Abstract
The conformational preferences of cyclosophoroheptadecaose (Cys-A), which is a member of a class of cyclic (1→2)-β-D-glucan, were characterized by molecular dynamics simulations. Simulated annealing and constant temperature molecular dynamics simulations were performed on the Cys-A. The simulations produced various types of compact and asymmetrical conformations of Cys-A. Excellent agreement was found between experimental data and corresponding values predicted by molecular modeling. Most glycosidic linkages were concentrated in the lowest energy region of φ-ψ energy map, and the values of radius of gyration (RG) and the nuclear Overhauser effect (NOE) distance data derived from our simulations were finely consistent with the reported experimental values. This result will also give novel insights for the molecular complexation mechanism of Cys-A with various guest chemicals.
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References
Abe, M., Amemura, A. and Higashi, S., Plant Soil, 64 (1982) 315.
Hisamatsu, M., Amemura, A., Koizumi, K., Utamura, T. and Okada, Y., Carbohydr. Res., 121 (1983) 31.
Miller, K.J., Kennedy, E.P. and Reinhold, V.N., Science, 231 (1986) 48.
Clarke, H. R., Leigh, J. A. and Douglas, C. J., Cell, 71 (1993) 191.
Dylan, T., Nagpal, P., Helinski, D.R. and Ditta, G.S., J. Bacteriol., 172 (1990) 1409.
Okada, Y., Horiyama, S. and Koizumi, K., Yakugaku Zasshi, 106 (1986) 240.
Kwon, C., Choi, Y., Kim, N., Yoo, J., Yang, C., Kim, H. and Jung, S., J. Incl. Phenom., 36 (2000) 55.
Palleschi, A. and Crescenzi, V., Gazz. Chim. Ital., 115 (1985) 243.
York, W.S., Thomsen, J.U. and Meyer, B., Carbohydr. Res., 248 (1993) 55.
André, I., Mazeau, K., Taravel, F.R. and Tvaroska, I., Int. J. Biol. Macromol., 17 (1995) 189.
Hargy, B.J. and Sarko, A., J. Comput. Chem., 14 (1993) 831.
Balaji, P.V., Qasba, P.K. and Rao, V.S., Glycobiology, 4 (1994) 497.
Asensio, J.L., Martin-Pastor, M. and Jimenez-Barbero, J., Int. J. Biol. Macromol., 17 (1995) 137.
Martín-Pastor, M., Espinosa, J.F., Asensio, J.L. and Jimenez-Barbero, Carbohyd. Res., 298 (1997) 15.
Chio, Y., Yang, C., Kim, H. and Jung, S., Carbohydr. Res., 326 (2000) 227.
Kim, H., Choi, J., Kim, H. and Jung, S., Carbohydr. Res., 337 (2002) 549.
Dauber-Osguthorpe, P., Roberts, V.A., Osguthorpe, D.J., Wolff, J., Genest, M. and Hagler, A.T., Proteins, 4 (1988) 31.
Choi, Y., Kang, S., Yang, C., Kim, H. and Jung, S., Bull. Korean Chem. Soc., 20 (1999) 753.
Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A. and Haak, J.R., J. Chem. Phys., 81 (1984) 3684.
Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F. and Hermans, J., In Pullman B (Ed.) Intermolecular Forces, Reidel, Dordrecht, 1981.
Swope, W.C., Anderson, H.C., Berens, P.H. and Wilson, K.R., J. Chem. Phys., 76 (1982) 637.
Ding, H.Q., Karasawa, N. and Goddard, W.A., J. Chem. Phys., 97 (1992) 4309.
Andersen, H.C., J. Comp. Physics., 52 (1983) 24.
Mimura, M., Kitamura, S., Gotoh, S., Takeo, K., Urakawa, H. and Kanjiwara, K., Carbohydr. Res., 289 (1996) 25.
Lemieux, R.U., Bock, K., Delbaere, L.T.J., Koto, S. and Rao, V.S., Can. J. Chem., 58 (1980) 631. 610
Bock, K., Pure Appl. Chem., 55 (1983) 605.
Dowd, M.K., French, A.D. and Reilly, P.J., Carbohydr. Res., 233 (1992) 15.
Ohanessian, P.J., Longchambon, F. and Arene, F., Acta. Crystallogr., Sect B, 34 (1978) 3666.
Spieser, S.A.H., van Kuik, J.A., Kroon-Batenburg, L.M.J. and Kroon, J., Carbohydr. Res., 322 (1999) 264.
Jeffrey, G.A., An Introduction to Hydrogen Bonding, Oxfod, New York, 1997.
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Kim, H., Jeong, K., Lee, S. et al. Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A). J Comput Aided Mol Des 16, 601–610 (2002). https://doi.org/10.1023/A:1021923815450
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DOI: https://doi.org/10.1023/A:1021923815450