Elucidating the binding efficacy of β-galactosidase on graphene by docking approach and its potential application in galacto-oligosaccharide production

Bioprocess and Biosystems Engineering

Volumn 39, Issue 5, 2016, Pages 807-814

  Satar, Rukhsana ^a   Ismail, Syed Ahmed ^a   Rehan, Mohd ^b   Ansari, Shakeel Ahmed ^b  

^a IBN SINA NATIONAL COLLEGE FOR MEDICAL STUDIES   (Saudi Arabia)

^b KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

Docking softwares; Galacto oligosaccharide production; Graphene; Galactosidase

Indexed keywords

CHEMICAL STABILITY; COMPLEXATION; ENZYMES; FOURIER TRANSFORM INFRARED SPECTROSCOPY; GRAPHENE; IODINE; MOLECULAR MODELING; OLIGOSACCHARIDES;

CHEMICAL DENATURANTS; FTIR SPECTROSCOPY; GALACTO-OLIGOSACCHARIDES; GALACTOSIDASES; IMMOBILIZED ENZYME; LIGAND COMPLEXES; MOLECULAR DOCKING; SYNTHESIS AND CHARACTERIZATIONS;

ENZYME IMMOBILIZATION;

ALCOHOL; BETA GALACTOSIDASE; GALACTOSE OLIGOSACCHARIDE; GRAPHENE OXIDE; HYDROXYL GROUP; IMMOBILIZED ENZYME; LACTOSE; LIGAND; POLYSILOXANE; GRAPHITE;

ARTICLE; ASPERGILLUS ORYZAE; BIOSENSOR; BIOTECHNOLOGY; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ECOSYSTEM RESTORATION; ENZYME ENGINEERING; ENZYME IMMOBILIZATION; HYDROLYSIS; INFRARED SPECTROSCOPY; MOLECULAR DOCKING; NANOFILTRATION; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; SUBSTRATE CONCENTRATION; SYNTHESIS; TRANSMISSION ELECTRON MICROSCOPY; ENZYMOLOGY; KINETICS; METABOLISM;

ASPERGILLUS ORYZAE; BETA-GALACTOSIDASE; GRAPHITE; KINETICS; MICROSCOPY, ELECTRON, TRANSMISSION; MOLECULAR DOCKING SIMULATION; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

EID: 84957677116     PISSN: 16157591     EISSN: 16157605     Source Type: Journal    
DOI: 10.1007/s00449-016-1560-6     Document Type: Article

References (34)

