Automated docking of monosaccharide substrates and analogues and methyl α-acarviosinide in the glucoamylase active site

Proteins: Structure, Function and Genetics

Volumn 27, Issue 2, 1997, Pages 235-248

  Coutinho, Pedro M ^a   Dowd, Michael K ^b   Reilly, Peter J ^a  

^a Iowa State University of Science and Technology   (United States)

^b SOUTHERN REGIONAL RESEARCH CENTER   (United States)

Author keywords

acarviosinide; active site; docking; glucoamylase; molecular mechanics; monosaccharides; simulated annealing

Indexed keywords

GLUCAN 1,4 ALPHA GLUCOSIDASE; MONOSACCHARIDE;

ARTICLE; BINDING KINETICS; ENZYME ACTIVE SITE; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

1-DEOXYNOJIRIMYCIN; ASPERGILLUS; AUTOMATION; BINDING SITES; CATALYSIS; COMPUTER SIMULATION; DISACCHARIDES; FUNGAL PROTEINS; GALACTOSE; GLUCAN 1,4-ALPHA-GLUCOSIDASE; GLUCONATES; GLUCOSE; MANNOSE; MODELS, MOLECULAR; MONOSACCHARIDES; SUBSTRATE SPECIFICITY;

EID: 0031058806     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199702)27:2<235::AID-PROT10>3.0.CO;2-N     Document Type: Article

References (60)

