Endo- and exo-inulinases: Enzyme-substrate interaction and rational immobilization

Biotechnology Progress

Volumn 26, Issue 2, 2010, Pages 397-405

  Basso, Alessandra ^a   Spizzo, Patrizia ^a   Ferrario, Valerio ^a   Knapic, Lorena ^a   Savko, Nina ^a   Braiuca, Paolo ^a   Ebert, Cynthia ^a   Ricca, Emanuele ^b   Calabrò, Vincenza ^b   Gardossi, Lucia ^a  

^a UNIVERSITY OF TRIESTE   (Italy)

^b UNIVERSITY OF CALABRIA   (Italy)

Author keywords

Docking; Endo inulinase; Exo inulinase; Homology modeling; Immobilization; Inulin; Molecular modeling

Indexed keywords

ASPERGILLUS AWAMORI; ASPERGILLUS NIGER; BACILLUS STEAROTHERMOPHILUS; CATALYTIC POTENTIAL; COMPUTATIONAL ANALYSIS; EFFECTIVE TOOL; ENDOINULINASE; ENZYME-SUBSTRATE INTERACTIONS; EXOINULINASE; HOMOLOGY MODELING; IMMOBILIZATION; IMMOBILIZED BIOCATALYSTS; INULINASE; MOLECULAR DYNAMICS SIMULATIONS; STRUCTURAL DIFFERENCES; STRUCTURAL FEATURE; SUBSTRATE SELECTIVITY; THREE-DIMENSIONAL MODEL;

BACTERIOLOGY; CATALYSTS; CRYSTAL STRUCTURE; DOCKING; ENZYMES; MOLECULAR DYNAMICS; MOLECULAR MODELING; SULFUR COMPOUNDS; SURFACE ANALYSIS; THREE DIMENSIONAL;

ENZYME IMMOBILIZATION;

BACTERIAL PROTEIN; FUNGAL PROTEIN; GLYCOSIDASE; IMMOBILIZED ENZYME; INULINASE;

ARTICLE; ASPERGILLUS NIGER; BIOLOGY; CHEMISTRY; ENZYMOLOGY; GEOBACILLUS STEAROTHERMOPHILUS; KINETICS; METABOLISM; METHODOLOGY; MOLECULAR DYNAMICS; PROTEIN BINDING; SURFACE PROPERTY;

ASPERGILLUS NIGER; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; ENZYMES, IMMOBILIZED; FUNGAL PROTEINS; GEOBACILLUS STEAROTHERMOPHILUS; GLYCOSIDE HYDROLASES; KINETICS; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; SURFACE PROPERTIES;

ASPERGILLUS AWAMORI; ASPERGILLUS NIGER; GEOBACILLUS STEAROTHERMOPHILUS;

EID: 77950893851     PISSN: 87567938     EISSN: 15206033     Source Type: Journal    
DOI: 10.1002/btpr.334     Document Type: Article

References (25)

1. Ricca E, Calabrò V, Curcio S, Iorio G. The state of the art in the production of fructose from inulin enzymatic hydrolysis. Crit Rev Biotechnol. 2007; 27: 129-145.
2. Sirisansaneeyakul S, Worawuthiyanan N, Vanichsriratana W, Srinophakun P, Chisti Y. Production of fructose from inulin using mixed inulinase from Aspergillus niger and Candida guilliermondii. World J Microb Bio. 2007; 23: 543-552.
3. Vandamme EJ, Derycke DG. Microbial inulinase: fermentation process, properties and applications. Adv App Microbiol. 1983; 29: 139-176.
4. Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D. BRENDA, the enzyme database: updates and major new developments. Nucl Acid Res. 2004; 32: 431-433.
5. Ohta K, Setsugu N, Nakamura T. Purification and properties of an extracellular inulinase from Rhizopus sp. strain TN-96. J Biosci Bioeng. 2002; 94: 78-80.
6. Nagem RPA, Rojas AL, Golubev AM, Korneeva OS, Eneyskaya EV, Kulminskaya AA, Neutroev KN, Palikarpov I. Crystal structure of exo-inulinase from Aspergillus awamori: the enzyme fold and structural determinants of substrate recognition. J Mol Biol. 2004; 344: 471-480.
7. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucl Acids Res. 2000; 28: 235-242.
8. The UniProt Consortium. The universal protein resource (UniProt). Nucl Acids Res. 2006; 36: 190-195.
9. Lengauer T, Rarey M. Computational methods for biomolecular docking. Curr Opin Struc Biol. 1996; 6: 402-406.
10. Alder BJ, Wainwright TE. Studies in molecular dynamics. I. General method. J Chem Phys. 1959; 31: 459-466.
11. Ghazi I, De Segura AG, Fernandez-Arrojo L, Alcalde M, Yates M, Rojas-Cervantes ML, Plou FJ, Ballesteros A. Immobilization of fructosyltransferase from Aspergillus aculeatus on epoxy-activated Sepabeads EC for the synthesis of fructo-oligosaccharides. J Mol Cat B: Enz. 2005; 35: 19-27.
12. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc. 1998; 117: 5179-5197.
13. Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem. 1985; 28: 849-857.
14. Basso A, Braiuca P, Cantone S, Ebert C, Linda P, Spizzo P, Caimi P, Hanefeld H, Degrassi G, Gardossi L. In Silico analysis of enzyme surface and glycosylation effect as a tool for efficient covalent immobilization of CalB and PGA on Sepabeads®. Adv Synth Catal. 2007; 349: 877-886.
15. Petrescu AJ, Milac AL, Petrescu SM, Dwek RA, Wormald MR. Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding. Glycobiology 2004; 14: 103-114.
16. Trimble RB, Atkinson PH, Tschopp JF, Townsend RR, Maley F. Structure of oligosaccharides on Saccharomyces SUC2 invertase secreted by the methylotrophic yeast Pichia pastoris. J Biol Chem. 1991; 34: 22807-22817.
17. Harte N, Silventoinen V, Quevillon E, Robinson S, Kallio K, Fustero X, Patel P, Jokinen P, Lopez R. Public web-based services from the European Bioinformatics Institute. Nucl Acids Res. 2004; 32: W3-W9.
18. Kallenberg AI, Van Rantwijk F, Sheldon RA. Immobilization of Penicillin G acylase: the key to optimum performance. Adv Synth Catal. 2005; 347: 905-926.
19. Hanefeld U, Gardossi L, Magner E. Understanding enzyme immobilization. Chem Soc Rev. 2009; 38: 453-468.
20. Fernández-Lafuente R, Rodriguez V, Mateo C, Penzal G, Hernández-Justiz O, Irazoqui G, Villarino A, Ovsejevi K, Batista F, Guisán JM. Stabilization of multimeric enzymes via immobilization and post-immobilization techniques. J Mol Cat B: Enz. 1999; 7: 181-189.
21. Mateo C, Abian O, Fernández-Lorente G, Pedroche J, Fernández-Lafuente R, Guisán J, Tam A, Daminati M. Epoxy-Sepabeads: a novel epoxy support for stabilisation of industrial enzymes via very intense multipoint covalent attachment. Biotechnol Prog. 2002; 18: 629-634.
22. Giacobini C, Villarino A, Franco-Fraguas L, Batista-Viera F. immobilization of beta-galactosidase from Kluyveromyces lactis on silica and agarose: comparison of different methods. J Mol Cat B: Enz. 1998; 4: 313-327.
23. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215: 403-410.
24. Gish W, States DJ. Identification of protein coding regions by database similarity search. Nat Genet. 1993; 3: 266-272.
25. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Nat Acad Sci USA. 1992; 89: 10915-10919.