In Silico Analysis of Glucose Oxidase H516r and H516d Mutations for an Enzymatic Fuel Cell
Abstract
Glucose oxidase (GOx) is an oxido-reductase enzyme that catalyzes glucose into hydrogen peroxide and glucono delta-lactone (GDL). GOx has the potential to be used in the medical field. Numerous research concerning the usage of GOx to create enzymatic biofuel cells have been done, nevertheless the results obtained have not been optimal. This research aims to increase the Km values of GOx in order to increase its potential as a material for an enzymatic fuel cell. The amino acid histidine in position 516 is a residue in the active site that plays an important part in the process of glucose oxidation. In this research we mutated H516 by in silico twice resulting in the mutants R516 and D516. The mutations resulted in a change of the docking area for both mutants and in the docking affinity for H516D resulting in higher Km values. This shows that the H516 residue plays an important part in the functions of glucose oxidase and mutation into aspartate could improve glucose oxidase based enzymatic fuel cells.
Keywords
References
Albert, B. (2010). Essential Cell Biology. New York (US): Garland Science.
Ambade, V. N., Sharma, Y. V., & Somani, B. L. (1998). Methods for estimation of blood glucose: A comparative evaluation. Medical journal, Armed Forces India, 54(2), 131-133
Ambarsari, L., Setyawati, I., Kurniasih, R., Kurniatin, P., & Maddu, A. (2016). Immobilization of Glucose Oxidase on Modified-Carbon-Paste-Electrodes for Microfuel Cell. Indonesian Journal of Chemistry, 16, 92-97.
Aquino Neto, S., & De Andrade, A. R. (2013). New energy sources: the enzymatic biofuel cell. Journal of the Brazilian Chemical Society, 24, 1891-1912.
Blanford, C. F. (2013). The birth of protein electrochemistry. Chemical Communications, 49(95), 11130-11132.
Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Di Costanzo, L., . . . Zardecki, C. (2019). RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Research, 47(D1), D464-D474.
Clark, R. M., Tavaré, S., & Doebley, J. (2005). Estimating a Nucleotide Substitution Rate for Maize from Polymorphism at a Major Domestication Locus. Molecular Biology and Evolution, 22(11), 2304-2312.
Elouarzaki, K., Cheng, D., Fisher, A., & Lee, J.-M. (2018). Coupling orientation and mediation strategies for efficient electron transfer in hybrid biofuel cells. Nature Energy, 3, 574–581.
Fikrika, H., Ambarsari, L., & Sumaryada, T. (2016). Molecular Docking Studies of Catechin and Its Derivatives as Anti-bacterial Inhibitor for Glucosamine-6-Phosphate Synthase. IOP Conference Series: Earth and Environmental Science, 31, 012009.
Goldrick, S., Lee, K., Spencer, C., Holmes, W., Kuiper, M., Turner, R., & Farid, S. (2017). On-Line Control of Glucose Concentration in High-Yielding Mammalian Cell Cultures Enabled Through Oxygen Transfer Rate Measurements. Biotechnology Journal, 13, 1700607.
Gupta, A., Chaudhary, N., Reddy, K., Pallu, R., & Polamarasetty, A. (2015). The Augmenting Effects of Desolvation and Conformational Energy Terms on the Predictions of Docking Programs against mPGES-1. PLoS ONE, 10, e0134472.
Hall, T. A. (1999). Bioedit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symposium Series, 41, 95-98.
Hollingsworth, S., & Karplus, P. (2010). A Fresh Look at the Ramachandran Plot and the Occurrence of Standard Structures in Proteins. Biomolecular concepts, 1, 271-283.
Ivanov, I., Vidaković-Koch, T., & Sundmacher, K. (2010). Recent Advances in Enzymatic Fuel Cells: Experiments and Modeling. Energies, 3(4), 803-846.
Ivnitski, D., Branch, B., Atanassov, P., & Apblett, C. (2006). Glucose oxidase anode for biofuel cell based on direct electron transfer. Electrochemistry Communications, 8(8), 1204-1210.
Kastritis, P., & Bonvin, A. (2013). On the binding affinity of macromolecular interactions: Daring to ask why proteins interact. Journal of the Royal Society, Interface / the Royal Society, 10, 20120835.
Krieger, E., Joo, K., Lee, J., Lee, J., Raman, S., Thompson, J., . . . Karplus, K. (2009). Improving Physical Realism, Stereochemistry, and Side-Chain Accuracy in Homology Modeling: Four Approaches That Performed Well in CASP8. Proteins: Structure, Function, and Bioinformatics, 77, 114-122.
