Molecular dynamics exploration of the binding mechanism and properties of single-walled carbon nanotube to WT and mutant VP35 FBP region of Ebola virus

Journal of Biological Physics

Volumn 43, Issue 1, 2017, Pages 149-165

  Zhang, Yan Jun ^a   Ding, Jing Na ^a   Zhong, Hui ^a   Sun, Chang Ping ^a,b   Han, Ju Guang ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b LINYI UNIVERSITY   (China)

Author keywords

EBOVs; MD simulations; MM GBSA; SWCNT; VP35

Indexed keywords

MUTANT PROTEIN; SINGLE WALLED NANOTUBE; UNCLASSIFIED DRUG; VIRAL PROTEIN; VIRAL PROTEIN 35; CARBON NANOTUBE; PROTEIN BINDING; VP35 PROTEIN, FILOVIRUS;

ARTICLE; BINDING AFFINITY; BINDING FREE ENERGY; COLLISIONALLY ACTIVATED DISSOCIATION; COMPARATIVE STUDY; CONTROLLED STUDY; DNA STRUCTURE; EBOLAVIRUS; ENERGY; FIRST BASIC PATCH; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NONHUMAN; PROTEIN CONFORMATION; PROTEIN INTERACTION; VIRUS INHIBITION; WILD TYPE; CHEMISTRY; GENETICS; METABOLISM; MUTATION; THERMODYNAMICS;

MOLECULAR DYNAMICS SIMULATION; MUTATION; NANOTUBES, CARBON; PROTEIN BINDING; PROTEIN CONFORMATION; THERMODYNAMICS; VIRAL REGULATORY AND ACCESSORY PROTEINS;

EID: 85009844424     PISSN: 00920606     EISSN: 15730689     Source Type: Journal    
DOI: 10.1007/s10867-016-9440-5     Document Type: Article

References (41)

