Automated docking of glucosyl disaccharides in the glucoamylase active site

Proteins: Structure, Function and Genetics

Volumn 28, Issue 2, 1997, Pages 162-173

  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

AutoDock; Cellobioside; Disaccharide; Docking; Gentiobioside; Glucoamylase; Kojibio side; Maltoside; Nigeroside; Simulated annealing; Trehalose

Indexed keywords

DISACCHARIDE; DOCKING PROTEIN; GLUCAN 1,4 ALPHA GLUCOSIDASE; GLUCOSE; HYDROXYL GROUP; TREHALASE;

ARTICLE; CATALYSIS; CRYSTALLOGRAPHY; ENERGY TRANSFER; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME SUBSTRATE COMPLEX; MOLECULAR INTERACTION; PRIORITY JOURNAL;

BINDING SITES; CARBOHYDRATE CONFORMATION; CATALYSIS; DISACCHARIDES; GLUCAN 1,4-ALPHA-GLUCOSIDASE; HYDROGEN BONDING;

RUMEX;

EID: 0031007588     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199706)28:2<162::AID-PROT5>3.0.CO;2-H     Document Type: Article

References (59)

1. Pazur, J.H., Kleppe, K. The hydrolysis of α-D-glucosides by amyloglucosidase from Aspergillus niger. J. Biol. Chem. 237:1002-1006, 1962.
2. Meagher, M.M., Reilly, P.J. Kinetics of the hydrolysis of diand trisaccharides by Aspergillus niger glucoamylases I and II. Biotechnol. Bioeng. 34:689-693, 1989.
3. Hehre, E.J., Okada, G., Genghof, D.S. Configurational specificity: Unappreciated key to understanding enzymic reversions and de novo glycosidic bond synthesis. I. Reversal of hydrolysis by α-, β-, and glucoamylases with donors of correct anomeric form. Arch. Biochem. Biophys. 135:74-89, 1969.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. Stoffer, B., Aleshin, A.E., Firsov, L.M., Svensson, B., Honzatko, R.B. Refined structure of the complex of D-glucodihydroacarbose 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.
13. 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.
14. Coutinho, P.M., Reilly, P.J. Structure-function relationships in the catalytic and starch-binding domains of glucoamylase. Protein Eng. 7:393-400, 1994.
15. 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.
16. Coutinho, P.M., Reilly, P.J. Structural similarities in glucoamylases by hydrophobic cluster analysis. Protein Eng. 7:749-760, 1994.
17. 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.
18. Goodsell, D.S., Olson, A.J. Automated docking of substrates to proteins by simulated annealing. Proteins 8:195-202, 1990.
19. 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.
20. Goodsell, D.S., Morris, G.M., Olson, A.J. Docking of flexible ligands: Applications of AutoDock. J. Mol. Recog., 9:1-5, 1996.
21. Stoddard, B.L., Koshland, D.E. Prediction of a receptor protein complex using a binary docking method. Nature 358:774-776, 1992.
22. Coutinho, P.M., Dowd, M.K., Reilly, P.J. Automated docking of monosaccharide substrates and analogues and methyl α-acarviosinide in the glucoamylase active site. Proteins, 27:235-248, 1997
23. Coutinho, P.M., Dowd, M.K., Reilly, P.J. Automated docking of isomaltose analogues in the glucoamylase active site. Carbohydr. Res., 297:309-324, 1997.
24. Quiocho, F.A. Protein-carbohydrate interactions: Basic molecular features. Pure Appl. Chem. 7:1293-1306, 1989.
25. Lemieux, R.U. The origin of the specificity in the recognition of oligosaccharides by proteins. Chem. Soc. Rev. 18:347-374, 1989.
26. Bock, K., Pedersen, H. The substrate specificity of the enzyme amyloglucosidase (AMG). Part I. Deoxy derivatives. Acta Chem. Scand. B41:617-628, 1987.
27. 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.
28. 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.
29. Bock, K., Skrydstrup, T., Refn, S. Synthesis of isomaltose analogues. J. Carbohydr. Chem. 10:969-980, 1991.
30. Lemieux, R.U., Spohr, U. How Emil Fisher was led to the lock and key concept for enzyme specificity. Adv. Carbohydr. Chem. Biochem. 50:1-20, 1994.
31. 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.
32. 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.
33. 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.
34. 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.
