Stochastic molecular dynamics of peanut lectin PNA complex with T-antigen disaccharide

Journal of Molecular Graphics and Modelling

Volumn 21, Issue 3, 2002, Pages 227-240

  Caffarena, Ernesto R ^a   Raul Grigera J ^b   Bisch, Paulo M ^a  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b Instituto de Fisica de Liquidos y Sistemas Biologicos   (Argentina)

Author keywords

Lectins; PNA; Stochastic molecular dynamics simulation; T antigen

Indexed keywords

ANTIGENS; CARBOHYDRATES; CHEMICAL BONDS; COMPUTER SIMULATION; ELECTROSTATICS; HYDROGEN BONDS; MOLECULAR DYNAMICS; WATER; X RAY ANALYSIS;

ACTIVE SITE;

PROTEINS;

DISACCHARIDE; HYDROGEN; OXYGEN; PLANT LECTIN; TUMOR ANTIGEN; WATER; PEANUT AGGLUTININ;

ARTICLE; ATOM; CARBOHYDRATE ANALYSIS; COMPLEX FORMATION; ELECTRIC POTENTIAL; HYDROGEN BOND; MOLECULAR DYNAMICS; PEANUT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; CONFORMATION; KINETICS; METABOLISM; SOLUTION AND SOLUBILITY; TIME; X RAY CRYSTALLOGRAPHY;

ARACHIS HYPOGAEA;

ANTIGENS, TUMOR-ASSOCIATED, CARBOHYDRATE; BINDING SITES; CARBOHYDRATE CONFORMATION; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DISACCHARIDES; HYDROGEN BONDING; KINETICS; MODELS, MOLECULAR; OXYGEN; PEANUT AGGLUTININ; SOLUTIONS; TIME FACTORS; WATER;

EID: 0036888373     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(02)00119-5     Document Type: Article

References (28)