1. Prins, K.C., Delpeut, S., Leung, D.W., Reynard, O., Volchkova, V.A., Reid, S.P., Ramanan, P., Cardenas, W.B., Amarasinghe, G.K., Volchkov, V.E., Basler, C.F.: Mutations abrogating VP35 interaction with double-stranded RNA render ebola virus avirulent in guinea pigs. J. Virol. 84(6), 3004–3015 (2010)
2. Kuhn, J.H., Becker, S., Ebihara, H., Geisbert, T.W., Johnson, K.M., Kawaoka, Y., Lipkin, W.I., Negredo, A.I., Netesov, S.V., Nichol, S.T., Palacios, G., Peters, C.J., Tenorio, A., Volchkov, V.E., Jahrling, P.B.: Proposal for a revised taxonomy of the family Filoviridae: classification, names of taxa and viruses, and virus abbreviations. Arch. Virol. 155(12), 2083–2103 (2010)
3. Feldmann, H., Sanchez, A., Geisbert, T.W.: Filoviridae: Marburg and Ebola viruses. In: Knipe, D.M., Howley, P.M. (eds.) Fields Virology, 6th ed. Lippincott Williams & Wilkins, Philadelphia (2007)
4. Salvaggio, M.R., Baddley, J.W.: Other viral bioweapons: Ebola and Marburg hemorrhagic fever. Dermatol. Clin 22(3), 291 (2004)
5. Reed, D.S., Mohamadzadeh, M.: Status and challenges of filovirus vaccines. Vaccine 25(11), 1923–1934 (2007)
6. Elliott, L.H., Kiley, M.P., McCormick, J.B.: Descriptive analysis of Ebola virus proteins. Virology 147(1), 169–176 (1985)
7. Muhlberger, E., Weik, M., Volchkov, V.E., Klenk, H.D., Becker, S.: Comparison of the transcription and replication strategies of Marburg virus and Ebola virus by using artificial replication systems. J. Virol. 73(3), 2333–2342 (1999)
8. Basler, C.F., Garcia-Sastre, A.: Viruses and the type I interferon antiviral system: induction and evasion. Int. Rev. Immunol. 21(4–5), 305–337 (2002)
9. Muhlberger, E., Lotfering, B., Klenk, H.D., Becker, S.: Three of four nucleocapsid proteins of Marburg virus, NP, VP35, and L, are sufficient to mediate replication and transcription of Marburg virus-specific monocistronic minigenomes. J. Virol. 72(11), 8756–8764 (1998)
10. Haasnoot, J., de Vries, W., Geutjes, E.J., Prins, M., de Haan, P., Berkhout, B.: The Ebola virus VP35 protein is a suppressor of RNA silencing. PLoS Pathogens 3(6), 794–803 (2007)
11. Brown, C.S., Lee, M.S., Leung, D.W., Wang, T.J., Xu, W., Luthra, P., Anantpadma, M., Shabman, R.S., Melito, L.M., MacMillan, K.S., Borek, D.M., Otwinowski, Z., Ramanan, P., Stubbs, A.J., Peterson, D.S., Binning, J.M., Tonelli, M., Olson, M.A., Davey, R.A., Ready, J.M., Basler, C.F., Amarasinghe, G.K.: In silico derived small molecules bind the filovirus VP35 protein and inhibit its polymerase cofactor activity. J. Mol. Biol. 426(10), 2045–2058 (2014)
12. Basler, C.F., Mikulasova, A., Martinez-Sobrido, L., Paragas, J., Muhlberger, E., Bray, M., Klenk, H.D., Palese, P., Garcia-Sastre, A.: The Ebola virus VP35 protein inhibits activation of interferon regulatory factor 3. J. Virol. 77(14), 7945–7956 (2003)
13. St Reid, P., Cardenas, W.B., Basler, C.F.: Homo-oligomerization facilitates the interferon-antagonist activity of the ebolavirus VP35 protein. Virology 341(2), 179–189 (2005)
14. Leung, D.W., Shabman, R.S., Farahbakhsh, M., Prins, K.C., Borek, D.M., Wang, T.J., Muhlberger, E., Basler, C.F., Amarasinghe, G.K.: Structural and functional characterization of reston ebola virus VP35 interferon inhibitory domain. J. Mol. Biol. 399(3), 347–357 (2010)
15. Leung, D.W., Ginder, N.D., Fulton, D.B., Nix, J., Basler, C.F., Honzatko, R.B., Amarasinghe, G.K.: Structure of the Ebola VP35 interferon inhibitory domain. Proc. Natl. Acad. Sci. U. S. A. 106(2), 411–416 (2009)
16. Laskowski, R.A., Swindells, M.B.: LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model. 51(10), 2778–2786 (2011)
17. Krammer, A., Kirchhoff, P.D., Jiang, X., Venkatachalam, C.M., Waldman, M.: LigScore: a novel scoring function for predicting binding affinities. J. Mol. Graph. Model. 23(5), 395–407 (2005)
18. Zhang, Y.J., Ding, J.N., Feng, T.T., Han, J.G.: Exploring interaction mechanisms of the inhibitor binding to the VP35 IID region of Ebola virus by all atom molecular dynamics simulation method. Proteins: Struct., Funct., Bioinf. 83(12), 2263–2278 (2015)
19. Iijima, S.: Helical microtubules of graphitic carbon. Nature 354(6348), 56–58 (1991)
20. Akita, S., Nishijima, H., Nakayama, Y., Tokumasu, F., Takeyasu, K.: Carbon nanotube tips for a scanning probe microscope: their fabrication and properties. J. Phys. D – Appl. Phys. 32(9), 1044–1048 (1999)
21. Friedman, S.H., Ganapathi, P.S., Rubin, Y., Kenyon, G.L.: Optimizing the binding of fullerene inhibitors of the HIV-1 protease through predicted increases in hydrophobic desolvation. J. Med. Chem. 41(13), 2424–2429 (1998)
22. Meher, B.R., Wang, Y.X.: Binding of single walled carbon nanotube to WT and mutant HIV-1 proteases: analysis of flap dynamics and binding mechanism. J. Mol. Graph. Model. 38, 430–445 (2012)
23. Bosi, S., Da Ros, T., Spalluto, G., Prato, M.: Fullerene derivatives: an attractive tool for biological applications. Eur. J. Med. Chem. 38(11-12), 913–923 (2003)
24. Zhu, Z.W., Schuster, D.I., Tuckerman, M.E.: Molecular dynamics study of the connection between flap closing and binding of fullerene-based inhibitors of the HIV-1 protease. Biochemistry 42(5), 1326–1333 (2003)
25. Schrodinger, LLC. The PyMOL Molecular Graphics System, Version 1.3r1. 2010.
26. Schrodinger, LLC. The JyMOL Molecular Graphics Development Component, Version 1.0. 2010.
27. Schrodinger, LLC. The AxPyMOL Molecular Graphics Plugin for Microsoft PowerPoint, Version 1.0. 2010.
28. Frey JT, Doren DJ. TubeGen 3.4. University of Delaware, Newark DE: University of Delaware, Newark DE; 2011.
29. Yong, D., Chun, W., Chowdhury, S., Lee, M.C., Guoming, X., Wei, Z., Rong, Y., Cieplak, P., Ray, L., Taisung, L., Caldwell, J., Junmei, W., Kollmann, P.: A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24(16), 1999–2012 (2003)
30. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., Wolfson, H.J.: PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 33, W363–W367 (2005)
31. Wang, J.M., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A.: Development and testing of a general amber force field. J. Comput. Chem. 25(9), 1157–1174 (2004)
32. Case, D., et al.: AMBER 12. University of California, San Francisco 2012.
33. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L.: Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79(2), 926–935 (1983)
34. Darden, T., York, D., Pedersen, L.: Particle Mesh Ewald - an N.LOG(N) method for Ewald Sums in large systems. J. Chem. Phys. 98(12), 10089–10092 (1993)
35. Ryckaert, J.P., Ciccotti, G., Berendsen, H.J.C.: Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes. J. Comput. Phys. 23(3), 327–341 (1977)
36. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E.: UCSF chimera - A visualization system for exploratory research and analysis. J. Comput. Chem. 25(13), 1605–1612 (2004)
37. Kollman, P.A., Massova, I., Reyes, C., Kuhn, B., Huo, S.H., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D.A., Cheatham, T.E.: Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33(12), 889–897 (2000)
38. Feig, M., Im, W., Brooks, C.L.: Implicit solvation based on generalized Born theory in different dielectric environments. J. Chem. Phys. 120(2), 903–911 (2004)
39. Gohlke, H., Kiel, C., Case, D.A.: Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RaIGDS complexes. J. Mol. Biol. 330(4), 891–913 (2003)
40. Zoete, V., Meuwly, M., Karplus, M.: Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition. Proteins-Struct Funct Bioinforma 61(1), 79–93 (2005)
41. Zhao, R.N., Fan, S., Han, J.G., Liu, G.: Molecular dynamics study of segment peptides of Bax, Bim, and Mcl-1 BH3 domain of the apoptosis-regulating proteins bound to the anti-apoptotic Mcl-1 protein. J. Biomol. Struct. Dyn. 33(5), 1067–1081 (2015)