Homology Modeling and Structural Dynamics of the Glucose Oxidase

Farhan Azhwin Maulana; Laksmi Ambarsari; Setyanto Tri Wahyudi

doi:10.22146/ijc.39135

Homology Modeling and Structural Dynamics of the Glucose Oxidase

https://doi.org/10.22146/ijc.39135

Farhan Azhwin Maulana^(1*), Laksmi Ambarsari⁽²⁾, Setyanto Tri Wahyudi⁽³⁾

(1) Master of Biochemistry Program, Postgraduate School, Bogor Agricultural University, Kampus IPB Dramaga, Bogor 16680, West Java, Indonesia
(2) Molecular Biology Division, Department of Biochemistry, Bogor Agricultural University, Kampus IPB Dramaga, Bogor 16680, West Java, Indonesia
(3) Computational Biophysics and Molecular Modeling Research Group, Department of Biophysics, Bogor Agricultural University, Kampus IPB Dramaga, Bogor 16680, West Java, Indonesia
(*) Corresponding Author

Abstract

Glucose oxidase from Aspergillus niger IPBCC.08.610 (GOD_IPBCC) is a locally sourced flavoenzyme from Indonesia that can potentially be developed in a variety of industrial processes. Although this enzyme has a high activity in catalyzing the redox reactions, the use of this enzyme was still limited to be applied as glucose biosensor. Using information from the amino acid sequences, a computational structure of GOD_IPBCC was therefore designed by homology modeling method using two homologous structures of GOD from protein data bank (1CF3 and 5NIT) as the templates. The quality of the resulting structures was evaluated geometrically for selection of the best model, and subsequently, 50 ns of MD simulations were carried out for the selected model as well as the corresponding template. Results obtained from the validation analysis showed that the 1CF3 template-built structure was selected as the best reliable model. The structural comparison exhibited that the best-modeled structure consisted of two functional domains and three catalytic residues similarly to the corresponding experimental structure. The overall dynamic behavior of the 50 ns of the structure was structurally stable and comparable with that of the positive control both from globally and locally observations. Implications of these stable nature within the best-modeled structure unfold the possibilities in search of notable residues and their roles to enhance enzyme thermostability.

Keywords

glucose oxidase; homology modeling; molecular dynamics; three-dimensional structure

Full Text:

Full Text PDF

References

[1] Leskovac, V., Trivić, S., Wohlfahrt, G., Kandrač, J., and Peričin, D., 2005, Glucose oxidase from Aspergillus niger: The mechanism of action with molecular oxygen, quinones, and one-electron acceptors, Int. J. Biochem. Cell Biol., 37 (4), 731–750.

[2] Petrović, D., Frank, D., Kamerlin, S.C.L., Hoffmann, K., and Strodel, B., 2017, Shuffling active site substrate populations affects catalytic activity: The case of glucose oxidase, ACS Catal., 7 (9), 6188–6197.

[3] Bankar, S.B., Bule, M.V., Singhal, R.S., and Ananthanarayan, L., 2009, Glucose oxidase-An overview, Biotechnol. Adv., 27 (4), 489-501.

[4] Kiess, M., Hecht, H.J., and Kalisz, H.M., 1998, Glucose oxidase from Penicillium amagasakiense. Primary structure and comparison with other glucose-methanol-choline (GMC) oxidoreductases, Eur. J. Biochem., 252 (1), 90–99.

[5] Rohmayanti, T., Ambarsari, L., and Maddu, A., 2017, Enzymatic activity of glucose oxidase from Aspergillus niger IPBCC.08.610 on modified carbon paste electrode as glucose biosensor, IOP Conf. Ser.: Earth Environ. Sci, 58 (1), 12046.

[6] Zhu, Z., Momeu, C., Zakhartsev, M., and Schwaneberg, U., 2006, Making glucose oxidase fit for biofuel cell applications by directed protein evolution, Biosens. Bioelectron., 21 (11), 2046–2051.

