Comparative of structure of three isozymes of Glucoamylase in order to determination demonstrator parameters thermal stability of proteins via molecular dynamics simulation

Mahnam, Karim; Mosharf Ghahfarokhi, Azin; Rafieepour, Hosein Ali

Comparative of structure of three isozymes of Glucoamylase in order to determination demonstrator parameters thermal stability of proteins via molecular dynamics simulation

Document Type : Original Research

Authors

karim mahnam ¹

Azin Mosharf Ghahfarokhi ²

Hosein Ali Rafieepour ²

¹ Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran

² Department of Cell and Molecular Biology, Faculty of Chemistry, Kashan University, Kashan, Iran

Abstract

Glucoamylase, is an important economic enzyme due to its ability to hydrolyze starch and β-D-glucose polymers. Understanding of factors affecting the thermal stability of the glucoamylase enzyme is critical in the production of isoenzymes with high heat or cold stability. In this study, the effect of temperature on the structure and properties of each of the isoenzymes of the mesophilic, thermophilic and psychrophilic glucoamylase were studied. For this purpose, molecular dynamics simulation was used to assess these factors and structural differences. 240 nanosecond of MD simulation was done for three isoenzymes of glucoamylase in four temperatures at 300, 350, 400 and 450 K. The variations of each of these parameters were compared for three isoenzymes, and it was found that among the computable factors in molecular dynamics simulation, electrostatic energy of protein with water, van der Waals energy between proteins and water, free energy solubility (∆G_solvation), instability parameter, nonpolar solvent accessible surface, and total solvent accessible surface can be used to predict thermal stability of a protein during increase of temperature.

Keywords

Glucoamylase enzyme

Mesophile

Thermophile

Psychrophile

Molecular dynamics simulation

Thermal stability

20.1001.1.23222115.1399.11.3.5.8

Subjects

Bioinformatics

[1] Pavezzi, F. C.,Gomes, E., andSilva, R. (2008) Production andcharacterization of glucoamylase from fungus aspergillus awamori expressed in yeast saccharomyces cerevisiae using different carbon sources. Braz. J Microbiol.39,108-114.
[2] Hyun, H. H., and Zeikus, J. G. (1985) General biochemical characterization of thermostable pullulanase and glucoamylase from clostridium thermohydrosulfuricum. Am. Soc Microbiol. 49,1168-1173.
[3] Sauer, J., Sigurskjold, B. W., Christensen, U., Frandsen, T. P., Mirgorodskaya, E.,Harrison, M., Roepstorff, P., andSvensson, B. (2000) Glucoamylase: structure/function relationships, and protein engineering. Biochim. Biophys Acta. 1543,275-293.
[4] Campos, L., and Felix, C. R. (1995) Purification and characterization of a glucoamylasefrom Humicola grisea. Am. Soc Microbiol. 61, 2436-2438.
[5] Jebor, M. A., Ali, Z. M., and Hassan, B. A.(2014) Purification and characterization of the glucoamylase from Aspergillus niger. Int. J Curr Microbiol App Sci.3,63-75.
[6] Daniel, A. M., Fuchs, E., Liu, Y., and Ford, C. (2008) Directed evolution of Aspergillus niger glucoamylase to increase thermostability. Microbiol. Biotechnol. 1,523-531.
[7] Liu, H-L., and Wang, W-C.(2003) Protein engineering to improve the thermostability ofglucoamylase from Aspergillus awamori based on moleculardynamics simulations. Protein. Eng.16,19-25.
[8] Kovacic, F., Mandrysch, A., Poojari, C., Strodel, B., andJaeger, K-E. (2016)Structural features determining thermal adaptation of esterases. Protein. Eng De Sel.29,65-76.
[9] Liu,Y., Meng, Z., Shi, R., Zhan, L., Hu, W., Xiang, H., and Xie, Q. (2015) Effects of temperature and additives on the thermal stability of glucoamylase from Aspergillus niger. J. Microbiol Biotechnol.25, 33-43.
[10] Zeiske, T.,Stafford, K. A., andPalmer, A. G. (2016) Thermostability of enzymes from molecular dynamics simulations. J. Chem Theory Comput. 12, 2489–2492.
[11] http://uniprot.org
[12] Chen, J., Zhang, Y. Q., Zhao, C. Q. A. N., Li, C. Q., Zhou, Q. X., andLi, D. C. (2007)Cloning of gene encoding thermostable glucoamylase from Chaetomium thermophilum and its expression in Pichia pastoris. J. Appl Microbiol.103,2277-2284.
[13] Notredame, C. A., Higgins, D. G., Heringa, J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment.J. Mol Biol.302, 205-217.
[14] Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J. (1990) Basic local alignment search tool. J. Mol Biol. 215, 403-410.
[15] States, D. J., Gish, W. (1994) Combined use of sequence similarity and codon bias for coding region identification. J. Comput Biol. 1, 39-50.
[16] Marti-Renom, M. A., Stuart, A. C., Fiser, A., Sanchez, R., Melo, F., and Sali, A.(2000) Comparative protein structure modeling of genes and genomes.Annu. Rev Biophys Biomol Struct.29, 291-325.
[17] Klepeis, J. L., Lindorff-Larsen, K., Dror, R. O., and Shaw, D. E. (2009)Long-timescale molecular dynamics simulations of proteinstructure and function. Curr. Opin Struct Biol.19,120-127.
[18] Abdulazeez, S. (2019) Molecular simulation studies on B-cell lymphoma/leukaemia 11A. (BCL11A). Am. J Transl. Res. 11, 3689-3697.
[19] Goswami, C., Jayraman, M., Bakthavachalam, T., Sethi, G., Krishna, R. (2017) Homology modeling, molecular dynamics simulation and essential dynamics on anopheles gambiae D7r1. Int. J Biochim. Biophys.5, 65-77.
[20] Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE and Berendsen HJC GROMACS: fast, flexible, and free. J. Comput. Chem. 2005; 26:1701-1718.
[21] Berendsen HJC, Van der Spoel D and Van Drunen R. GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun.1995; 91:43-56.
[22] Chong, L. T., Duan, Y., Wang, L., Massova, I., and Kollman, P. A. (1999) Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Biophys. 96, 14330-14335.
[23] Baker, N. A., Sept, D., Joseph, S., Holst, M. J., andMcCammon, J. A. (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. chem. biophys.98, 10037-10041.