Current Science

Open Access Open Access  Restricted Access Subscription Access

Molecular Dynamics Study of the Interaction Between RNA-Binding Domain of NS1 Influenza A Virus and Various Types of Carbon Nanotubes


Affiliations
1 Department of Chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran, Islamic Republic of
 

Adsorption of biomolecules on the surface of carbon nanotubes (CNTs) is important in biological fields. Given the fact that RNA-binding domain (RBD) of NS1 protects the virus against antiviral materials, molecular dynamics simulation was employed to study the adsorption of RBD on the surface of CNTs. It was observed that RBD has a greater tendency to chiral CNTs. The results of Rg (radius of gyration), ischolar_main mean square fluctuation, hydrogen bonds, and secondary structure analysis indicate that the main chain of RBD is strongly stretched and CNT can function as a good adsorbent for RBD.

Keywords

Adsorption, Carbon Nanotubes, Influenza A Virus, Molecular Dynamics Simulation, RNA-Binding Domain.
User
Notifications
Font Size

  • Mansoori, G. A., Mohazzabi, P., Mccormack, P. and Jabbari, S., Nanotechnology in cancer prevention, detection and treatment: bright future lies ahead. WRSTSD, 2007, 4, 226-257.

  • Iijima, S., Helical microtubules of graphitic carbon. Nature, 1991, 354, 56-58.

  • Kam, N. W. S., Jessop, T. C., Wender, P. A. and Dai, H., Nanotube molecular transporters: internalization of carbon nanotube-protein conjugates into mammalian cells. J. Am. Chem. Soc., 2004, 126, 6850-6851.

  • Lin, Y. et al., Advances toward bioapplications of carbon nanotubes. J. Mater. Chem., 2004, 14, 527-541.

  • Mandal, H. S., Su, Z., Ward, A. and Tang, X., Carbon nanotube thin film biosensors for sensitive and reproducible whole virus detection. Theranostics, 2012, 2, 251-257.

  • Boero, C., Carrara, S., Vecchio, G. D., Calza, V. and Micheli, G. D., Targeting of multiple metabolites in neural cells monitored by using protein-based carbon nanotubes. Sensor. Actuate. B. Chem., 2011, 157, 216-224.

  • Jana, A. K. and Sengupta, N., Surface induced collapse of Aβ1-42 with the F19A replacement following adsorption on a single walled carbon nanotube. Biophys. Chem., 2013, 184, 108-115.

  • Mitchell, D. T., Lee, S. B., Trofin, L., Li, N., Nevanen, T. K., Soderlund, H. and Martin, C. R., Smart nanotubes for bioseparations and biocatalysis. J. Am. Chem. Soc., 2002, 124, 11864-11865.

  • Bi, Y. H., Huang, Z. L. and Zhao, Y. D., Interactions of cytochrome c with DNA at glassy carbon surface. Biophys. Chem., 2005, 116, 193-198.

  • Azamian, B. R., Davis, J. J., Coleman, K. S., Bagshaw, C. B. and Green, M. L., Bioelectrochemical single-walled carbon nanotubes. J. Am. Chem. Soc., 2002, 124, 12664-12665.

  • Veetil, J. V. and Ye, K., Development of immunosensors using carbon nanotubes. Biotechnol. Prog., 2007, 23, 517-531.

  • Vatsyayan, P., Bordoloi, S. and Goswami, P., Large catalase based bioelectrode for biosensor application. Biophys. Chem., 2010, 153, 36-42.

  • Kam, N. W. S., O'Connell, M., Wisdom, J. A. and Dai, H., Carbon nanotubes as multifunctional biological transporters and nearinfrared agents for selective cancer cell destruction. Proc. Natl. Acad. Sci. USA, 2005, 102, 11600-11605.

  • Kang, Y., Wang, Q., Liu, Y. C., Wu, T., Chen, Q. and Guan, W. J., Dynamic mechanism of collagen-like peptide encapsulated into carbon nanotubes. J. Phys. Chem. B., 2008, 112, 4801-4807.

