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Computational approaches for evaluating the effect of sequence variations and the intrinsically disordered C-terminal region of the Helicobacter pylori CagA protein on the interaction with tyrosine kinase Src

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Abstract

The Helicobacter pylori CagA protein was the first bacterial oncoprotein to be identified as important in the development of human malignancies such as gastric cancer. It is not clear how it is able to deregulate a set of cell control mechanisms to induce carcinogenesis following translocation into human gastric epithelial cells. It is likely, however, that structural variations in the CagA sequence alter its affinity with the host proteins inducing differences in the pathogenicity of different H. pylori strains. Using the recently elucidated N-terminal 3D structure of H. pylori CagA, information on the full cagA gene sequence, and intrinsically disordered protein structure predictions methods we evaluated the interaction of different CagA variants with the kinase Src. An automated docking followed by molecular dynamics simulations were performed to explore CagA interaction modes with Src, one of its cellular partners. The computational approach let us establish that even in the presence of the same number and type of EPIYA motifs, CagA protein can reveal different spatial distributions. Based on the lowest affinity energy and higher number of interactions it was established that the principal forces governing the CagA-Src interaction are electrostatic. Results showed that EPIYA-D models presents higher affinity with some host proteins than EPIYA-C. Thus, we highlight the importance and advantage of the use of computational tools in combining chemical and biological data with bioinformatics for modeling and prediction purposes in some cases where experimental techniques present limitations.

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References

  1. Jones KR, Whitmire JM, Merrell DS (2010) A tale of two toxins: Helicobacter pylori CagA and VacA modulate host pathways that impact disease. Front Microbiol 1:115

    Article  CAS  Google Scholar 

  2. Hunt RH, Xiao SD, Megraud F, Bazzoli F, Hamid S, Vakil N, Malfertheiner P, Leon-Barua R, Merwe SV, Wong BCY, Goh KL, Cohen H, Coeecho LG, Fock KM, Fefail S, Krahshuis JH (2010) Helicobacter pylori in developing countries. [http:/ / www.omge.org/ assets/ downloads/ en/ pdf/ guidelines/ 11_helicobacter_pylori_developing_c ountries_en.pdf] webcite

  3. López AM, Delgado MP, Jaramillo C, Amézqita A, Parra G, Echeverry MM (2009) Characterization of the Helicobacter pylori vacuolating cytotoxin gene in gastric biopsy specimens from patients living in Tolima, Colombia. Rev Argent Microbiol 41(1):4–10

    Google Scholar 

  4. Atherton JC (1998) H. pylori virulence factors. Br Med Bull 54(1):105–120

    Article  CAS  Google Scholar 

  5. Cendron L, Zanotti G (2011) Structural and functional aspects of unique type IV secretory components in the Helicobacter pylori cag-pathogenicity island. FEBS J 278:1223–1231. doi:10.1111/j.1742-4658.2011.08038.x

    Article  CAS  Google Scholar 

  6. Backert S, Tegtmeyer N, Selbach M (2010) The versatility of Helicobacter pylori CagA effector protein functions: the master key hypothesis. Helicobacter 15(3):163–176

    Article  CAS  Google Scholar 

  7. Acosta N, Quiroga A, Delgado P, Bravo MM, Jaramillo C (2010) Helicobacter pylori CagA protein polymorphisms and their lack of association with pathogenesis. World J Gastroenterol 16(31):3936–3943

    Article  CAS  Google Scholar 

  8. Panayotopoulou EG, Sgouras DN, Papadakos K, Kalliaropoulos A, Papatheodoridis G, Mentis AF, Archimandritis AJ (2007) Strategy to characterize the number and type of repeating EPIYA phosphorylation motifs in the carboxyl terminus of CagA protein in Helicobacter pylori clinical isolates. J Clin Microbiol 45(2):488–495

    Article  CAS  Google Scholar 

  9. Shiota S, Matsunari O, Watada M, Yamaoka Y (2010) Serum Helicobacter pylori CagA antibody as a biomarker for gastric cancer in east-Asian countries. Future Microbiol 5(12):1885–1893

