In silico analysis suggests interaction between Ebola virus and the extracellular matrix

Frontiers in Microbiology

Volumn 6, Issue FEB, 2015, Pages

  Veljkovic, Veljko ^a   Glisic, Sanja ^a   Muller, Claude P ^b   Scotch, Matthew ^c   Branch, Donald R ^d   Perovic, Vladimir R ^a   Sencanski, Milan ^e   Veljkovic, Nevena ^a   Colombatti, Alfonso ^f  

^a UNIVERSITY OF BELGRADE   (Serbia)

^b LABORATOIRE NATIONAL DE SANTÉ   (Luxembourg)

^c ARIZONA STATE UNIVERSITY   (United States)

^d CANADIAN BLOOD SERVICES   (Canada)

^e UNIVERSITY OF BELGRADE   (Serbia)

^f CENTRO DI RIFERIMENTO ONCOLOGICO   (Italy)

Author keywords

Ebola virus; EMILINs; Endothelial extracellular matrix; Glycoprotein GP; In silico analysis

Indexed keywords

AMODIAQUINE; ELASTIN MICROFIBRIL INTERFACE LOCATED PROTEIN; GLYCOPROTEIN; PROTEIN; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ARTICLE; COMPUTER MODEL; EBOLA HEMORRHAGIC FEVER; EBOLA VIRUS; ELECTRON ION INTERACTION POTENTIAL; EXTRACELLULAR MATRIX; HUMAN; INFORMATIONAL SPECTRUM METHOD; MOLECULAR DOCKING; NONHUMAN; PATHOGENESIS; PROTEIN PROTEIN INTERACTION; REVERTANT;

EBOLA VIRUS;

EID: 84927523630     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2015.00135     Document Type: Article

References (62)