  • Pei, Q. X., Lim, C. G., Cheng, Y. and Gao, H., Molecular dynamics study on DNA oligonucleotide translocation through carbon nanotubes. J. Chem. Phys., 2008, 129, 125101-125108.

  • Tsang, S. C., Davis, J. J., Green, M. L. H., Hill, H. A. O., Leung, Y. C. and Sadler, P. J., Immobilization of small proteins in carbon nanotubes: high-resolution transmission electron microscopy study and catalytic activity. J. Chem. Soc. Chem. Commun., 1995, 17, 2579-2580.

  • Hilder, T. A. and Hill, J. M., Probability of encapsulation of paclitaxel and doxorubicin into carbon nanotubes. Micro. Nano. Lett., 2008, 3, 41-49.

  • Chen, Q., Wang, Q., Liu, Y. C., Wu, T., Kang, Y., Moore, J. D. and Gubbins, K. G., Energetics investigation on encapsulation of protein/peptide drugs in carbon nanotubes. J. Chem. Phys., 2009, 131, 015101-015106.

  • Chen, B. D., Yang, C. L., Yang, J. S., Wang, M. S. and Ma, X. G., Dynamic mechanism of HIV replication inhibitor peptide encapsulated into carbon nanotubes. Curr. Appl. Phys., 2013, 13, 1001-1007.

  • Fu, Z. M., Luo, Y., Derreumaux, P. and Wei, G. H., Induced βbarrel formation of the Alzheimer's Aβ25-35 oligomers on carbon nanotube surfaces: implication for amyloid fibril inhibition. Biophys. J., 2009, 97, 1795-1803.

  • Webster, R. G., Bean, W. J., Gorman, O. T., Chambers, T. M. and Kawaoka, Y., Evolution and ecology of influenza A viruses. Microbiol. Rev., 1992, 56, 152-179.

  • Seo, S. H., Hoffmann, E. and Webster, R. G., Lethal H5N1 influenza viruses escape host anti-viral cytokine responses. Nat. Med., 2002, 8, 950-954.

  • Lu, P. S., Early diagnosis of avian influenza. Science, 2006, 312, 337.

  • Horimoto, T. and Kawaoka, Y., Influenza: lessons from past pandemics, warnings from current incidents. Nat. Rev. Microbiol., 2005, 3, 591-600.

  • Noah, D. L. and Krug, R. M., Influenza virus virulence and its molecular determinants. Adv. Virus. Res., 2005, 65, 121-145.

  • Solorzano, A., Webby, R. J., Lager, K. M., Janke, B. H., GarciaSastre, A. and Richt, J. A., Mutations in the NS1 protein of swine influenza virus impair anti-interferon activity and confer attenuation in pigs. J. Virol., 2005, 79, 7535-7543.

  • Qian, X. Y., Lu, Y., Montelione, G. T. and Krug, R. M., An amino-terminal polypeptide fragment of the influenza virus NS1 protein possesses specific RNA-binding activity and largely helical backbone structure. RNA, 1995, 1, 948-956.

  • Van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E. and Berendsen, H. J. C., GROMACS: fast, flexible, and free. J. Comput. Chem., 2005, 26, 1701-1718.

  • Jorgensen, W. L., Maxwell, D. S. and Tirado-Rives, J., Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc., 1996, 118, 11225-11236.

  • Liu, J., Lynch, P. A., Chien, C. Y., Montelione, G. T., Krug, R. M. and Berman, H. M., Crystal structure of the unique RNA-binding domain of the influenza virus NS1 protein. Nat. Struct. Mol. Biol., 1997, 4, 896-899.

  • http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/memtutorial.pdf

  • Humphrey, W., Dalke, A. and Schulten, K., VMD: Visual molecular dynamics. J. Mol. Graph., 1996, 14, 33-38.

  • Kaukonen, M., Gulans, A., Havu, P. and Kauppinen, E., Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations. J. Comput. Chem., 2012, 33, 652.

  • Jorgensen, W. L. and Schyman, P., Exploring adsorption of water and ions on carbon surfaces using a polarizable force field. J. Phys. Chem. Lett., 2013, 4, 468.