[7] Holland, J.T., Lau, C., Brozik, S., Atanassov, P., and Banta, S., 2011, Engineering of glucose oxidase for direct electron transfer via site-specific gold nanoparticle conjugation, J. Am. Chem. Soc., 133 (48), 19262–19265.

[8] Holland, J.T., Harper, J.C., Dolan, P.L., Manginell, M.M., Arango, D.C., Rawlings, J.A., Apblett, C.A., and Brozik, S.M., 2012, Rational redesign of Glucose oxidase for improved catalytic function and stability, PLoS One, 7 (6), e37924.

[9] Altschul, S.F., Boguski, M.S., Gish, W., and Wootton, J.C., 1994, Issues in searching molecular sequence databases, Nat. Genet., 6 (2), 119–129.

[10] He, Y., Rackovsky, S., Yin, Y., and Scheraga, H.A., 2015, Alternative approach to protein structure prediction based on sequential similarity of physical properties, Proc. Natl. Acad. Sci. U.S.A., 112 (16), 5029–5032.

[11] Marín-Navarro, J., Roupain, N., Talens-Perales, D., and Polaina, J., 2015, Identification and structural analysis of amino acid substitutions that increase the stability and activity of Aspergillus niger glucose oxidase, PLoS One, 10 (12), e0144289.

[12] Wohlfahrt, G., Witt, S., Hendle, J., Schomburg, D., Kalisz, H.M., and Hecht, H.J., 1999, 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 Crystallogr., Sect. D: Biol. Crystallogr., 55 (Pt 5), 969–977.

[13] Robert, X., and Gouet, P., 2014, Deciphering key features in protein structures with the new ENDscript server, Nucleic Acids Res., 42 (Web Server issue), W320–W324.

[14] DeLano, W.L., 2002, The PyMOL molecular graphics system, Proteins, 30, 442–454.

[15] Case, D.A., Betz, R.M., Botello-Smith, W., Cerutti, D.S., Cheatham, III, T.E., Darden, T.A., Duke, R.E., Giese, T.J., Gohlke, H., Goetz, A.W., Homeyer, N., Izadi, S., Janowski, P., Kaus, J., Kovalenko, A., Lee, T.S., LeGrand, S., Li, P., Lin, C., Luchko, T., Luo, R., Madej, B., Mermelstein, D., Merz, KM., Monard, G., Nguyen, H., Nguyen, H.T., Omelyan, I., Onufriev, A., Roe, D.R., Roitberg, A., Sagui, C., Simmerling, C.L., Botello-Smith, W.M., Swails, J., Walker, R.C., Wang, J., Wolf, R.M., Wu, X., Xiao, L., and Kollman P.A., 2016, AMBER 2016, University of California, San Francisco

[16] Reetz, M.T., Carballeira, J.D., and Vogel, A., 2006, Iterative saturation mutagenesis on the basis of b factors as a strategy for increasing protein thermostability, Angew. Chem. Int. Ed., 45 (46), 7745–7751.

[17] Humphrey, W., Dalke, A., and Schulten, K., 1996, VMD: Visual molecular dynamics, J. Mol. Graphics, 14 (1), 33–38.

[18] Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D., and Bairoch, A., 2005, “Protein Identification and Analysis Tools on the ExPASy Server” in The Proteomics Protocols Handbook, Eds., Walker J.M., Humana Press, New York City.

[19] Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T.G., Bertoni, M., Bordoli, L., and Swede, T., 2014, SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information, Nucleic Acids Res., 42 (Web Server issue), W252–W258.

[20] Laskowski, R.A., Jabłońska, J., Pravda, L., Vařeková, R.S., and Thornton, J.M., 2018, PDBsum: Structural summaries of PDB entries, Protein Sci., 27 (1), 129–134.

[21] Chen, V.B., Arendall, W.B., Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., Murray, L.W., Richardson, J.S., and Richardson, D.C., 2010, MolProbity: All-atom structure validation for macromolecular crystallography, Acta Crystallogr., Sect. D: Biol. Crystallogr., 66 (Pt 1), 12–21.