    Article  CAS  Google Scholar 

  10. Higashi H, Tsutsumi R, Fujita A, Yamazaki S, Asaka M, Azuma T, Hatakeyama M (2002) Biological activity of the Helicobacter pylori virulence factor CagA is determined by variation in the tyrosine phosphorylation sites. Proc Natl Acad Sci 99(22):14428–14433

    Article  CAS  Google Scholar 

  11. Argent RH, Hale JL, El-Omar EM, Atherton JC (2008) Differences in Helicobacter pylori CagA tyrosine phosphorylation motif patterns between western and East Asian strains, and influences on interleukin-8 secretion. J Med Microbiol 57(9):1062–1067

    Article  Google Scholar 

  12. Argent RH, Kidd M, Owen RJ, Thomas RJ, Limb MC, Atherton JC (2004) Determinants and consequences of different levels of CagA phosphorylation for clinical isolates of Helicobacter pylori. Gastroenterology 127(2):514–523

    Article  CAS  Google Scholar 

  13. Basso D, Zambon CF, Letley DP, Stranges A, Marchet A, Rhead JL, Schiavon S, Guariso G, Ceroti M, Nitti D (2008) Clinical Relevance of Helicobacter pylori cagA and vacA Gene Polymorphisms. Gastroenterology 135(1):91–99

    Article  CAS  Google Scholar 

  14. Jones KR, Joo YM, Jang S, Yoo YJ, Lee HS, Chung IS, Olsen CH, Whitmire JM, Merrell DS, Cha JH (2009) Polymorphism in the CagA EPIYA motif impacts development of gastric cancer. J Clin Microbiol 47(4):959–968

    Article  CAS  Google Scholar 

  15. Miura M, Ohnishi N, Tanaka S, Yanagiya K, Hatakeyama M (2009) Differential oncogenic potential of geographically distinct Helicobacter pylori CagA isoforms in mice. Int J Cancer 125(11):2497–2504

    CAS  Google Scholar 

  16. Naito M, Yamazaki T, Tsutsumi R, Higashi H, Onoe K, Yamazaki S, Azuma T, Hatakeyama M (2006) Influence of EPIYA-repeat polymorphism on the phosphorylation-dependent biological activity of Helicobacter pylori CagA. Gastroenterology 130(4):1181–1190

    Article  CAS  Google Scholar 

  17. Xia Y, Yamaoka Y, Zhu Q, Matha I, Gao X (2009) A comprehensive sequence and disease correlation analyses for the C-terminal region of CagA protein of Helicobacter pylori. PLoS One 4(11):e7736

    Article  Google Scholar 

  18. Zhang Y, Argent RH, Letley DP, Thomas RJ, Atherton JC (2005) Tyrosine phosphorylation of CagA from Chinese Helicobacter pylori isolates in AGS gastric epithelial cells. J Clin Microbiol 43(2):786–790

    Article  CAS  Google Scholar 

  19. Hayashi T, Senda M, Morohashi H, Higashi H, Horio M, Kashiba Y, Nagase L, Sasaya D, Shimizu T, Venugopalan N (2012) Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA. Cell Host Microbe 12(1):20–33

    Article  CAS  Google Scholar 

  20. Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CM, Hipps KW, Ausio J, Nissen MS, Reeves R, Kang C, Kissinger CR, Bailey CW, Griswold MD, Chiu W, Garner EC, Obradovic Z (2001) Intrinsically disordered protein. J Mol Graph Model 19(1):26–59

    CAS  Google Scholar 

  21. Jha AK, Colubri A, Freed KF, Sosnick TR (2005) Statistical coil model of the unfolded state: Resolving the reconciliation problem. Proc Natl Acad Sci 102(37):13099–13104

    Article  CAS  Google Scholar 

  22. Beltrán G (2005) ¿Está cambiando la epidemiología del cáncer de colon en Colombia?. Rev Col Gastroenterol [online]. 20(1):5-6. Available from:http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-99572005000100002&lng=en&nrm=iso>

  23. Otero W, Gómez MA, Castro D (2009) Gastric carcinogenesis. Rev Col Gastroenterol 24(3):314–329

    Google Scholar 

  24. Bravo LE, Cortés A, Carrascal E, Jaramillo R, García LS, Bravo PE, Badel A, Bravo PA (2003) Helicobacter pylori: patología y prevalencia en biopsias gástricas en Colombia. Colomb Méd 34(3):124–131