  • Jorgensen, W. L. and Severance, D. L., Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene. J. Am. Chem. Soc., 1990, 112, 4768.

  • Jorgensen, W. L., Maxwell, D. S. and Tirado-Rives, J., Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc., 1996, 118, 11225.

  • Darden, T., York, D. and Pedersen, L., Particle mesh Ewald: An N ⋅ log (N) method for Ewald sums in large systems. J. Chem. Phys., 1993, 98, 10089-10092.

  • Van der Spoel, D. and Lindahl, E., Brute-force molecular dynamics simulations of Villin headpiece: comparison with NMR parameters. J. Phys. Chem. B., 2003, 107, 11178-11187.

  • Parrinello, M. and Rahman, A., Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys., 1981, 52, 7182-7190.

  • Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. and Haak, J. R., Molecular-dynamics with coupling to an external bath. J. Chem. Phys., 1984, 81, 3684-3690.

  • Shen, J. W., Wu, T., Wang, Q. and Kang, Y., Induced stepwise conformational change of human serum albumin on carbon nanotube surfaces. Biomaterials, 2008, 29, 3847-3855.

  • Mosaddeghi, H., Alavi, S., Kowsari, M. H. and Najafi, B., Simulations of structural and dynamic anisotropy in nano-confined water between parallel graphite plates. J. Chem. Phys., 2012, 137, 184703-184712.

  • Az'hari, S. and Ghayeb, Y., Effect of chirality, length and diameter of carbon nanotubes on the adsorption of 20 amino acids: a molecular dynamics simulation study. Mol. Simulat., 2014, 40, 392-398.

  • Santosh, M., Panigrahi, S., Bhattacharyya, D., Sood, A. K. and Maiti, P. K., Unzipping and binding of small interfering RNA with single walled carbon nanotube: a platform for small interfering RNA delivery. J. Chem. Phys., 2012, 136, 065106.

  • Vasumathi, V., Pramanik, D., Sood, A. K. and Maiti, P. K., Structure of a carbon nanotube-dendrimer composite. Soft Matter., 2013, 9, 1372-1380.

  • Feher, J., Quantitative Human Physiology, Academic Press, Massachusetts, 2012, pp. 100-109.

  • Chamberlain, A. K. and Bowie, J. U., Evaluation of C-H…O hydrogen bonds in native and misfolded proteins. J. Mol. Biol., 2002, 322, 497-503.

  • Pauling, L., Corey, R. B. and Branson, H. R., The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. USA, 1957, 37, 205-211.

  • Toniolo, C. and Benedetti, E., Intramolecularly hydrogen-bonded peptide conformation. CRC. Crit. Rev. Biochem., 1980, 9, 1-44.


Abstract Views: 248

PDF Views: 80




  • Molecular Dynamics Study of the Interaction Between RNA-Binding Domain of NS1 Influenza A Virus and Various Types of Carbon Nanotubes

Abstract Views: 248  |  PDF Views: 80

Authors

Sara Az'hari
Department of Chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran, Islamic Republic of
Hamid Mosaddeghi
Department of Chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran, Islamic Republic of
Yousef Ghayeb
Department of Chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran, Islamic Republic of

Abstract


Adsorption of biomolecules on the surface of carbon nanotubes (CNTs) is important in biological fields. Given the fact that RNA-binding domain (RBD) of NS1 protects the virus against antiviral materials, molecular dynamics simulation was employed to study the adsorption of RBD on the surface of CNTs. It was observed that RBD has a greater tendency to chiral CNTs. The results of Rg (radius of gyration), ischolar_main mean square fluctuation, hydrogen bonds, and secondary structure analysis indicate that the main chain of RBD is strongly stretched and CNT can function as a good adsorbent for RBD.

Keywords


Adsorption, Carbon Nanotubes, Influenza A Virus, Molecular Dynamics Simulation, RNA-Binding Domain.

References





DOI: https://doi.org/10.18520/cs%2Fv116%2Fi3%2F398-404