1. Baskerville, A., Fisher-Hoch, S. P., Neild, G. H., and Dowsett, A. B. (1985). Ultrastructural pathology of experimental Ebola haemorrhagic fever virus infection. J. Pathol. 147, 199-209. doi: 10.1002/path.1711470308.
2. Basler, C. F. (2013). A novel mechanism of immune evasion mediated by Ebola virus soluble glycoprotein. Expert Rev. Anti Infect. Ther. 11, 475-478. doi: 10.1586/eri.13.30.
3. Colombatti, A., Spessotto, P., Doliana, R., Mongiat, M., Bressan, G. M., and Esposito, G. (2012). The EMILIN/Multimerin family. Front. Immunol. 2:93. doi: 10.3389/fimmu.2011.00093.
4. Cosic, I. (1997). The Resonant Recognition Model of Macromolecular Bioreactivity: Theory & Application. Berlin. doi: 10.1007/978-3-0348-7475-5.
5. Danussi, C., Petrucco, A., Wassermann, B., Modica, T. M., Pivetta, E., Del Bel Belluz, L., et al. (2012). An EMILIN1-negative microenvironment promotes tumor cell proliferation and lymph node invasion. Cancer Prev. Res. 5, 1131-1143. doi: 10.1158/1940-6207.CAPR-12-0076-T.
6. Davis, K. J., Anderson, A. O., Geisbert, T. W., Steele, K. E., Geisbert, J. B., Vogel, P., et al. (1997). Pathology of experimental Ebola virus infection in African green monkeys. Arch. Pathol. Lab. Med. 121, 805-819.
7. Deng, S. P., and Huang, D. S. (2014). SFAPS: an R package for structure/function analysis of protein sequences based on informational spectrum method. Methods. 69, 207-212. doi: 10.1016/j.ymeth.2014.08.004.
8. Doliana, R., Veljkovic, V., Prljic, J., Veljkovic, N., De Lorenzo, E., Mongiati, M., et al. (2008). EMILINs interact with anthrax protective antigen and Inhibit toxin action in vitro. Matrix Biol. 27, 96-106. doi: 10.1016/j.matbio.2007.09.008.
9. Fröhlich, H. (1968). Long-range coherence and energy storage in biological systems. Int. J. Quantum Chem. 2, 641-649. doi: 10.1002/qua.560020505.
10. Fröhlich, H. (1970). Long range coherence and the action of enzymes. Nature 228:1093. doi: 10.1038/2281093a0.
11. Fröhlich, H. (1975). The extraordinary dielectric properties of biological materials and the action of enzymes. Proc. Natl. Acad. Sci. U.S.A. 72, 4211-4215. doi: 10.1073/pnas.72.11.4211.
12. Geisbert, T. W., Jahrling, P. B., Hanes, M. A., and Zack, P. M. (1992). Association of Ebola related Reston virus particles and antigen with tissue lesions of monkeys imported to the United States. J. Comp. Pathol. 106, 137-152. doi: 10.1016/0021-9975(92)90043-T.
13. Geisbert, T. W., Young, H. A., Jahrling, P. B., Davis, K. J., Larsen, T., Kagan, E., et al. (2003). Pathogenesis of Ebola hemorrhagic fever in primate models: evidence that hemorrhage is not a direct effect of virus-induced cytolysis of endothelial cells. Am. J. Pathol. 163, 2371-2382. doi: 10.1016/S0002-9440(10)63592-4.
14. Gire, S. K., Goba, A., Andersen, K. G., Sealfon, R. S., Park, D. J., Kanneh, L., et al. (2014). Genomic surveivallence elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345, 1369-1372. doi: 10.1126/science.1259657.
15. Glisic, S., Veljkovic, N., Jovanovic-Cupic, S., Vasiljevic, N., Prljic, J., Gemovic, B., et al. (2012). Assessment of hepatitis C virus protein sequences with regard to interferon/ribavirin combination therapy response in patients with HCV genotype 1b. Protein J. 31, 129-136. doi: 10.1007/s10930-011-9381-6.
16. Holty, J. E., Kim, R. Y., and Bravata, D. M. (2006). Anthrax: a systematic review of atypical presentations. Ann. Emerg. Med. 48, 270-280. doi: 10.1016/j.annemergmed.2005.11.035.
17. Huang, J., Tan, P. H., Li, K. B., Matsumoto, K., Tsujimoto, M., and Bay, B. H. (2005). Y-box binding protein, YB-1, as a marker of tumor aggressiveness and response to adjuvant chemotherapy in breast cancer. Int. J. Oncol. 26, 607-613. doi: 10.3892/ijo.26.3.607.
18. Jaax, N. K., Davis, K. J., Geisbert, T. W., Vogel, P., Jaax, G. P., Topper, M., et al. (1996). Lethal experimental infection of rhesus monkeys with Ebola-Zaire (Mayinga) virus by the oral and conjunctival route of exposure. Arch. Pathol. Lab. Med. 120, 140-155.
19. Kelley, L. A., and Sternberg, M. J. E. (2009). Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 4, 363-371. doi: 10.1038/nprot.2009.2.
20. Kugelman, J. R., Sanchez-Lockhart, M., Andersen, K. G., Gire, S., Park, D. J., Sealfon, R., et al. (2015). Evaluation of the potential impact of ebola virus genomic drift on the efficacy of sequence-based candidate therapeutics. MBio 6, e02227-e02214. doi: 10.1128/mBio.02227-14.