    Google Scholar 

  25. Acosta PN, Delgado MP, Montealegre MC, Echeverry de Polanco M, Jaramillo CA (2009) Molecular and bioinformatic characterization of Helicobacter pylori CagA protein using gastric biopsies of Colombian patients. Rev Col Gastroenterol 24(4):353–362

    Google Scholar 

  26. Quiroga AJ, Huertas A, Cómbita AL, Bravo MM (2010) Variation in the number of EPIYA-C repeats in CagA protein from Colombian Helicobacter pylori strains and its ability middle to induce hummingbird phenotype in gastric epithelial cells. Biomedica 30:251–258

    Article  Google Scholar 

  27. Huang J, Ru B, Dai P (2002) Prediction of protein interaction sites using mimotope analysis. In: Cai W and Hong H (Eds.) Protein protein interactions-computational and experimental tools. InTech, 2012, pp 189–206

  28. Tovchigrechko A, Wells CA, Vakser IA (2002) Docking of protein models. Protein Sci 11(8):1888–1896. doi:10.1110/ps.4730102

    Article  CAS  Google Scholar 

  29. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, Sayers EW (2012) GenBank. Nucleic Acids Res 40(D1):D48–D53

    Article  CAS  Google Scholar 

  30. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling. Electrophoresis 18(15):2714–2723

    Article  CAS  Google Scholar 

  31. Froimowitz M (1993) HyperChem: a software package for computational chemistry and molecular modeling. Biotechniques 14(6):1010–1013

    CAS  Google Scholar 

  32. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26(2):283–291. doi:10.1107/S0021889892009944

    Article  CAS  Google Scholar 

  33. Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8(1):52–56

    Article  CAS  Google Scholar 

  34. Comeau SR, Gatchell DW, Vajda S, Camacho CJ (2004) ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20(1):45–50

    Article  CAS  Google Scholar 

  35. Sjoerd J, van D M, Bonvin A. The HADDOCK web server for data-driven biomolecular docking. Nature Protocols 5:883–897 doi:10.1038/nprot.2010.32.

  36. Hof P, Pluskey S, Dhe-Paganon S, Eck MJ, Shoelson SE (1998) Crystal structure of the tyrosine phosphatase SHP-2. Cell 92(4):441–450

    Article  CAS  Google Scholar 

  37. Wang Z, Ling B, Zhang R, Suo Y, Liu Y, Yu Z, Liu C (2009) Docking and molecular dynamics studies toward the binding of new natural phenolic marine inhibitors and aldose reductase. J Mol Graph Modell 28(2):162–169

    Google Scholar 

  38. Handa O, Naito Y, Yoshikawa T (2007) CagA protein of Helicobacter pylori: a hijacker of gastric epithelial cell signaling. Biochem Pharmacol 73(11):1697–1702

    Article  CAS  Google Scholar 

  39. Hatakeyama M, Higashi H (2005) Helicobacter pylori CagA: a new paradigm for bacterial carcinogenesis. Cancer Sci 96(12):835–843

    Article  CAS  Google Scholar 

  40. Ren S, Higashi H, Lu H, Azuma T, Hatakeyama M (2006) Structural basis and functional consequence of Helicobacter pylori CagA multimerization in cells. J Biol Chem 281(43):32344–32352

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was sponsored by the Departamento Administrativo de Ciencia, Tecnología e Innovación (Colciencias) under contract No. 757 de 2010. We also thank the Faculty of Sciences, Universidad de los Andes, Bogotá (Colombia) for it financial support. We would like to thank Tiziana Laudato for her proof reading of the manuscript.

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Correspondence to María del Pilar Delgado.

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Delgado, P., Peñaranda, N., Zamora, M.A. et al. Computational approaches for evaluating the effect of sequence variations and the intrinsically disordered C-terminal region of the Helicobacter pylori CagA protein on the interaction with tyrosine kinase Src. J Mol Model 20, 2406 (2014). https://doi.org/10.1007/s00894-014-2406-2

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