JBiSE  Vol.2 No.1 , February 2009
Computer-Assisted analysis of subcellular localization signals and post-translational modifications of human prion proteins
ABSTRACT
In the present work, computational analyses were applied to study the subcellular localiza-tion and posttranslational modifications of hu-man prion proteins (PrPs). The tentative location of prion protein was determined to be in the nu-cleolus inside the nucleus by the following bio-informatics tools: Hum-PLoc, Euk-PLoc and Nuc-PLoc. Based on our results signal peptides with average of 22 base pairs in N-terminal were identified in human PrPs. This theoretical study demonstrates that PrP is post-translationally modified by: 1) attachment of two N-linked complex carbohydrate moieties (N181 and N197), 2) attachmet of glycosylphosphatidylinositol (GPI) at serine 230 and 3) formation of two di-sulfide bonds between “6–22” and “179–214” cysteines. Furthermore, ten protein kinase phosphorylation sites were predicted in human PrP. The above-noted phosphorylation was car-ried out by PKC and CK2. By using bioinfor-matics tools, we have shown that computation-ally human PrPs locate particularly into the nu-cleolus.

Cite this paper
nullMoosawi, F. and Mohabatkar, H. (2009) Computer-Assisted analysis of subcellular localization signals and post-translational modifications of human prion proteins. Journal of Biomedical Science and Engineering, 2, 70-75. doi: 10.4236/jbise.2009.21012.
References
[1]   G. G. Kovacs and H. Budka, (2008) Prion Diseases: From Protein to Cell Pathology. The American Journa of Pathology, 172(3): 555-565.

[2]   R. G. Will, J. W. Ironside, M. Zeidler, S. N. Cousens, K. Estibiro, A. Alperovitch, S. Poser, M. Pocchiari, A. Hofman and P. G. Smitch, (1996) A new variant of Creutsfeldt-Jakob disease in the UK. Lancet, 347: 921-925.

[3]   M. E. Bruce, (2006) New variant Creutsfeldt-Jakob disease and bovine spongiform encephalopathy. Nature medicine, 6: 258- 259.

[4]   I. Loredana, N. Beatriz, Z. Andrea, C. Franco, A. Raquel, S. Marco, B. Simona, I. Marcello, L. Quanguo, V. Vito, L. Mei, F. Franco, C. Salvatore, F. Antonio and P. Maurizio, (2006) Scrapie infectivity is quickly cleared in tissues of orally-infected farmed fish. BMC Veterinary Research, 2: 21.

[5]   D. A. Lysek, C. Schorn, L. G. Nivon, V. Esteve-Moya, B. Chris-ten, L. Calzolai, C. Von Schroetter, F. Fiorito, T. Herrmann, P. Guntert and K. (2005) Wuthrich, Prion protein NMR structure of cats, dogs, pigs and sheep. Proceedings of the National Academy of Sciences of the United States of America, 102: 640-645.

[6]   K. M. Pan, M. Baldwin, J. Nguyen, M. Gasset, A. Serban, D. Groth, I. Mehlhorn, Z. Huang, R. J. Fletterick and F. E. Cohen, et al. (1993) Conversion of alphahelices into beta-sheets features in the formation of the scrapie prion proteins. Proceedings of National Academy of Sciences of the United States of America, 90(23): 10962-10966.

[7]   B. P. Stantley, (1998) Proceedings of the National Academy of Sciences of the United States of America, 95: 13363-13383.

[8]   H. A. Kretzschmar, L. E. Stowring, D. Westaway, W. H. Stubblebine, S. B. Prusiner and S. J. DeArmond, (1986) Molecular cloning of a human prion protein cDNA. DNA, 5: 315–324.

[9]   N. Stahl, D. R. Borchelt, K. Hsiao and S. B. Prusiner, (1987) Scrapie prion protein contains a phosphatidylinositol glycolipid. Cell, 51: 229-240.

[10]   N. Stahl, D. R. Borchelt and S. B. Prusiner, (1990) Differential release ofcellular and scrapie prion proteins fromcellular membranes by phosphatidylinositol-specific phospholipase C. Biochemistry, 29: 5405-5412.

[11]   B. Caughey and G. J. Raymond, (1991) The scrapie-associated form of PrP is made from a cell surface precursor that is both protease and phospholipase-sensitive. The Journal of biological chemistry, 266: 18217–18223.

