Molecular Modeling and Docking of Mannose-binding Lectin from Lycoris radiata

doi:10.1007/s40242-013-3259-4

Abstract

Abstract:

Lycoris radiata mannose-binding lectin(LRL) is a protein which binds mannose residues specifically. The maturation peptide and three mannose-binding domains(residues 49―57, 80―88 and 113―121) of LRL were identified by sequence analysis. The 3D structure of LRL constructed by homology modeling shaped a fistular triangular prism. Three flanks of the prism are mainly composed of β-sheets and each flank has a mannose-binding domain. According to the docking and dynamics simulation, the bindings of residues 49―57 and 80―88 with mannose are more stable than that of residues 113―121 with it. The key residues for binding mannose are Gln80, Asp82, Asn84 and Tyr88. The study preliminarily analyzed the interaction sites and mechanism of LRL with mannoses, which could be useful for the study on insect-resistance and related drug discovery of LRL.

Key words: Mannose-binding lectin, Lycoris radiata, Molecular modeling, Molecular docking, Dynamics simulation

ZHU Qian-kun, ZHU Meng-li, ZOU Jia-xin, FENG Pei-chun, FAN Gao-tao, LIU Zu-bi, WANG Wan-jun. Molecular Modeling and Docking of Mannose-binding Lectin from Lycoris radiata[J]. Chemical Research in Chinese Universities, 2013, 29(6): 1153-1158.

References

[1] Chrispeels M. J., Raikhel N. V., Plant Cell, 1991, 3, 1
[2] Peumans W. J., van Damme E. J., Histochem. J., 1995, 27, 253
[3] Peumans W. J., van Damme E., Plant Physiol., 1995, 109, 347
[4] Vandenborre G., Smagghe G., van Damme E. J., Phytochemistry, 2011, 72, 1538
[5] Chang T., Zhu Z., Hereditas, 2002, 24, 493
[6] Lopez S., Armand-Ugon M., Bastida J., Viladomat F., Este J. A., Stewart D., Codina C., Planta Med., 2003, 69, 109
[7] Heinrich M., Lee Teoh H., J. Ethnopharmacol., 2004, 92, 147
[8] Yuan J. H., J. Anhui Agr. Sci., 2010, 2, 053
[9] Zhao X., Yao J., Sun X., Tang K., Mitochondr. DNA, 2003, 14, 223
[10] Sauerborn M. K., Wright L. M., Reynolds C. D., Grossmann J. G., Rizkallah P. J., J. Mol. Biol., 1999, 290, 185
[11] Hester G., Kaku H., Goldstein I. J., Wright C. S., Nat. Struct. Mol. Biol., 1995, 2, 472
[12] van Damme E. J., Smeets K., van Leuven F., Peumans W. J., Plant Mol. Biol., 1994, 24, 825
[13] Pang Y. Z., Shen G. A., Liao Z. H., Yao J. H., Fei J., Sun X. F., Tan F., Tang K. X., Mitochondr. DNA, 2003, 14, 163
[14] Wright C. S., Kaku H., Goldstein I. J., J. Biol. Chem., 1990, 265, 1676
[15] Wu C. F., Li J., An J., Chang L. Q., Chen F., Bao J. K., J. Int. Plant Biol., 2006, 48, 223
[16] Liu W., Yang N., Ding J., Huang R. H., Hu Z., Wang D. C., J. Biol. Chem., 2005, 280, 14865
[17] Larkin M., Blackshields G., Brown N., Chenna R., McGettigan P., McWilliam H., Valentin F., Wallace I., Wilm A., Lopez R., Bioinformatics, 2007, 23, 2947
[18] Zhu Q., Zhou J., Zhang G., Liao H., Chin. J. Chem., 2012, 30, 2533
[19] Johnson M. S., Mol. Med. Today, 1995, 1, 188
[20] Brooks B. R., Bruccoleri R. E., Olafson B. D., Swaminathan S., Karplus M., J. Comput. Chem., 1983, 4, 187
[21] Lan H. N., Wang Y. X., Zheng M. Z., Han W. W., Zheng X., Chem. Res. Chinese Universities, 2013, 29(1), 139
[22] Li J. L., Wang J. P., Hu D. H., Shao C., Su Z. M., Chem. J. Chinese Universities, 2010, 31(8), 1636
[23] Elumalai P., Liu H. L., Int. J. Biol. Macromol., 2011, 49, 134
[24] Wang Y., Zhou Y. H., Guo Y. J., Xu X. L., Si D. Y., Zhou H., Li Z. S., Chem. Res. Chinese Universities, 2009, 25(6), 904
[25] Xu X., Cannistraro S., Bizzarri A., Zeng Y., Wang C., Chem. Res. Chinese Universities, 2013, 29(2), 299
[26] Zhou Y. H., Luo Q., Han W. W., Yao Y., Li Z. S., Chem. J. Chinese Universities, 2009, 30(7), 1423
[27] Colovos C., Yeates T. O., Protein Sci., 1993, 2, 1511
[28] Wiederstein M., Sippl M. J., Nucleic Acids Res., 2007, 35, 407
[29] Yuan X. H., Qu Z. Y., Wu X. M., Wang Y. C., Wei F. X., Zhang H. Y., Liu L., Yang Z. W., Chem. J. Chinese Universities, 2009, 30(8), 1636
[30] Wallace A. C., Laskowski R. A., Thornton J. M., Protein Eng., 1995, 8, 127
[31] Gajendrarao P., Krishnamoorthy N., Sakkiah S., Lazar P., Lee K. W., J. Mol. Graph. Model., 2010, 28, 524
[32] Shan S., Xia L., Ding X., Zhang Y., Hu S., Sun Y., Yu Z., Han L., Chin. J. Chem., 2011, 29, 427
[33] Bodade R., Beedkar S., Manwar A., Khobragade C., Int. J. Biol. Macromol., 2010, 47, 298