1. Meagher, M.M., Reilly, P.J. Kinetics of the hydrolysis of di-and trisaccharides by Aspergillus niger glucoamylases I and II. Biotechnol. Bioeng. 34:689-693, 1989.
2. Nikolov, Z.L., Meagher, M.M., Reilly, P. J. Kinetics, equilibria, and modeling of the formation of oligosaccharides from D-glucose by Aspergillus niger glucoamylases I and II. Biotechnol. Bioeng. 34:694-704, 1989.
3. Nakano, H., Hamayasu, K.-I., Fujita, K., Hara, K., Ohi, M., Yoshizumi, H., Kitahata, S. Synthesis of 2-deoxyglucooligosaccharides through condensation of 2-deoxy-D-glucose by glucoamylase and α-glucosidase. Biosci. Biotechnol. Bioeng. 59:1732-1736, 1995.
4. Pestlin, S., Prinz, D., Starr, J.N., Reilly, P.J. Kinetics and equilibria of condensation reactions between monosaccharide pairs catalyzed by Aspergillus niger glucoamylase. Biotechnol. Bioeng., submitted for publication, 1996.
5. Coutinho, P.M., Reilly, P.J. Structural similarities in glucoamylases by hydrophobic cluster analysis. Protein Eng. 7:749-760, 1994.
6. Aleshin, A.E., Golubev, A., Firsov, L.M., Honzatko, R.B. Crystal structure of glucoamylase from Aspergillus awamori var. X100 to 2.2-Å resolution. J. Biol. Chem. 267: 19291-19298, 1992.
7. Aleshin, A.E., Hoffman, C., Firsov, L.M., Honzatko, R.B. Refined crystal structures of glucoamylase from Aspergillus awamori var. X100. J. Mol. Biol. 238:575-591, 1994.
8. Harris, E.M.S., Aleshin, A.E., Firsov, L.M., Honzatko, R.B. Refined structure for the complex of 1-deoxynojirimycin with glucoamylase from Aspergillus awamori var. X100 to 2.4-Å resolution. Biochemistry 32:1618-1626, 1993.
9. Aleshin, A.E., Firsov, L.M., Honzatko, R.B. Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. X100 to 2.4-Å resolution. J. Biol. Chem. 269:15631-15639, 1994.
10. Stoffer, B., Aleshin, A.E., Firsov, L.M., Svensson, B., Honzatko, R.B. Refined structure of the complex of D-gluco-dihydroacarbose with glucoamylase from Aspergillus awamori var. X100 to 2.2 Å resolution: Dual conformations for extended inhibitors bound to the active site of glucoamylase. FEBS Lett. 358:57-61, 1995.
11. Aleshin, A.E., Stoffer, B., Firsov, L.M., Svensson, B., Honzatko, R.B. Crystallographic complexes of glucoamylase with maltooligosaccharide analogs: Relationship of stereochemical distortions at the non-reducing end to the catalytic mechanism. Biochemistry, 35:8319-8328, 1996.
12. Savel'ev, A.N., Sergeev, V.R., Firsov, L.M. Study of the active site of glucoamylase from Aspergillus awamori. Biokhimiya 47:390-397, 1982.
13. Meagher, M.M., Nikolov, Z.L., Reilly, P.J. Subsite mapping of Aspergillus niger glucoamylases I and II with malto-and isomaltooligosaccharides. Biotechnol. Bioeng. 34:681-688, 1989.
14. Ermer, J., Rose, K., Hübner, G., Schellenberger, A. Subsite affinities of Aspergillus niger glucoamylase II determined with p-nitrophenylmaltooligosaccharides. Biol. Chem. Hoppe-Seyler 374:123-128, 1993.
15. Coutinho, P.M., Reilly, P.J. Structure-function relationships in the catalytic and starch-binding domains of glucoamylase. Protein Eng. 7:393-400, 1994.
16. Henrissat, B., Coutinho, P.M., Reilly, P.J. Reading-frame shift in Saccharomyces glucoamylases restores catalytic base, extends sequence and improves alignment with other glucoamylases. Protein Eng. 7:1281-1282, 1994.
17. Dowd, M.K., Zeng, J., French, A.D., Reilly, P.J. Conformational analysis of the anomeric forms of kojibiose, nigerose, and maltose using MM3. Carbohydr. Res. 230:223-244, 1992.
18. Andrews, J.S., Weimar, T., Frandsen, T.B., Svensson, B., Pinto, B.M. Novel disaccharides containing sulfur in the ring and nitrogen in the interglycosidic linkage: Conformation of methyl 5′-thio-4-N-α-maltoside bound to glucoamylase and its activity as a competitive inhibitor. J. Am. Chem. Soc. 117:10799-10804, 1995.
19. Sigurskjold, B.W., Berland, C.R., Svensson, B. Thermodynamics of inhibitor binding to the catalytic site of glucoamylase from Aspergillus niger determined by displacement titration calorimetry. Biochemistry 33:10191-10199, 1994.
20. Raimbaud, E., Buléon, A., Pérez, S. Molecular modelling of acarviosine, the pseudo-disaccharide moiety of acarbose, and other inhibitors of alpha-amylases. Carbohydr. Res. 227:351-363, 1992.
21. Bock, K., Meldal, M., Refn, S. Controlled reduction of acarbose: Conformational analysis of acarbose and the resulting saturated products. Carbohydr. Res. 221:1-16, 1991.
22. Howard, A.E., Kollman, P.A. An analysis of current methodologies for conformational searching of complex molecules. J. Med. Chem. 31:1669-1675, 1988.
23. Mukhopadhay, C., Rao, V.S.R. Computer modelling approach to study the modes of binding of α-and β-L-arabinose to L-arabinose-binding protein. Int. J. Biol. Macromol. 10:217-226, 1988.
24. Mukhopadhay, C., Rao, V.S.R. Computer modelling approach to study the modes of binding of α-and β-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein. Int. J. Biol. Macromol. 11:194-200, 1989.
25. Biswas, M., Sekharudu, Y.C., Rao, V.S.R. The conformation of glycans of the oligo-D-mannosidic type, and their interaction with concanavalin A: A computer-modelling study. Carbohydr. Res. 160:151-170, 1987.
26. Petukhov, M.G., Mazur, A.K. Modeling of possible methods of substrate binding in the active site of α-amylase A from Aspergillus oryzae. Molek. Biol. 26:292-299, 1992.
27. Casset, F., Imberty, A., Haser, R., Payan, F., Pérez, S. Molecular modelling of the interaction between the catalytic site of pig pancreatic α-amylase and amylose fragments. Eur. J. Biochem. 232:284-293, 1995.