[12]   G. C. Telling, M. Scott, J. Mastrianni, R. Gabizon, M. Torchia, F. E. Cohen, S. J. DeArmond and S. B. Prusiner, (1995) Prion propagation in mice expressing human and chimeric PrP transgenes implicates the interaction of cellular PrP with another protein. Cell, 83: 79-90.

[13]   B. Oesch, D. B. Teplow, N. Stahl, D. Serban, L. E. Hood and S. B. Prusiner, (1990) Identification of cellular proteins binding to the scrapie prion. Biochemistry, 29: 5848–5855.

[14]   B. Oesch, (1994) Characterization of PrP binding proteins. Philosophical transactions of the Royal Society of London. Series B, Biological, 343: 443–445.

[15]   B. Caughey, K. Neary, R. Buller, D. Ernst, L. Perry, B. Chesebro and R. Race, (1990) Normal and scrapie-associated forms of prion protein differ in their sensitivities to phospholipase and proteases in intact neuroblastoma cells. Journal of virology, 64: 1093-1101.

[16]   A. Taraboulos, M. Rogers, D. R. Borchelt, M. P. McKinley, M. Scott, D. Serban and S. B. Prusiner, (1990) Acquisition of prote-aseresistance by prion proteins in scrapie-infected cells does not-require asparagine-linked glycosylation. Proceedings of the National Academy of Sciences of the United States of America, 87: 8262-8266.

[17]   M. P. McKinley, A. Taraboulos, L. Kenaga, D. Serban, A. Stieber, S. J. DeArmond, S. B. Prusiner and N. Gonatas, (1991) Ultra-structural localization of scrapie prion proteins in cytoplasmic vesicles of infected cultured cells. Laboratory investigation, 65: 622-630.

[18]   K. Pfeifer, M. Bachmann, H. C. Schroder, J. Forrest and W. E. G. Muller, (1993) Kinetics of expression of prion protein in unin-fected and scrapieinfected N2 (a) mouse neuroblastoma cells. Cell biochemistry and function, 11: 1-11.

[19]   J. Alexandre, M. Franck, M. Jean, C. Bertrand, P. D. Jean and D. Dominique, (1998) Search for a Nuclear Localization Signal in the Prion Protein. Molecular and Cellular Neuroscience, 11: 127-133.

[20]   L. Otvos and M. Cudic, (2002) Post-translational modifications in prion proteins. Current protein and peptide science, 3(6): 643-652.

[21]   T. Haraguchi, S. Fisher, S. Olofsson, T. Endo, D. Groth, A. Tarentino, D. R. Borchelt, D. Teplow, L. Hood, and A. Burlingame, et al. (1989) Asparagine-linked glycosylation of the scrapie and cellular prion proteins. Archives of biochemistry and biophysics, 274(1): 1-13.

[22]   H. B. Shen, J. Yang and K. C. Chou, (2007) Euk-PLoc: an en-semble classifier for large-scale eukaryotic protein subcellular location prediction. Amino Acids, 33(1): 57-67.

[23]   K. C. Chou and H. B. Shen, (2007) Signal-CF: a subsite-coupled and window fusing approach for predicting signal peptides. Bio-chemical and biophysical research communications, 357(3): 633-640.

[24]   K. C. Chou, and H. B. Shen, (2006) Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization. Biochemical and biophysical research communications, 347(1): 150-157.

[25]   H. B. Shen, and K. C. Chou, (2007) Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM. Protein engineering, design and selection, 20(11): 561-567.

[26]   B. Eisenhaber, G. Schneider, M. Wildpaner and F. Eisenhaber, (2004) A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to ge-nome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosac-charomyces pombe. Journal of molecular biology, 337(2): 243-253.

[27]   F. Ferre, and P. Clote, (2005) Clote. DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Research, 33: 230-232.

[28]   K. C. Chou, (2001) Using subsite coupling to predict signal peptides. Protein Engineering, 2: 75-79.

[29]   Y. Gu, J. Hinnerwisch, R. Fredricks, S. Kalepu, R. S. Mishra and N. Singh, (2002) Identification of cryptic nuclear localization signals in the prion protein. Neurobiology of Disease, 12: 133-149.

[30]   Z. P. Feng, (2002) An overview on predicting the subcellular location of a protein. In silico biology, 2: 291-303.

