Homology Modeling and Structural Dynamics of the Glucose Oxidase

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.

Molecular Dynamics Simulation of E412 Catalytic Residue Mutation of GOx-IPBCC

“…To compare and validate the binding site, the 3-dimensional structure of the GOx-IPBCC enzyme and the 3-dimensional structure of the GOx 1CF3 enzyme with known binding site was aligned (25). On the other hand, the use of the 1CF3 structure is based on the position of this structure as the template structure for the GOx-IPBCC builder (13).…”

“…This enzyme has a total activity of 92.87 U and a Km value of 2.9 mM (11,12). The 3-dimensional structure of the GOx-IPBCC enzyme was successfully predicted from the sequence of its constituent genetic code (https://www.ncbi.nlm.nih.gov/ with access number MH593586.1) (13,14). This study was conducted to predict the molecular dynamics of E412 residue catalytic mutation belonging to the GOx-IPBCC enzyme.…”

The Effect of H133V of α-Amylase Bacillus licheniformis F11 in High Temperature using Molecular Dynamics Simulation

“…The overall stability of all structures was assessed by root-mean-square deviation (RMSD) analysis which calculates the deviation of backbone atoms of the protein referred to initial structure's backbone atoms, averaged over backbone atoms (18). A continuous increase in RMSDs value from the initial structure indicated a labile conformation or instability model and also offers the perception of tertiary structure (19)(20)(21). The RMSD profile of the positive control showed a constant profile in the average value of 1.23 Å through 100 ns simulation which considered good global stability.…”

Molecular Dynamic Simulation of Asiatic Acid Derivatives Complex With Inducible Nitric Oxide Synthase Enzyme as an Anti-Inflammatory

“…By observing the result, AA5 is the compound that is predicted to have the best bond stability because the results of visualization using VMD (Visual Molecular Dynamic) show the strong bond between the ligand (AA5) and receptor (iNOS). Beside considering the RMSD the stability of the bond between the ligands and receptors could be determined by calculating the non-bonded energy [26], and the LIE (Linear Interaction Energy) [27,28] of each system. LIE allows researchers to analyze changes in the energy of interactions between ligands and proteins on average during the simulation process [29].…”