1. Peumans W.J., van Damme E.J.M. Lectins as plant defense proteins. Plant Physiol. 109:1995;347.
2. K. Suguna, A. Surolia, M. Vijayan, Structural Diversity and Carbohydrate Specificity of Plant Lectins. Perspectives in Structural Biology, Universities Press (India) Ltd., 1999, pp. 367-379.
3. Reeke G.N. Jr., Becker J.W. Carbohydrate-binding sites of plant lectins. Curr. Topics Microbiol. Immunol. 120:1985;35-58.
4. Baneerj R., Mande S., Ganesh V., Das K., Dhanarj V., Mantha S., Suguna K., Surolia A., Vijayan M. Crystal structure of peanut lectin, a protein with a unusual quaternary structure. Proc. Natl. Acad. Sci. U.S.A. 91:1994;227-231.
5. Toone J.E. Structure and energetics of protein-carbohydrate complexes. Curr. Opin. Struc. Biol. 4:1994;719-728.
6. Loris R., Casset F., Bouckaert J., Pletinckx J., Dao-Thi M., Poortmans F., Imberty A., Perez S., Wyns L. The monosaccharide binding site of lectil lectin: an X-ray and molecular modelling study. Glycoconjugate J. 11:1994;507-517.
7. Baneerj R., Das K., Ravishankar R., Suguna K., Surolia A., Vijayan M. Conformation, protein carbohydrate interactions and a novel subunit association in the refined structure of peanut lectin-lactose complex. J. Mol. Biol. 259:1996;281-296.
8. Ravishankar R., Suguna K., Surolia A., Vijayan M. Crystal structure of the peanut-T-antigen complex. Carbohydrate specificity generated by water bridges. Curr. Sci. 72(11):1997;855-861.
9. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242.
10. Springer G. T and tn, general carcinoma auto-antigens. Science. 224:1984;1198-1206.
11. Irimura T., Kawaguchi T., Terao T., Osawa T. Carbohydrate-binding specificity of so-called galactose-specific phytohemagglutinins. Carbohydr. Res. 39:1975;317-327.
12. Lotan R., Skutelsky E., Danon D., Sharon N. Purification, composition, and specificity of anti-T lectin from peanut (arachis-hypogaea). J. Biol. Chem. 250:1975;8518-8523.
13. Lee X., Thompson A., Zhang Z., Ton-that H., Biesterfeldt J., Ogata C., Xu L., Jhonston R., Young M. Structure of the complex of Maclura Pomifera agglutinin and the T-antigen disaccharide, Galβ(1-3)GalNAc. J. Biol. Chem. 273(11):1998;6312-6318.
14. Bradbrook G.M., Gleichmann T., Harrop S.J., Habash J., Raftery J., Kalb(Gilboa) J., Yariv J., Hilier I.H., Helliwell J.R. X-ray and molecular dynamics studies of concanavalin-A glucoside and mannoside complexes. Relating structure to thermodynamics. Faraday Trans. 94:1998;1603-1611.
15. Loris R., Stas P.P.G., Wyns L.J. Conserved waters in legume lectin crystal structures. J. Biol. Chem. 269(43):1994;26722-26733.
16. Naidoo K.J., Brady J.W. Molecular dynamics simulations of a glycoprotein: the lectin from Erythrina corallodendron. J. Mol. Struc. (Theochem.). 395-396:1997;469-475.
17. Bradbrook G.M., Forshaw J.R., Pérez S. Structure/thermodynamics relationships of lectin saccharide complexes. The Erythrina corallodendron case. Eur. J. Biochem. 267:2000;4545-4555.
18. Åqvist J., Mowbray S.L. Sugar recognition by a glucose/galactose receptor. J. Biol. Chem. 270(17):1995;9978-9981.
19. Pascutti P., El-Jaik L., Bisch P., Mundim K., Ito A. Molecular dynamics simulation of α-melanocyte stimulating hormone in a water-membrane model interface. Eur. Biophys. J. 28(6):1999;499-509.
20. W.F. Van Gunsteren, H.J.C. Berendsen, GROMOS from BIOMOS, n.v, Nijenborg 4, 9747, AG Groningen, 1987.
21. W.F. Van Gunsteren, S. Billeter, A. Eising, P. Hünenberger, P. Krüger, A. Mark, W. Scott, I. Tironi, Biomolecular Simulation: The Gromos96 Manual and User guide, vdf Hochschulverlag AG na der ETH Zürich and BIOMOS b.v., Zürich, Groningen, 1996.
22. Berendsen H.J.C., Grigera J.R., Straatsma T.P. The missing term in the effective pair potentials. J. Phys. Chem. 91:1987;6269-6271.
23. Brooks C.L., Karplus M. Solvent effect on protein motion and protein effects on solvent motions. Dynamics of the active site region of lisozyme. J. Mol. Biol. 208:1989;159-181.
24. Van Gunsteren W.F., Berendsen H.J.C. A leap frog algorithm for stochastic dynamics. Mol. Simul. 1:1988;173-185.
25. Post C., Brooks B., Karplus M., Dobson C., Artymiuk P., Cheetham J., Phillips D. Molecular dynamics simulations of native and substrate-bound lysozyme. J. Mol. Biol. 190:1986;455-479.
26. Oberlin D., Scheraga H.A. B-spline method for energy minimization in grid-based molecular mechanics calculations. J. Comp. Chem. 19(1):1998;71-85.
27. Caffarena E.R., Bisch P.M. Hydration of T-antigen Galβ(1-3)GalNAc and the isomer Galβ(1-3)GlcNAc by molecular dynamics simulations. J. Mol. Graph. Mod. 18:2000;119-125.
28. Podjarny A.D., Howard E.I., Urzhumtsev A., Grigera J.R. A multicopy modelling of the water distribution in macromolecular crystals. Proteins: Struc. Function Genet. 28:1997;303-312.