DOI: https://doi.org/10.14710/jksa.25.5.169-178

Molecular Docking Study of IPBCC.08.610 Glucose Oxidase Mutant for Increasing Gluconic Acid Production

1Department of Biochemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, Indonesia

2Department of Physics, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, Indonesia

3Tropical Biopharmaca Research Center, IPB University, Bogor, Indonesia

Received: 25 Feb 2022; Revised: 30 Apr 2022; Accepted: 18 May 2022; Published: 31 May 2022.
Open Access Copyright 2022 Jurnal Kimia Sains dan Aplikasi under http://creativecommons.org/licenses/by-sa/4.0.

Citation Format:
Cover Image
Abstract

Glucose oxidase (GOD) is an oxidoreductase enzyme that catalyzes the oxidation of glucose to gluconolactone and hydrogen peroxide. Then, gluconolactone will be hydrolyzed to gluconic acid. The wide application of gluconic acid in various industries has increased production demand. However, glucose concentrations higher than 40% (w/w) inhibited the conversion of glucose to gluconic acid due to a decrease in the oxygen solubility concentration at pH 6, 30℃, and 1 bar pressure. Therefore, decreasing the value of Km is predicted to reduce saturation and enhance gluconic acid production. This study aimed to analyze the interaction between the IPBCC.08.610 GOD mutant with β-D-Glucose in improving gluconic acid production by decreasing the Km value. Mutations were performed in silico using Chimera and then docked using AutoDock Vina. The mutations resulted in distinct ligand poses in the binding pocket, different -OH conformations of the ligands, and changes in the T554M/D578P mutant’s hydrophobicity index (554 mutated from threonine to methionine, and 578 mutated from aspartate to proline), and decreased ΔG and Km values in the H559D mutant (559 mutated from histidine to aspartate), D578P and T554M/D578P. This decrease might strengthen the ligand-receptor interaction, increasing gluconic acid production. The H559D was the best mutant to increase production based on the ΔG, Km value, and stability due to the addition of hydrogen bonds.

Fulltext View|Download
Keywords: gluconic acid; glucose oxidase; mutation; molecular docking
Funding: Institut Pertanian Bogor

Article Metrics:

Article Info
Section: Research Articles
Language : EN
Recent articles
Functionalized Alkaline Lignin for Removal of Lead in Aqueous Solution Synthesis of Surfactant-Modified Activated Carbon (SMAC) Above Critical Micelle Concentration as Cr(VI) Ion Adsorbent Synthesis and Tyrosinase Inhibitory Activity of (E)-5-Benzyl-7- (3-Bromobenzylidene)-3-(3-Bromophenyl)-2-Phenyl-3,3a, 4,5,6,7-Hexahydro-2H-Pyrazolo[4,3-c]Pyridine More recent articles
Most cited articles
Pra-Standarisasi: Produksi dan Analisis Minyak Virgin Coconut Oil (VCO) Skrining Metabolit Sekunder Bakteri Endofit yang Berfungsi sebagai Antidiabetes dari Daun Mimba (Azadirachta Indica) Synthesis of Alginate-Chitosan Polyelectrolyte Complex (PEC) Membrane and Its Physical-Mechanical Properties Pengaruh Keasaman Medium dan Imobilisasi Gugus Organik pada Karakter Silika Gel dari Abu Sekam Padi Polimerisasi Eugenol Dengan Katalis Asam Sulfat Pekat More cited articles
  1. Muhammad Anjum Zia, Ayesha Riaz, Samreen Rasul, Rao Zahid Abbas, Evaluation of antimicrobial activity of glucose oxidase from Aspergillus niger EBL-A and Penicillium notatum, Brazilian Archives of Biology and Technology, 56, 6, (2013), 956-961 https://doi.org/10.1590/S1516-89132013005000010
  2. Shweta V. Bhat, B.R. Swathi, Maria Rosy, M. Govindappa, Isolation and charecterization of glucose oxidase (GOD) from Aspergillus flavus and Penicillium sp., International Journal of Current Microbiology and Applied Sciences, 2, 6, (2013), 153-161
  3. Manish K. Dubey, Andleeb Zehra, Mohd Aamir, Mukesh Meena, Laxmi Ahirwal, Siddhartha Singh, Shruti Shukla, Ram S. Upadhyay, Ruben Bueno-Mari, Vivek K. Bajpai, Improvement strategies, cost effective production, and potential applications of fungal glucose oxidase (GOD): current updates, Frontiers in Microbiology, 8, 1032, (2017), 1-22 https://doi.org/10.3389/fmicb.2017.01032
  4. Chun Ming Wong, Kwun Hei Wong, Xiao Dong Chen, Glucose oxidase: natural occurrence, function, properties and industrial applications, Applied Microbiology and Biotechnology, 78, 6, (2008), 927-938 https://doi.org/10.1007/s00253-008-1407-4
  5. Hui-Chen Wang, An-Rong Lee, Recent developments in blood glucose sensors, Journal of Food and Drug Analysis, 23, 2, (2015), 191-200 https://doi.org/10.1016/j.jfda.2014.12.001
  6. Andi Mulyadi, Biosensor Glukosa Termodifikasi Nanoserat Polianilin dari Glukosa Oksidase Aspergillus niger IPBCC. 08.610 sebagai Detektor Kematangan Buah, Master Thesis, Department of Biochemistry, IPB University, Bogor, 2019
  7. Laksmi Ambarsari, Akhiruddin Maddu, Titi Rohmayanti, Waras Nurcholis, An optimized glucose biosensor as a potential micro-fuel cell, Rasayan Journal of Chemistry, 11, 1, (2018), 32-36 http://dx.doi.org/10.7324/RJC.2018.1111981
  8. José C. Soares, Patrícia R. Moreira, A. Catarina Queiroga, José Morgado, F. Xavier Malcata, Manuela E. Pintado, Application of immobilized enzyme technologies for the textile industry: a review, Biocatalysis and Biotransformation, 29, 6, (2011), 223-237 https://doi.org/10.3109/10242422.2011.635301
  9. MR Hakim, T. Sumaryada, L. Ambarsari, Antibacterial based on IPBCC. 08.610 glucose oxidase against UDP-N-acetyl glucosamine enolpyruvyl transferase and elongation factor G enzymes in silico, IOP Conference Series: Earth and Environmental Science, 2019 https://doi.org/10.1088/1755-1315/299/1/012035
  10. Qingxuan Mu, Yinglu Cui, Meirong Hu, Yong Tao, Bian Wu, Thermostability improvement of the glucose oxidase from Aspergillus niger for efficient gluconic acid production via computational design, International Journal of Biological Macromolecules, 136, (2019), 1060-1068 https://doi.org/10.1016/j.ijbiomac.2019.06.094