[31]   A. Reinhardt and T. Hubbard, (1998) Using neural networks for prediction of the subcellular location of proteins. Nucleic acids research, 26: 2230-2236.

[32]   S. Hua and Z. Sun, (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics, 17: 721-728.

[33]   K. C. Chou, (2001) Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins, 43: 246-255.

[34]   J. D. Bendtsen, H. Nielsen, G. Heijne and S. Brunak, (2004) Improved prediction of signal peptides: SignalP 3.0. Journal of molecular biology, 340: 783-795.

[35]   O. Emanuelsson, H. Nielsen, S. Brunak and G. Heijne, (2000) Predicting subcellular localization of proteins based on their Nterminal amino acid sequence. Journal of molecular biology, 300: 1005-1016.

[36]   E. M. Marcotte, I. Xenarios, A. M. Der Bliek and D. Eisenberg, (2000) Localizing proteins in the cell from their phylogenetic profiles. Proceedings of the National Academy of Sciences of the United States of America, 97: 12115-12120.

[37]   Z. Lu, D. Szafron, R. Greiner, P. Lu, D. S. Wishart, B. Poulin, J. Anvik, C. Macdonell and R. Eisner, (2004) Predicting subcellular localization of proteins using machine-learned classifiers. Bioinformatics, 20: 547-556.

[38]   K. Nakai and M. Kanehisa, (1992) A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics, 14: 897-911.

[39]   A. Drawid and M. Gerstein, (2000) A Bayesian system integrating expression data with sequence patterns for localizing pro-teins: comprehensive application to the yeast genome. Journal of molecular biology, 301: 1059-1075.

[40]   M. S. Scott, D. Y. Thomas, and M. T. Hallett, (2004) Predicting subcellular localization via protein motif cooccurrence. Genome research, 14: 1957-1966.

[41]   Y. D. Cai, and K. C. Chou, (2004) Predicting subcellular localization of proteins in a hybridization space. Bioinformatics, 20(7): 1151-1156.

[42]   R. Rieger, F. Edenhofer, C. I. Lasme磟as, and S. Weiss, (1997) The human 37-kDA laminin receptor precursor interacts with the prion protein in eukaryotic cells. Nature medicine, 3: 1383-1388.

[43]   W. E. Muller, U. Scheffer, S. Perovic, J. Forrest and H. C. Schroder, (1997) Interaction of prion protein mRNA with CBP35 and other cellular proteins Possible implications for prion replication and age-dependent changes. Archives of ger-ontology and geriatrics , 25(1): 41-58.

[44]   J. F. Bazan, R. J. Fletterick, M. P. McKinley and S. B. Prusiner, (1987) Pre-dicted secondary structure and membrane topology of the scrapie prion protein. Protein engineering, 2: 125-135.

[45]   R. Haltiwanger and J. Lowe, (2004) role of glycosylation in development. Annual Review of Biochemistry, 73: 491-537.

[46]   P. Mentesana and J. Konopka, (2001) Mutational analysis of the role of N glycosylation in alpha-factor receptor function. Biochemistry, 40(32): 9685-9694.

[47]   K. Pilobello and L. Mahal, (2007) Deciphering the glycocode: the complexity and analytical challenge of glycomics. Current opinion in chemical biology, 11(3): 300-305.

[48]   S. Miyamoto, (2006) Clinical applications of glycomic ap-proaches for the detection of cancer and other diseases. Current opinion in molecular therapeutics, 8: 507-513.

[49]   R. Gupta and S. Brunak, (2002) Prediction of glycosylation across the human proteome and the correlation to protein function. Pacific Symposium on Biocomputing, 310-322.

[50]   C. W. Von der Lieth, A. Bohne-Lang, K. K. Lohmann and M. Frank, (2004) Bioinformatics for glycomics: Status, methods, requirements and perspectives. Briefings in Bioinformatics, 5(2): 164-178.

[51]   B. Eisenhaber, P. Bork and F. Eisenhaber, (1999) Prediction of Potential GPI-modification Sites in Protein Sequences. Journal of molecular biology, 292: 741-758.

[52]   S. M. Muskal, S. R. Holbrook and S. H. Kim, Prediction of the disulfide-bonding state of cysteine in proteins. Protein Engineering 1990, 3(8): 667-672.

 
 
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