21. Lazovic, J. (1996). Selection of amino acid parameters for Fourier transform-based analysis of proteins. Comp. Appl. Bio. Sci. 16, 553-558.
22. Lee, J. E., Fusco, M. L., Hessell, A. J., Oswald, W. B., Burton, D. R., and Saphire, E. O. (2008). Nature 454, 177-182. doi: 10.1038/nature07082.
23. Madrid, P. B., Chopra, S., Manger, I. D., Gilfillan, L., Keepers, T. R., Shurtleff, A. C., et al. (2013). A systematic screen of FDA-approved drugs for inhibitors of biological threat agents. PLoS ONE 8:e60579. doi: 10.1371/journal.pone.0060579.
24. Mayer, T. A., Bersoff-Matcha, S., Murphy, C., Earls, J., Harper, S., Pauze, D., et al. (2001). Clinical presentation of inhalational anthrax following bioterrorism exposure: report of 2 surviving patients. JAMA 286, 2549-2553. doi: 10.1001/jama.286.20.2549.
25. Mohan, G. S., Li, W., Ye, L., Compans, R. W., and Yang, C. (2012). Antigenic subversion: a novel mechanism of host immune evasion by Ebola virus. PLoS Pathog. 8:e1003065. doi: 10.1371/journal.ppat.1003065.
26. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., et al. (2009). Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Comput. Chem. 16, 2785-2791. doi: 10.1002/jcc.21256.
27. Nwankwo, N. (2013). A digital signal processing-based bioinformatics approach to identifying the origins of HIV-1 non B subtypes infecting US Army personnel serving abroad. Curr. HIV Res. 11, 271-280. doi: 10.2174/1570162X113119990046.
28. Pedretti, A., Villa, L., and Vistoli, G. (2004). Vega-an open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. J Comput. Aided Mol. Des. 18, 167-173. doi: 10.1023/B:JCAM.0000035186.90683.f2.
29. Perovic, V. (2013). Novel algorithm for phylogenetic analysis of proteins: application to analysis of the evolution of H5N1 influenza viruses. J. Mathem. Chem. 51, 2238-2255. doi: 10.1007/s10910-013-0212-1.
30. Perovic, V. R., Muller, C. P., Niman, H. L., Veljkovic, N., Dietrich, U., Tosic, D. D., et al. (2013). Novel phylogenetic algorithm to monitor human tropism in Egyptian H5N1-HPAIV reveals evolution toward efficient human-to-human transmission. PLoS ONE 8:e61572. doi: 10.1371/journal.pone.0061572.
31. Peters, C. J., and Khan, A. S. (1999). Filovirus diseases. Curr. Top. Microbiol. Immunol. 235, 85-95. doi: 10.1007/978-3-642-59949-1_6.
32. Pirogova, E., Coloe, P. J., Cosic, I., and Istivan, T. S. (2012). A bioactive peptide analogue for myxoma virus protein with a targeted cytotoxicity for human skin cancer in vitro. J. Biomed. Sci. 19:65. doi: 10.1186/1423-0127-19-65.
33. Pirogova, E., Istivan, T., Gan, E., and Cosic, I. (2011). Advances in methods for therapeutic peptide discovery, design and development. Curr. Pharm. Biotechnol. 12, 1117-1127. doi: 10.2174/138920111796117436.
34. Rodriguez, L. L., De Roo, A., Guimard, Y., Trappier, S. G., Sanchez, A., Bressler, D., et al. (1999). Persistence and genetic stability of Ebola virus during the outbreak in Kikwit, Democratic Republic of the Congo, 1995. J. Infect. Dis. 179(Suppl. 1), S170-S176.
35. Ryabchikova, E. I., Kolesnikova, L. V., and Netesov, S. V. (1999). Animal pathology of filoviral infections. Curr. Top. Microbiol. Immunol. 235, 145-173. doi: 10.1007/978-3-642-59949-1_9.
36. Sa, Q., Hart, E., Nadeau, J. H., and Hoover-Plow, J. L. (2010). Mouse chromosome 17 candidate modifier genes for thrombosis. Mamm. Genome. 21, 337-349. doi: 10.1007/s00335-010-9274-6.
37. Sa, Q., and Hoover-Plow, J. L. (2011). EMILIN2 (Elastin microfibril interface located protein), potential modifier of thrombosis. Thromb. J. 9:9. doi: 10.1186/1477-9560-9-9.
38. Sanner, M., F. (1999). Python: a programming language for software integration and development. J. Mol. Graph. Mod. 17, 57-61.
39. Srdic-Rajic, T., Kekovic, G., Davidovic, D. M., and Metlas, R. (2013). Phosphocholine-binding antibody activities are hierarchically encoded in the sequence of the heavy-chain variable region: dominance of self-association activity in the T15 idiotype. Int. Immunol. 25, 345-352. doi: 10.1093/intimm/dxs156.
40. Sullivan, N., Yang, Z. Y., and Nabel, G. J. (2003). Ebola virus pathogenesis: implications for vaccines and therapies. J. Virol. 77, 9733-9737 doi: 10.1128/JVI.77.18.9733-9737.2003.
41. Takada, A., Ebihara, H., Feldmann, H., Geisbert, T. W., and Kawaoka, Y. (2007). Epitopes required for antibody-dependent enhancement of Ebola virus infection. J. Infect. Dis. 196(Suppl. 2), S347-S356. doi: 10.1086/520581.
42. Takada, A., Feldmann, H., Ksiazek, T. G., and Kawaoka, Y. (2003). Antibody-dependent enhancement of Ebola virus infection. J. Virol. 77, 7539-7544. doi: 10.1128/JVI.77.13.7539-7544.2003.