[22] Finn, R.D., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Mistry, J., Mitchell, A.L., Potter, S.C., Punta, M., Qureshi, M., Sangrador-Vegas, A., Salazar, G.A., Tate, J., and Bateman, A., 2016, The Pfam protein families database: Towards a more sustainable future, Nucleic Acids Res., 44 (D1), D279–D285.

[23] Laskowski, R.A., 2001, PDBsum: Summaries and analyses of PDB structures, Nucleic Acids Res., 29 (1), 221–222.

[24] Anandakrishnan, R., Aguilar, B., and Onufriev, A.V., 2012, H++ 3.0: Automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations, Nucleic Acids Res., 40 (Web Server issue), W537–W541.

[25] Myers, J., Grothaus, G., Narayanan, S., and Onufriev, A., 2006, A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules, Proteins, 63 (4), 928–938.

[26] Case, D.A., Cheatham, T.E., Darden, T., Gohlke, H., Luo, R., Merz, K.M., Onufriev, A., Simmerling, C., Wang, B., and Woods, R.J., 2005, The Amber biomolecular simulation programs, J. Comput. Chem., 26 (16), 1668–1688.

[27] Benkert, P., Biasini, M., and Schwede, T., 2011, Toward the estimation of the absolute quality of individual protein structure models, Bioinformatics, 27 (3), 343–350.

[28] Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M., 1993, PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr., 26, 283–291.

[29] Yusuf, M., Baroroh, U., Hasan, K., Rachman, S.D., Ishmayana, S., and Subroto, T., 2017, Computational model of the effect of a surface-binding site on the Saccharomycopsis fibuligera R64 α-amylase to the substrate adsorption, Bioinf. Biol. Insights, 11, 1177932217738764.

[30] Hecht, H.J., Kalisz, H.M., Hendle, J., Schmid, R.D., and Schomburg, D., 1993, Crystal structure of glucose oxidase from Aspergillus niger refined at 2.3 Å resolution, J. Mol. Biol., 229 (1), 153-172.

[31] Janati-Fard, F., Housaindokht, M.R., and Monhemi, H., 2016, Investigation of structural stability and enzymatic activity of glucose oxidase and its subunits, J. Mol. Catal. B: Enzym., 134 (Part A), 16–24.

[32] Liao, S.M., Du, Q.S., Meng, J.Z., Pang, Z.W., and Huang, R.B., 2013, The multiple roles of histidine in protein interactions, Chem. Cent. J., 7 (1), 44.

[33] Meyer, E.A., Castellano, R.K., and Diederich, F., 2003, Interactions with aromatic rings in chemical and biological recognition, Angew. Chem. Int. Ed., 42 (11), 1210–1250.

[34] Yu, H., Yan, Y., Zhang, C., and Dalby, P.A., 2017, Two strategies to engineer flexible loops for improved enzyme thermostability, Sci. Rep., 7, 41212.

[35] Tsai, M.Y., Zheng, W., Balamurugan, D., Schafer, N.P., Kim, B.L., Cheung, M.S., and Wolynes, P.G., 2016, Electrostatics, structure prediction, and the energy landscapes for protein folding and binding, Protein Sci., 25 (1), 255–269.

[36] Todde, G., Hovmöller, S., Laaksonen, A., and Mocci, F., 2014, Glucose oxidase from Penicillium amagasakiense: Characterization of the transition state of its denaturation from molecular dynamics simulations, Proteins, 82 (10), 2353–2363.

[37] Caves, M.S., Derham, B.K., Jezek, J., and Freedman, R.B., 2011, The mechanism of inactivation of glucose oxidase from Penicillium amagasakiense under ambient storage conditions, Enzyme Microb. Technol., 49 (1), 79–87.

DOI: https://doi.org/10.22146/ijc.39135