  11. Sumitra Ramachandran, Pierre Fontanille, Ashok Pandey, Christian Larroche, Gluconic acid: properties, applications and microbial production, Food Technology & Biotechnology, 44, 2, (2006), 185-195
  12. Ester Junko Tomotani, Luiz Carlos Martins das Neves, Michele Vitolo, Oxidation of glucose to gluconic acid by glucose oxidase in a membrane bioreactor, Applied Biochemistry and Biotechnology, 121, 1, (2005), 149-162 https://doi.org/10.1385/ABAB:121:1-3:0149
  13. Oreste J. Lantero, Jayarama K. Shetty, Process for the preparation of gluconic acid and gluconic acid produced thereby, Google Patents, United States, 2005
  14. Savas Anastassiadis, Igor G. Morgunov, Gluconic acid production, Recent Patents on Biotechnology, 1, 2, (2007), 167-180 http://dx.doi.org/10.2174/187220807780809472
  15. Annisa Dhiya Athiyyah Khanza, Karakterisasi dan Kloning Gen Penyandi Glukosa Oksidase (GGOx) dari Aspergillus niger IPBCC 08.610, Undergraduate Thesis, Department of Biochemistry, IPB University, Bogor, 2016
  16. Julia Marín-Navarro, Nicole Roupain, David Talens-Perales, Julio Polaina, Identification and structural analysis of amino acid substitutions that increase the stability and activity of Aspergillus niger glucose oxidase, PloS One, 10, 12, (2015), 1-14 https://doi.org/10.1371/journal.pone.0144289
  17. Dušan Petrović, David Frank, Shina Caroline Lynn Kamerlin, Kurt Hoffmann, Birgit Strodel, Shuffling active site substate populations affects catalytic activity: the case of glucose oxidase, ACS Catalysis, 7, 9, (2017), 6188-6197 https://doi.org/10.1021/acscatal.7b01575
  18. Farhan Azhwin Maulana, Simulasi Termostabilitas Struktur Glukosa Oksidase Aspergillus niger IPBCC. 08.610 In-Silico, Master Thesis, Departement of Biochemistry, IPB University, Bogor, 2017
  19. Puspa Julistia Puspita, Laksmi Ambarsari, Adrian Adiva, Tony Ibnu Sumaryada, In Silico Analysis of Glucose Oxidase H516r and H516d Mutations for an Enzymatic Fuel Cell, Jurnal Kimia Valensi, 7, 2, (2021), 83-93 https://doi.org/10.15408/jkv.v7i2.20733
  20. Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T. Heer, Tjaart A. P. de Beer, Christine Rempfer, Lorenza Bordoli, SWISS-MODEL: homology modelling of protein structures and complexes, Nucleic Acids Research, 46, W1, (2018), W296-W303 https://doi.org/10.1093/nar/gky427
  21. Pilot Pipeline, in: Dassault Systèmes BIOVIA discovery studio modeling environment, In Release, 2016
  22. Zheng Yang, Keren Lasker, Dina Schneidman-Duhovny, Ben Webb, Conrad C. Huang, Eric F. Pettersen, Thomas D. Goddard, Elaine C. Meng, Andrej Sali, Thomas E. Ferrin, UCSF Chimera, MODELLER, and IMP: an integrated modeling system, Journal of Structural Biology, 179, 3, (2012), 269-278 https://doi.org/10.1016/j.jsb.2011.09.006
  23. Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin, UCSF Chimera—a visualization system for exploratory research and analysis, Journal of Computational Chemistry, 25, 13, (2004), 1605-1612 https://doi.org/10.1002/jcc.20084
  24. Elmar Krieger, Keehyoung Joo, Jinwoo Lee, Jooyoung Lee, Srivatsan Raman, James Thompson, Mike Tyka, David Baker, Kevin Karplus, Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8, Proteins: Structure, Function, and Bioinformatics, 77, S9, (2009), 114-122 https://doi.org/10.1002/prot.22570
  25. Ch. Surendhar Reddy, K. Vijayasarathy, E. Srinivas, G. Madhavi Sastry, G. Narahari Sastry, Homology modeling of membrane proteins: a critical assessment, Computational Biology and Chemistry, 30, 2, (2006), 120-126 https://doi.org/10.1016/j.compbiolchem.2005.12.002
  26. Scott A. Hollingsworth, P. Andrew Karplus, A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins, BioMolecular Concepts, 1, (2010), 271-283 https://doi.org/10.1515/bmc.2010.022