43. Takada, A., Watanabe, S., Okazaki, K., Kida, H., and Kawaoka, Y. (2001). Infectivity-enhancing antibodies to Ebola virus glycoprotein. J. Virol. 75, 2324-2330. doi: 10.1128/JVI.75.5.2324-2330.2001.
44. Tintori, C., Veljkovic, N., Veljkovic, V., and Botta, M. (2010). Computational studies of the interaction between the HIV-1 integrase tetramer and the cofactor LEDGF/p75: insights from molecular dynamics simulations and the informational spectrum method. Proteins 78, 3396-3408. doi: 10.1002/prot.22847.
45. Trott, O., and Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J. Comput. Chem. 31, 455-461. doi: 10.1002/jcc.21334.
46. Veljkovic, N., Branch, D. R., Metlas, R., Prljic, J., Vlahovicek, K., Pongor, S., et al. (2003). Design of peptide mimetics of HIV-1 gp120 for prevention and therapy of HIV disease. J. Pept. Res. 62, 158-166. doi: 10.1034/j.1399-3011.2003.00081.x.
47. Veljkovic, N., Glisic, S., Prljic, J., Perovic, V., Botta, M., et al. (2008). Discovery of new therapeutic targets by the informational spectrum method. Curr. Protein Pept. Sci. 9, 493-506. doi: 10.2174/138920308785915245.
48. Veljkovic, V. (1973). The dependence of the Fermi energy on the atomic number. Phys. Lett. 45A, 41-42. doi: 10.1016/0375-9601(73)90497-0.
49. Veljkovic, V. (1980). A Theoretical Approach to Preselection of Carcinogens and Chemical Carcinogenesis. New York, NY: Gordon & Breach.
50. Veljkovic, V., and Cosic, I. (1987). A novel method of protein analysis for prediction of biological function. Cancer Biochem. Biophys. 9, 139-148.
51. Veljkovic, V., Cosic, I., Dimitrijevic, B., and Lalovic, D. (1985). Is it possible to analyze DNA and protein sequence by the method of digital signal processing? IEEE Trans. Biomed. Eng. 32, 337-341. doi: 10.1109/TBME.1985.325549.
52. Veljkovic, V., Glisic, S., Veljkovic, N., Bojic, T., Dietrich, U., Perovic, V. R., et al. (2014). Influenza vaccine as prevention for cardiovascular diseases: possible molecular mechanism. Vaccine. 32, 6569-6575. doi: 10.1016/j.vaccine.2014.07.007.
53. Veljkovic, V., and Lalovic, D. (1973). General model pseudopotential for positive ions. Phys. Lett. 45A, 59-60. doi: 10.1016/0375-9601(73)90506-9.
54. Veljkovic, V., Niman, H. L., Glisic, S., Veljkovic, N., Perovic, V., and Muller, C. P. (2009b). Identification of hemagglutinin structural domain and polymorphisms which may modulate swine H1N1 interactions with human receptor. BMC Struct. Biol. 9:62. doi: 10.1186/1472-6807-9-62.
55. Veljkovic, V., and Slavic, I. (1972). Simple general-model pseudopotential. Phys. Rev. Lett. 29, 105-107. doi: 10.1103/PhysRevLett.29.105.
56. Veljkovic, V., Veljkovic, N., Muller, C. P., Müller, S., Glisic, S., Perovic, V., et al. (2009a). Characterization of conserved properties of hemagglutinin of H5N1 and human influenza viruses: possible consequences for therapy and infection control. BMC Struct. Biol. 9:21. doi: 10.1186/1472-6807-9-21.
57. Vergara-Alert, J., Argilaguet, J. M., Busquets, N., Ballester, M., Martin-Valls, G. E., Rivas, R., et al. (2012). Conserved synthetic peptides from the hemagglutinin of influenza viruses induce broad humoral and T-cell responses in a pig model. PLoS ONE 7:e40524. doi: 10.1371/journal.pone.0040524.
58. Veljkovic, V., and Lalovic, D. (1976). Theoretical prediction of mutagenicity and carcinogenicity of chemical substances. Cancer Biochem. Biophys. 1, 295-298.
59. Wahl-Jensen, V. M., Afanasieva, T. A., Seebach, J., Ströher, U., Feldmann, H., and Schnittler, H. J. (2005). Effects of Ebola virus glycoproteins on endothelial cell activation and barrier function. J. Virol. 79, 10442-10450. doi: 10.1128/JVI.79.16.10442-10450.2005.
60. Wilson, J. A., Hevey, M., Bakken, R., Guest, S., Bray, M., Schmaljohn, A. L., et al. (2000). Epitopes involved in antibody-mediated protection from Ebola virus. Science 287, 1664-1666. doi: 10.1126/science.287.5458.1664.
61. Yang, Z., Delgado, R., Xu, L., Todd, R. F., Nabel, E. G., Sanchez, A., et al. (1998). Distinct cellular interactions of secreted and transmembrane Ebola virus glycoproteins. Science 279, 1034-1037. doi: 10.1126/science.279.5353.1034.
62. Yang, Z., Duckers, H. J., Sullivan, N. J., Sanchez, A., Nabel, E. G., and Nabel, G. J. (2000). Identification of the Ebola virus glycoprotein as the main viral determinant of vascular cell cytotoxicity and injury. Nat. Med. 6, 886-889. doi: 10.1038/78645.