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Study of the Conformational Variety of the Oligosaccharide Substrates of Neuraminidases from Pathogens using Molecular Modeling

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Moscow University Chemistry Bulletin Aims and scope

Abstract

Analysis of the conformational variety of the oligosaccharide fragments of the human glycan receptors LSTa (α-D-Neu5Ac-(2-3)-β-D-Gal-(1-3)-β-D-GlcNAc-(1-3)-β-D-Gal(1-4)-D-Glc) and LSTc (α-D-Neu5Ac-(2-6)-β-D-Gal-(1-3)-β-D-GlcNAc-(1-3)-β-D-Gal(1-4)-D-Glc) in aqueous solution has been performed with the comprehensive use of molecular modeling and statistical data processing followed by determination of major and minor stabilized conformers and selection of relevant topologies. The sialic acid ring conformational free energy landscape for both pentasaccharides has been reconstructed and analyzed giving a specification of the most probable distorted ring conformations of the basic chair 1C4 structure. The obtained results are in a good agreement with experimental data generated by nuclear magnetic resonance spectroscopy and X-ray crystallography.

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References

  1. Geissner, A. and Seeberger, P.H., Annu. Rev. Anal. Chem., 2016, vol. 9, p. 223.

    Article  CAS  Google Scholar 

  2. Agre, P., Bertozzi, C., Bissell, M., Campbell, K.P., Cummings, R.D., Desai, U.R., and Ginsburg, D., J. Clin. Invest., 2016, vol. 126, no. 2, p. 405.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Domenech, M., Garcia, E., and Moscoso, M., Microb. Biotechnol., 2012, vol. 5, no. 4, p. 455.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Manco, S., Hernon, F., Yesilkaya, H., Paton, J.C., Andrew, P.W., and Kadioglu, A., Infect. Immun., 2006, vol. 74, no. 7, p. 4014.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Smith, D.F. and Cummings, R.D., Curr. Opin. Virol., 2014, vol. 7, p. 79.

    Article  CAS  PubMed  Google Scholar 

  6. Chandrasekaran, A., Srinivasan, A., Raman, R., Viswanathan, K., Raguram, S., Tumpey, T.M., and Sasisekharan, R., Nat. Biotechnol., 2008, vol. 26, no. 1, p. 107.

    Article  CAS  PubMed  Google Scholar 

  7. Case, D.A., Berryman, J.T., Betz, R.M., Cerutti, D.S., Cheatham, T.E., Darden, T.A., Duke, R.E., Giese, T.J., Smith, W., Swails, J., Walker, R.C., Wang, J., Wolf, R.M., Wu, X., York, D.M., and Kollman, P.A., AMBER 2015, San Francisco, 2015.

    Google Scholar 

  8. Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., and Parrinello, M., Comput. Phys. Commun., 2009, vol. 180, no. 10, p. 1961.

    Article  CAS  Google Scholar 

  9. Cremer, D. and Pople, J.A., J. Am. Chem. Soc., 1975, vol. 97, no. 6, p. 1354.

    Article  CAS  Google Scholar 

  10. Iglesias-Fernández, J., Raich, L., Ardèvol, A., and Rovira, C., Chem. Sci., 2015, vol. 6, no. 2, p. 1167.

    Article  CAS  PubMed  Google Scholar 

  11. Costa, S.I., Torezzan, C., Campello, A., and Vaishampayan, V.A., IEEE Information Theory and Applications Workshop (ITA), 2013, p. 1.

    Google Scholar 

  12. Straub, J., Campbell, T., How, J.P., and Fisher, J.W., IEEE Conf. on Computer Vision and Pattern Recognition (CVPR), 2015, p. 334.

    Google Scholar 

  13. Pierce, L.C., Salomon-Ferrer, R., Augusto F. de Oliveira, C., McCammon, J.A., and Walker, R.C., J. Chem. Theory Comput., 2012, vol. 8, no. 9, p. 2997.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Laio, A. and Parrinello, M., Proc. Natl. Acad. Sci. U. S. A., 2002, vol. 99, no. 20, p. 12562.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Sassaki, G.L., Elli, S., Rudd, T.R., Macchi, E., Yates, E.A., Naggi, A., and Guerrini, M., Biochemistry, 2013, vol. 52, no. 41, p. 7217.

    Article  CAS  PubMed  Google Scholar 

  16. Sabesan, S., Bock, K., and Paulson, J.C., Carbohydr. Res., 1991, vol. 218, p. 27.

    Article  CAS  PubMed  Google Scholar 

  17. Poppe, L., Dabrowski, J., Lieth, C.W., Numata, M., and Ogawa, T., FEBS J., 1989, vol. 180, no. 2, p. 337.

    CAS  Google Scholar 

  18. Ohrui, H., Nishida, Y., Itoh, H., and Meguro, H., J. Org. Chem., 1991, vol. 56, no. 5, p. 1726.

    Article  CAS  Google Scholar 

  19. Xu, D., Newhouse, E.I., Amaro, R.E., Pao, H.C., Cheng, L.S., Markwick, P.R., and Arzberger, P.W., J. Mol. Biol., 2009, vol. 387, no. 2, p. 465.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Thompson, A.J., Dabin, J., Iglesias-Fernandez, J., Ardevol, A., Dinev, Z., Williams, S.J., and Smith, D.K., Angew. Chem., Int. Ed., 2012, vol. 51, no. 44, p. 10997.

    Article  CAS  Google Scholar 

  21. Chan, J., Lu, A., and Bennet, A.J., J. Am. Chem. Soc., 2011, vol. 133, no. 9, p. 2989.

    Article  CAS  PubMed  Google Scholar 

  22. Sadovnichy, V., Tikhonravov, A., Voevodin, V., and Opanasenko, V., “Lomonosov”: Supercomputing at Moscow State University, in Contemporary High Performance Computing: From Petascale toward Exascale, Boca Raton: CRC, 2013.

    Google Scholar 

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Authors and Affiliations

  1. Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology, Moscow State University, Moscow, 119991, Russia

    E. M. Kirilin & V. K. Švedas

Authors
  1. E. M. Kirilin
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  2. V. K. Švedas
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Correspondence to V. K. Švedas.

Additional information

Original Russian Text © E.M. Kirilin, V.K. Švedas, 2018, published in Vestnik Moskovskogo Universiteta, Seriya 2: Khimiya, 2018, No. 2, pp. 117–124.

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Kirilin, E.M., Švedas, V.K. Study of the Conformational Variety of the Oligosaccharide Substrates of Neuraminidases from Pathogens using Molecular Modeling. Moscow Univ. Chem. Bull. 73, 39–45 (2018). https://doi.org/10.3103/S0027131418020050

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  • DOI: https://doi.org/10.3103/S0027131418020050

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