35. French, A.D., Dowd, M.K. Exploration of disaccharide conformations by molecular mechanics. J. Mol. Struct. (Theochem) 186:183-201, 1993.
36. Allinger, N.L., Yuh, Y.H., Lu, J.H. Molecular mechanics. The MM3 force field for hydrocarbons. J. Am. Chem. Soc. 111:8551-8566, 1989.
37. Lu, 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.
38. Allinger, N.L., Rahman, M., Lu, J.H. A molecular mechanics force field (MM3) for alcohols and ethers. J. Am. Chem. Soc. 112:8293-8307, 1990.
39. 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.
40. Gasteiger, J., Marsili, M. Iterative partial equalization of orbital electronegativity: A rapid access to atomic charges. Tetrahedron 36:3219-3228, 1980.
41. Goodford, P.J. A computational procedure for determining energetically favorable binding sites on biologically important molecules. J. Med. Chem. 28:849-857, 1985.
42. Mehler, E.L., Solmajer, T. Electrostatic effects in proteins: Comparison of dielectric and charge models. Protein Eng. 4:903-910, 1991.
43. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950, 1991.
44. Bock, K., Fernandez-Bolaños Guzmán, J., Duus, J.Ø. A nuclear resonance spectroscopic and conformational study of eight pseudo-trehaloses (D-glucopyranosyl 5a-carba-D-and L-glucopyranosides). Carbohydr. Res. 209:51-65, 1991.
45. Alvarado, E. "The Conformational Properties of Maltose, Maltotriose and Amylose." Doctoral thesis, University of Alberta, Edmonton, Alberta, Canada, 1987.
46. Hiromi, K., Kawai, M., Suetsugu, N., Nitta, Y., Hosotani, T. Kinetic studies on glucoamylase. VI. Inhibition of substrate analogues. J. Biochem. 74:935-943, 1973.
47. Palcic, M.M., Skrydstrup, T., Bock, K., Le, N., Lemieux, R.U. Substrate recognition by amyloglucosidase: Evaluation of conformationally biased isomaltosides. Carbohydr. Res. 250:87-92, 1993.
48. 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.
49. Alderhorst, K., Bock, K., Pedersen, H., and Refn, S. The substrate specificity of the enzyme amyloglucosidase (AMG). Part III. Synthesis of epimers and mono-O-methyl ethers of methyl β-maltoside. Acta Chem. Scand. B42:196-201, 1988.
50. Remaud-Simeon, M., López-Mungia, A., Pelenc, V., Paul, F., Monsan, P. Production and use of glycosyltransferases from Leuconostoc mesenteroides NRRL B-1299 for the synthesis of oligosaccharides containing α-(1,2) linkages. Appl. Biochem. Biotechnol. 44:101-117, 1994.
51. Evers, B., Thiem, J. Synthesis of 2-deoxy-maltooligosaccharides with phosphorylase and their degradation with amylases. Starch/Stärke 11:434-439, 1995.
52. Nakano, H., Hamayasu, K.-I., Fujita, K., Hara, K., Ohi, M., Yoshizumi, H., Kitahata, S. Synthesis of 2-deoxy-glucooligosaccharides through condensation of 2-deoxy-D-glucose by glucoamylase and α-glucosidase. Biosci. Biotechnol. Bioeng. 59:1732-1736, 1995.
53. Côté, G.L., Biely, P. Enzymically produced cyclic α-1,3-linked and α-1,6-linked oligosaccharides of D-glucose. Eur. J. Biochem. 226:641-648, 1994.
54. Okada, Y., Koizumi, K., Kitahata, S. Isolation by HPLC of the positional isomers of heterogeneous doubly branched cyclomaltohexaose having one α-D-galactosyl and one α-D-glucosyl side chain and determination of their structures by enzymatic degradation. Carbohydr. Res. 287:213-223, 1996.
55. Omichi, K., Matsushima, Y. Studies on the substrate specificity of Taka-amylase Al. XIV. Preparation of 6-deoxy-6-halogenomaltotrioses and their hydrolysis by Takaamylase A. J. Biochem. 84:835-841, 1978.
56. 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.
57. Abe, J.I., Takeda, Y., Hizukuri, S. Action of glucoamylase from Aspergillus niger on phosphorylated substrate. Biochim. Biophys. Acta 703:26-33, 1982.
58. Takeda, Y., Hizukuri, S., Ozono, Y. Suetake, M. Actions of porcine pancreatic and Bacillus subtilis alpha-amylases and Aspergillus niger glucoamylase on phosphorylated (1-4)-α-D-glucan. Biochim. Biophys. Acta 749:302-311, 1983.
59. Kimura, A., Robyt, J.F. Reaction of enzymes with starch granules: Enhanced reaction of glucoamylase with gelatinized starch granules. Carbohydr. Res. 288:233-240, 1996.