[59]
Qiu, W-R.; Sun, B-Q.; Xiao, X.; Xu, Z-C.; Jia, J-H.; Chou, K-C. Genomics, 2017, 5, 239-246.
[60]
Xu, Y.; Wang, Z.; Li, C.; Chou, K-C. Med. Chem., 2017, 13, 544-551.
[61]
Chou, K-C. Med. Chem., 2015, 11, 218-234.
[62]
Chou, K-C. Curr. Top. Med. Chem., 2017, 17, 2337-2358.
[63]
Chen, W.; Yang, H.; Feng, P.; Ding, H.; Lin, H. Bioinformatics, 2017, 33, 3518-3523.
[64]
Dao, F-Y.; Yang, H.; Su, Z-D.; Yang, W.; Wu, Y.; Hui, D.; Chen, W.; Tang, H.; Lin, H. Molecules, 2017, 22, 1057.
[65]
Feng, P.; Yang, H.; Ding, H.; Lin, H.; Chen, W.; Chou, K-C. Genomics, 2018, 111, 96-102.
[66]
Zhao, Y-W.; Su, Z-D.; Yang, W.; Lin, H.; Chen, W.; Tang, H. Int. J. Mol. Sci., 2017, 18, 1838.
[67]
Feng, P.; Ding, H.; Lin, H.; Chen, W. Sci. Rep., 2017, 7, 7449.
[68]
He, B.; Chai, G.; Duan, Y.; Yan, Z.; Qiu, L.; Zhang, H.; Liu, Z.; He, Q.; Han, K.; Ru, B. Nucleic Acids Res., 2015, 44, D1127-D1132.
[69]
He, B.; Jiang, L.; Duan, Y.; Chai, G.; Fang, Y.; Kang, J.; Yu, M.; Li, N.; Tang, Z.; Yao, P. Database, 2018, 2018
[70]
Liang, Z-Y.; Lai, H-Y.; Yang, H.; Zhang, C-J.; Yang, H.; Wei, H-H.; Chen, X-X.; Zhao, Y-W.; Su, Z-D.; Li, W-C. Bioinformatics, 2017, 33, 467-469.
[71]
Zhang, T.; Tan, P.; Wang, L.; Jin, N.; Li, Y.; Zhang, L.; Yang, H.; Hu, Z.; Zhang, L.; Hu, C. Nucleic Acids Res., 2016, 45, D135-D138.


Rights & PermissionsPrintExport Cite as

Article Details

VOLUME: 16
ISSUE: 4
Year: 2019
Page: [283 - 293]
Pages: 11
DOI: 10.2174/1570178615666180802122953
Price: $58

Article Metrics

PDF: 14
HTML: 2
EPUB: 1
PRC: 1