28. Imberty, A., Hardman, K.D., Carver, J.P., Pérez, S. Molecular modelling of protein-carbohydrate interactions: Docking of monosaccharides in the binding site of concanavalin A. Glycobiology 1:631-642, 1991.
29. Oshiro, C.M., Kuntz, I.D., Scott Dixon, J. Flexible ligand docking using a genetic algorithm. J. Comput. Aided Mol. Des. 9:113-130, 1995.
30. Sobolev, V., Wade, R.C., Vriend, G., Edelman, M. Molecular docking using surface complementarity. Proteins 25: 120-129, 1996.
31. Goodsell, D.S., Olson, A.J. Automated docking of substrates to proteins by simulated annealing. Proteins 8:195-202, 1990.
32. Goodsell, D.S., Lauble, H., Stout, C.D., Olson, A.J. Automated docking in crystallography: Analysis of the substrates of aconitase. Proteins 17:1-10, 1993.
33. Goodsell, D.S., Morris, G.M., Olson, A.J. Docking of flexible ligands. Applications of AutoDock. J. Mol. Recognition, 9:1-5, 1996.
34. Clark, K.P., Ajay. Flexible ligand docking without parameter adjustment across four ligand-receptor complexes. J. Comput. Chem. 16:1210-1226, 1995.
35. Coutinho, P.M., Dowd, M.K., Reilly, P.J. Automated docking of isomaltose analogues in the glucoamylase active site. Carbohydr. Res., in press, 1996.
36. Coutinho, P.M., Dowd, M.K., Reilly, P.J. Automated docking of disaccharides in the glucoamylase active site. Proteins, submitted for publication, 1996.
37. Dowd, M.K., French, A.D., Reilly, P.J. Modeling of aldopyranosyl ring puckering with MM3(92). Carbohydr. Res. 264:1-19, 1994.
38. Allinger, N.L., Yuh, Y.H., Lii, J.H. Molecular mechanics: The MM3 force field for hydrocarbons. J. Am. Chem. Soc. 111:8551-8566, 1989.
39. Lii, J.H., Allinger, N.L. Molecular mechanics. The MM3 force field for hydrocarbons. Vibrational frequencies and thermodynamics. J. Am. Chem. Soc. 111:8566-8575, 1989.
40. Allinger, N.L., Rahman, M., Lii, J.H. A molecular mechanics force field (MM3) for alcohols and ethers. J. Am. Chem. Soc. 112:8293-8307, 1990.
41. Dowd, M.K., Reilly, P.J., French, A.D. Conformational analysis of trehalose disaccharides and analogues using MM3. J. Comput. Chem. 13:102-114, 1992.
42. Dowd, M.K., French, A.D., Reilly, P.J. Conformational analysis of the anomeric forms of sophorose, laminarabiose, and cellobiose using MM3. Carbohydr. Res. 233:15-34, 1992.
43. Dowd, M.K., French, A.D., Reilly, P.J. Molecular modeling of two disaccharides containing fructopyranose linked to glucopyranose. J. Carbohydr. Chem. 12:449-457, 1993.
44. Dowd, M.K., Reilly, P.J., French, A.D. Relaxed-residue conformational mapping of the three linkage bonds of isomaltose and gentiobiose with MM3(92). Biopolymers 34: 625-638, 1994.
45. French, A.D., Dowd, M.K. Exploration of disaccharide conformations by molecular mechanics. J. Mol. Struct. (Theochem.) 186:183-201, 1993.
46. Gasteiger, J., Marsili, M. Iterative partial equalization of orbital electronegativity - A rapid access to atomic charges. Tetrahedron 36:3219-3228, 1980.
47. Goodford, P.J. A computational procedure for determining energetically favorable binding sites on biologically important molecules. J. Med. Chem. 28:849-857, 1985.
48. Mehler, E.L., Solmajer, T. Electrostatic effects in proteins: comparison of dielectric and charge models. Protein Eng. 4:903-910, 1991.
49. Bock, K., Pedersen, H. The solution conformation of acarbose. Carbohydr. Res. 132:142-149, 1984.
50. Lemieux, R.U., Spohr, U., Bach, M., Cameron, D.R., Frandsen, T.B., Svensson, B., Palcic, M.M. Chemical mapping of the active site of the glucoamylase of Aspergillus niger. Can. J. Chem. 74:319-335, 1996.
51. Bock, K., Pedersen, H. The substrate specificity of the enzyme amyloglucosidase (AMG). Part I. Deoxy derivatives. Acta Chem. Scand. 641:617-628, 1987.
52. Sierks, M.R., Bock, K., Refn, S., Svensson, B. Active site similarities of glucose dehydrogenase, glucose oxidase, and glucoamylase probed by deoxygenated substrates. Biochemistry 31:8972-8977, 1992.
53. El-Sayed, H., László, E. Condensation of glucose by the reversed hydrolysis reaction of glucoamylase. II. Effect of inhibition of glucose derivatives and pH. Acta Aliment. 23:59-70, 1994.
54. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl. Crystallogr. 24:946-950, 1991.
55. Ohnishi, M., Matsumoto, T., Yamanaka, T., Hiromi, K. Binding of isomaltose and maltose to the glucoamylase from Aspergillus niger, as studied by fluorescence spectrophotometry and steady-state kinetics. Carbohydr. Res. 204:187-196, 1990.
56. László, E., Holló, J., Hoschke, A., Sárosi, G. A study by means of lactone inhibition of the role of a "half-chair" glycosyl conformation at the active centre of amylolytic enzymes. Carbohydr. Res. 61:387-394, 1978.
57. Hiromi, K., Kawai, M., Suetsugo, N., Nitta, Y., Hosotani, T. Kinetic studies on glucoamylase. VI. J. Biochem. 74: 935-943, 1973.
58. Tanaka, Y., Tao, W., Blanchard, J.S., Hehre, E.J. Transition state structures for the hydrolysis of α-D-glucopyranosyl fluoride by retaining and inverting reactions of glycosylases. J. Biol. Chem. 269:32306-32316, 1994.
59. Sierks, M.R., Svensson, B. Kinetic identification of a hydrogen bonding pair in the glucoamylase-maltose transition state complex. Protein Eng. 5:185-188, 1992.
60. Bock, K., Pedersen, H. The substrate specificity of the enzyme amyloglucosidase (AMG). Part II. 6-Substituted maltose derivatives. Acta Chem. Scand. B42:75-85, 1988.