1. Kiehl K, Straube T, Opwis K, Gutmann JS (2015) Strategies for permanent immobilization of enzymes on textile carriers. Eng Life Sci 15:622–626
2. Mohamad NR, Marzuki NHC, Buang NA, Huyop F, Wahab RA (2015) An overview of technologies for immobilization of enzymes and surface analysis techniques for immobilized enzymes. Biotechnol Biotechnol Equip 29:205–220
3. Homaei AA, Sariri R, Vianello F, Stevanato R (2013) Enzyme immobilization: an update. J Chem Biol 6:185–205
4. Ansari SA, Husain Q (2012) Potential application of enzymes immobilized on/in nano materials: a review. Biotechnol Adv 30:512–523
5. Cipolatti EP, Silva MJA, Klein MP, Federn V, Feltes MMC, Oliveira JV (2014) Current status and trends in enzymatic nanoimmobilization. J Mol Catal B Enzym 99:56–67
6. Fei L, Perrett S (2009) Effect of nanoparticles on protein folding and fibrillogenesis. Int J Mol Sci 10:646–655
7. Goenka S, Sant V, Sant S (2014) Graphene-based nanomaterials for drug delivery and tissue engineering. J Control Release 173:75–88
8. Soldano C, Mahmood A, Dujardin E (2010) Production, properties and potential of graphene. Carbon 48:2127–2150
9. Singh V, Joung D, Zhai L, Das S, Khondaker SI, Seal S (2011) Graphene based materials: past, present and future. Prog Mat Sci 56:1178–1271
10. Georgakilas V, Otyepka M, Bourlinos AB, Chandra V, Kim N, Kemp KC, Hobza P, Zboril R, Kim KS (2012) Functionalization of graphene: covalent and non-covalent approaches, derivatives and application. Chem Rev 112:6156–6214
11. Hauser AS, Windshugel B (2016) A benchmark data set for assessment of peptide docking performance. J Chem Inf Mod. doi:10.1021/acs.jcim.5b00234
12. Panneerselvam S, Choi S (2014) Nanoinformatics: emerging databases and available tools. Int J Mol Sci 15:7158–7182
13. Suresh PS, Kumar A, Kumar R, Singh VP (2008) An insilico approach to bioremediation: laccase as a case study. J Mol Graph Mod 26:845–849
14. Morris GM, Huey R, Olson AJ (2008) Using autoDock for ligand-receptor docking. Curr Protoc Bioinform 8(8):14
15. Yang ST, Wang H, Guo L, Gao Y, Liu Y, Cao A (2008) Interaction of fullerenol with lysozyme investigated by experimental and computational approaches. Nanotechnology 19:395101
16. Diez-Municio M, Herrero M, Olano A, Moreno FJ (2014) Synthesis of novel bioactive lactose-derived oligosaccharides by microbial glycoside hydrolases. Microb Biotechnol 7:315–331
17. Otieno DO (2010) Synthesis of β-galactooligosaccharides from lactose using microbial β-galactosidases. Comp Rev Food Sci Food Saf 9:471–482
18. Zhao X, Liu L, Li X, Zeng J, Jia X, Liu P (2014) Biocompatible graphene oxide nanoparticle-based drug delivery platform for tumor microenvironment-responsive triggered release of doxorubicin. Langmuir 30:10419–10429
19. Ewing TJ, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aid Mol Des 15:411–428
20. DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos
21. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612
22. Wallace AC, Laskowski RA, Thornton JM (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 8:127–134
23. Laskowski RA, Swindells MB (2011) LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 51:2778–2786
24. Ansari SA, Satar R, Zaidi SK (2015) Carboxylation of silver nanoparticles for the immobilization of β-galactosidase and its efficacy in galacto-oligosaccharides production. Quim Nova 38:387–392
25. Fai AEC, Postore GM (2015) Galactooligosaccharides: production, health benefits, application to foods and perspectives. Agropecuaria 6:69–81
26. Neri DFM, Balcao VM, Costa RS, Rocha ICAP, Ferreria EMFC, Torres DPM, Rodriguez LRM, Carvalho LB Jr, Teixeria JA (2009) Galacto-oligosaccharides production during lactose hydrolysis by free Aspergillus oryzae β-galactosidase and immobilized on magnetic polysiloxane-polyvinyl alcohol. Food Chem 115:92–99
27. Srivastava G, Singh K, Talat M, Srivastava ON, Kayastha AM (2014) Functionalized graphene sheets as immobilization matrix for fenugreek β-amylase: enzyme kinetics and stability studies. PLoS ONE 9:e113408
28. Hsu CA, Lee SL, Chou CC (2007) Enzymatic production of galactooligosaccharides by beta-galactosidase from Bifidobacterium longum BCRC 15708. J Agric Food Chem 21:2225–2230
29. Barbara RC, Miguel AA, Lucia FA, Roseri B, Ana P, Jesus JB, Dietmar H, Antonio OO, Maria FL, Francisco JP (2011) Production of galacto-oligosaccharides by β-galactosidase from Kluyveromyces lactis: comparative analysis of permeabilized cells versus soluble enzyme. J Agric Food Chem 59:10477–10484
30. Warmerdam A, Boom RM, Janssen AEM (2013) β galactosidase stability at high substrate concentrations. Springer Plus 2:402–409
31. Palai T, Kumar A, Bhattacharya BK (2015) Kinetic studies and model development for the formation of galacto-oligosaccharides from lactose using synthesized thermo-responsive bioconjugates. Enzym Microb Technol 70:42–49
32. Albayrak N, Yang ST (2002) Production of galacto-oligosaccharides from lactose by Aspergillus oryzae beta-galactosidase immobilized on cotton cloth. Biotechnol Bioeng 5:8–19
33. Pruksasri S, Nguyen TH, Haltrich D, Novalin S (2015) Fractionation of a galacto-oligosaccharides solution at low and high temperature using nanofiltration. Sep Purif Technol 4:124–130
34. Sen P, Bhattacharjee C, Bhattacharya P (2016) Experimental studies and two-dimensional modeling of a packed bed bioreactor used for production of galacto-oligosaccharides (GOS) from milk whey. Bioprocess Biosyst Eng. doi:10.1007/s00449-015-1516-2