Kurniatin, P., Ambarsari, L., Khanza, A., Setyawati, I., Seno, D., & Nurcholis, W. (2020). Characteristics of Glucose Oxidase Gene (GGOx) from Aspergillus niger IPBCC 08.610. Jurnal Kimia Valensi, 6, 10-19.
Laskowski, R., & Swindells, M. (2011). LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery. Journal of chemical information and modeling, 51, 2778-2786.
Leskovac, V., Trivic, S., Wohlfahrt, G., Kandrac, J., & Pericin, D. (2005). Glucose oxidase from Aspergillus Niger: The mechanism of action with molecular oxygen, quinones, and one-electron acceptors. The international journal of biochemistry & cell biology, 37, 731-750.
Marco, M., Longo, E., & Scampicchio, M. (2016). Monitoring of Glucose in Beer Brewing by a Carbon Nanotubes Based Nylon Nanofibrous Biosensor. Journal of Nanomaterials, 2016, 1-11.
Meyer, M., Wohlfahrt, G., Knblein, J., & Enzymologie, A. (1998). Aspects of the mechanism of catalysis of glucoseoxidase: A docking, molecular mechanics and quantum chemical study. Journal of Computer-Aided Molecular Design, 12(5), 425–440.
O'Boyle, N., Banck, M., James, C., Morley, C., Vandermeersch, T., & Hutchison, G. (2011). Open Babel: An Open Chemical Toolbox. Journal of cheminformatics, 3, 33.
Petrović, D., Frank, D., Kamerlin, S. C. L., Hoffmann, K., & Strodel, B. (2017). Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase. ACS catalysis, 7(9), 6188-6197.
Pettersen, E. F., Goddard, T. D., Huang, C., Couch, G., Greenblatt, D. M., & Meng, E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. J Comput Chem, 25.
Pilot, P. (2016). Dassault Systèmes BIOVIA, discovery studio modelling environment. In: Release.
Reddy, C. S., Vijayasarathy, K., Srinivas, E., Sastry, G. M., & Sastry, G. N. (2006). Homology modeling of membrane proteins: A critical assessment. Computational Biology and Chemistry, 30(2), 120-126.
Rohmayanti, T., Ambarsari, L., & Maddu, A. (2017). Enzymatic activity of Glucose Oxidase from Aspergillus niger IPBCC.08.610 On Modified Carbon Paste Electrode as Glucose Biosensor. IOP Conference Series: Earth and Environmental Science, 58, 012046.
Song, Y., Penmatsa, V., and Wang, C. (2011). Recent development of miniatured enzymatic biofuel cell, in Energy Harvesting and Storage: Materials, Devices, and Applications II. 8035.
Studer, R., Dessailly, B., & Orengo, C. (2013). Residue mutations and their impact on protein structure and function: Detecting beneficial and pathogenic changes. The Biochemical journal, 449, 581-594.
Syahputra, G. (2014). Docking Simulation of Curcumin and Its Analogs as Inhibitors on 12-Lipoxygenase Enzyme. Master Thesis, Department of Biochemistry, IPB University.
Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., . . . Schwede, T. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296-W303.
Wedemeyer MJ, M. B., Bender BJ, Meiler J, Volkman BF. (2019). Methods in Cell Biology. Amsterdam (NL): Elsevier. Amsterdam (NL): Elsevier.
Wong, C., Wong, K., & Chen, X. (2008). Glucose oxidase: Natural occurrence, function, properties and industrial applications. Applied Microbiology and Biotechnology, 78, 927-938.
Yang, Z., Lasker, K., Schneidman-Duhovny, D., Webb, B., Huang, C. C., Pettersen, E. F., . . . Ferrin, T. E. (2012). UCSF Chimera, MODELLER, and IMP: An integrated modeling system. Journal of Structural Biology, 179(3), 269-278.
Yu, C.-M., & Chen, L.-C. (2009). Turning Glucose and Starch into Electricity with an Enzymatic Fuel Cell. Engineering in Agriculture, Environment and Food, 2(1), 1-6.
Yuen, C. M., & Liu, D. R. (2007). Dissecting protein structure and function using directed evolution. Nature methods, 4(12), 995-997.
DOI: 10.15408/jkv.v7i2.20733
Refbacks
- There are currently no refbacks.
Copyright (c) 2021 Puspa Julistia Puspita
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