  27. Noel M. O'Boyle, Michael Banck, Craig A. James, Chris Morley, Tim Vandermeersch, Geoffrey R. Hutchison, Open Babel: An open chemical toolbox, Journal of Cheminformatics, 3, 1, (2011), 1-14 https://doi.org/10.1186/1758-2946-3-33
  28. Tom Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symposium Series, 1999
  29. Gita Syahputra, Simulasi docking kurkumin enol, bisdemetoksikurkumin dan analognya sebagai inhibitor enzim12-lipoksigenase, Jurnal Biofisika, 10, 1, (2014), 55-67
  30. Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell, Arthur J. Olson, AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility, Journal of Computational Chemistry, 30, 16, (2009), 2785-2791 https://doi.org/10.1002/jcc.21256
  31. Roman A. Laskowski, Mark B. Swindells, LigPlot+: multiple ligand–protein interaction diagrams for drug discovery, Journal of Chemical Information and Modeling, 51, 10, (2011), 2778–2786 https://doi.org/10.1021/ci200227u
  32. Shuguang Yuan, H.C. Stephen Chan, Zhenquan Hu, Using PyMOL as a platform for computational drug design, Wiley Interdisciplinary Reviews: Computational Molecular Science, 7, 2, (2017), 1-10 https://doi.org/10.1002/wcms.1298
  33. Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin, On the binding affinity of macromolecular interactions: daring to ask why proteins interact, Journal of The Royal Society Interface, 10, 79, (2013), 1-27 https://doi.org/10.1098/rsif.2012.0835
  34. Tareq Hameduh, Yazan Haddad, Vojtech Adam, Zbynek Heger, Homology modeling in the time of collective and artificial intelligence, Computational and Structural Biotechnology Journal, 18, (2020), 3494-3506 https://doi.org/10.1016/j.csbj.2020.11.007
  35. Jamal Raiyn, Anwar Rayan, How Much Sequence Identity Guarantee Good Models in Homology Modeling-Proteins from Serine Protease Family as a Test Case?, International Conference on Bio-inspired Systems and Signal Processing, 2009 https://doi.org/10.5220/0001379204550458
  36. Vincent B. Chen, W. Bryan Arendall, Jeffrey J. Headd, Daniel A. Keedy, Robert M. Immormino, Gary J. Kapral, Laura W. Murray, Jane S. Richardson, David C. Richardson, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallographica Section D: Biological Crystallography, 66, 1, (2010), 12-21 https://doi.org/10.1107/S0907444909042073
  37. Mallory R. Tollefson, Jacob M. Litman, Guowei Qi, Claire E. O’Connell, Matthew J. Wipfler, Robert J. Marini, Hernan V. Bernabe, William T.A. Tollefson, Terry A. Braun, Thomas L. Casavant, Structural insights into hearing loss genetics from polarizable protein repacking, Biophysical Journal, 117, 3, (2019), 602-612 https://doi.org/10.1016/j.bpj.2019.06.030
  38. Gabriel Studer, Christine Rempfer, Andrew M. Waterhouse, Rafal Gumienny, Juergen Haas, Torsten Schwede, QMEANDisCo—distance constraints applied on model quality estimation, Bioinformatics, 36, 6, (2020), 1765-1771 https://doi.org/10.1093/bioinformatics/btz828
  39. Marco Biasini, Stefan Bienert, Andrew Waterhouse, Konstantin Arnold, Gabriel Studer, Tobias Schmidt, Florian Kiefer, Tiziano Gallo Cassarino, Martino Bertoni, Lorenza Bordoli, SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information, Nucleic Acids Research, 42, W1, (2014), W252-W258 https://doi.org/10.1093/nar/gku340
  40. Pascal Benkert, Marco Biasini, Torsten Schwede, Toward the estimation of the absolute quality of individual protein structure models, Bioinformatics, 27, 3, (2011), 343-350 https://doi.org/10.1093/bioinformatics/btq662
  41. Peter I. Maxwell, Paul L.A. Popelier, Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective, Journal of Computational Chemistry, 38, 29, (2017), 2459-2474 https://doi.org/10.1002/jcc.24904
  42. Andrio Suhadi, Rizarullah Rizarullah, Feriyani Feriyani, Simulasi docking senyawa aktif daun binahong sebagai inhibitor enzyme aldose reductase, Sel Jurnal Penelitian Kesehatan, 6, 2, (2019), 55-65 http://dx.doi.org/10.22435/sel.v6i2.1651
  43. Romain A. Studer, Benoit H. Dessailly, Christine A. Orengo, Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes, Biochemical Journal, 449, 3, (2013), 581-594 https://doi.org/10.1042/BJ20121221
  44. Richard M. Clark, Simon Tavaré, John Doebley, Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus, Molecular Biology and Evolution, 22, 11, (2005), 2304-2312 https://doi.org/10.1093/molbev/msi228
  45. Michael Meyer, Gerd Wohlfahrt, Jörg Knäblein, Dietmar Schomburg, Aspects of the mechanism of catalysis of glucose oxidase: A docking, molecular mechanics and quantum chemical study, Journal of Computer-Aided Molecular Design, 12, 5, (1998), 425-440 https://doi.org/10.1023/A:1008020124326
  46. Rollando Rollando, Pendekatan Struktur Aktivitas dan Penambatan Molekul Senyawa 2-iminoethyl 2-(2-(1-hydroxypentan-2-yl) phenyl) acetate Hasil Isolasi Fungi Endofit Genus Fusarium sp pada Enzim β-ketoasil-ACP KasA Sintase dan Enzim Asam Mikolat Siklopropana Sintase, Pharmaceutical Journal of Indonesia, 3, 2, (2018), 45-51
  47. Mohammad Rizki Fadhil Pratama, Eko Suhartono, Understanding the Interaction Between Glutathione and Acetaminophen: A Docking Study Approach, Dentino: Jurnal Kedokteran Gigi, 3, 2, (2018), 215-219
  48. Gerd Wohlfahrt, Susanne Witt, Jörg Hendle, Dietmar Schomburg, Henryk M. Kalisz, H.-J. Hecht, 1.8 and 1.9 Å resolution structures of the Penicillium amagasakiense and Aspergillus niger glucose oxidases as a basis for modelling substrate complexes, Acta Crystallographica Section D: Biological Crystallography, 55, 5, (1999), 969-977 https://doi.org/10.1107/S0907444999003431
  49. Navid Nezafat, Zeinab Karimi, Mahboobeh Eslami, Milad Mohkam, Sanam Zandian, Younes Ghasemi, Designing an efficient multi-epitope peptide vaccine against Vibrio cholerae via combined immunoinformatics and protein interaction based approaches, Computational Biology and Chemistry, 62, (2016), 82-95 https://doi.org/10.1016/j.compbiolchem.2016.04.006
  50. Christopher C. Valley, Alessandro Cembran, Jason D. Perlmutter, Andrew K. Lewis, Nicholas P. Labello, Jiali Gao, Jonathan N. Sachs, The methionine-aromatic motif plays a unique role in stabilizing protein structure, Journal of Biological Chemistry, 287, 42, (2012), 34979-34991 https://doi.org/10.1074/jbc.M112.374504
  51. Qoonita Fadhilah, Daryono Hadi Tjahjono, Hubungan Kuantitatif Struktur dan Aktivitas Senyawa Turunan 3-Haloasilaminobenzoilurea sebagai Inhibitor Pembentukan Mikrotubulus, Acta Pharmaceutica Indonesia, 37, 3, (2012), 76-82
  52. Sandeep Kumar, Chung-Jung Tsai, Ruth Nussinov, Factors enhancing protein thermostability, Protein Engineering, Design and Selection, 13, 3, (2000), 179-191 https://doi.org/10.1093/protein/13.3.179
  53. Dipali Mhaindarkar, Raphael Gasper, Natalie Lupilov, Eckhard Hofmann, Lars I. Leichert, Loss of a conserved salt bridge in bacterial glycosyl hydrolase BgIM-G1 improves substrate binding in temperate environments, Communications Biology, 1, 1, (2018), 1-11 https://doi.org/10.1038/s42003-018-0167-7
  54. James B. Bassingthwaighte, Tamara M. Chinn, Reexamining Michaelis-Menten enzyme kinetics for xanthine oxidase, Advances in Physiology Education, 37, 1, (2013), 37-48 https://doi.org/10.1152/advan.00107.2012
  55. Zatta Yumni Ihdhar Syarafina, Mega Safithri, Maria Bintang, Rini Kurniasih, In Silico Screening of Cinnamon (Cinnamomum burmannii) Bioactive Compounds as Acetylcholinesterase Inhibitors, Jurnal Kimia Sains dan Aplikasi, 25, 3, (2022), 97-107 https://doi.org/10.14710/jksa.25.3.97-107

Last update:

No citation recorded.

Last update: 2024-11-13 16:47:42

No citation recorded.