scholarly journals Homology Modeling and Structural Dynamics of the Glucose Oxidase

2019 ◽  
Vol 20 (1) ◽  
pp. 43
Author(s):  
Farhan Azhwin Maulana ◽  
Laksmi Ambarsari ◽  
Setyanto Tri Wahyudi
Keyword(s):  
Homology Modeling ◽  
Glucose Oxidase ◽  
Md Simulations ◽  
Data Bank ◽  
Positive Control ◽  
Glucose Biosensor ◽  
Amino Acid Sequences ◽  
Enzyme Thermostability ◽  
Modeled Structure ◽  
Reliable Model

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.

scholarly journals DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics

2020 ◽  
Vol 49 (D1) ◽  
pp. D288-D297 ◽  
Author(s):  
Malak Pirtskhalava ◽  
Anthony A Amstrong ◽  
Maia Grigolava ◽  
Mindia Chubinidze ◽  
Evgenia Alimbarashvili ◽  
...  
Keyword(s):  
De Novo ◽  
Biological Activities ◽  
Antimicrobial Properties ◽  
Md Simulations ◽  
Data Bank ◽  
Amino Acid Sequences ◽  
Production Costs ◽  
Web Browser ◽  
Initial Release ◽  
High Production

Abstract The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is an open-access, comprehensive database containing information on amino acid sequences, chemical modifications, 3D structures, bioactivities and toxicities of peptides that possess antimicrobial properties. DBAASP is updated continuously, and at present, version 3.0 (DBAASP v3) contains >15 700 entries (8000 more than the previous version), including >14 500 monomers and nearly 400 homo- and hetero-multimers. Of the monomeric antimicrobial peptides (AMPs), >12 000 are synthetic, about 2700 are ribosomally synthesized, and about 170 are non-ribosomally synthesized. Approximately 3/4 of the entries were added after the initial release of the database in 2014 reflecting the recent sharp increase in interest in AMPs. Despite the increased interest, adoption of peptide antimicrobials in clinical practice is still limited as a consequence of several factors including side effects, problems with bioavailability and high production costs. To assist in developing and optimizing de novo peptides with desired biological activities, DBAASP offers several tools including a sophisticated multifactor analysis of relevant physicochemical properties. Furthermore, DBAASP has implemented a structure modelling pipeline that automates the setup, execution and upload of molecular dynamics (MD) simulations of database peptides. At present, >3200 peptides have been populated with MD trajectories and related analyses that are both viewable within the web browser and available for download. More than 400 DBAASP entries also have links to experimentally determined structures in the Protein Data Bank. DBAASP v3 is freely accessible at http://dbaasp.org.

Temperature-induced amperometric glucose biosensor based on a poly(N-vinylcaprolactam)/graphene oxide composite film

The Analyst ◽  
2019 ◽  
Vol 144 (6) ◽  
pp. 1960-1967 ◽  
Author(s):  
Chao Chen ◽  
Pengcheng Zhao ◽  
Meijun Ni ◽  
Chunyan Li ◽  
Yixi Xie ◽  
...  
Keyword(s):  
Graphene Oxide ◽  
Composite Film ◽  
Glucose Oxidase ◽  
Glassy Carbon Electrode ◽  
Glassy Carbon ◽  
Glucose Biosensor ◽  
Carbon Electrode ◽  
Oxide Composite

A temperature-induced sensing film consisting of poly(N-vinylcaprolactam) (PVCL), graphene oxide (GO) and glucose oxidase (GOD) was fabricated and used to modify a glassy carbon electrode (GCE).

scholarly journals Biosensing Membrane Base on Ferulic Acid and Glucose Oxidase for an Amperometric Glucose Biosensor

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3757
Author(s):  
Gabriela Valdés-Ramírez ◽  
Laura Galicia
Keyword(s):  
Ferulic Acid ◽  
Glucose Oxidase ◽  
Aqueous Media ◽  
Glucose Biosensor ◽  
Single Step ◽  
Coefficient Of Determination ◽  
The Novel ◽  
Carbon Paste ◽  
Glucose Response ◽  
Glucose Biosensors

A biosensing membrane base on ferulic acid and glucose oxidase is synthesized onto a carbon paste electrode by electropolymerization via cyclic voltammetry in aqueous media at neutral pH at a single step. The developed biosensors exhibit a linear response from 0.082 to 34 mM glucose concentration, with a coefficient of determination R2 equal to 0.997. The biosensors display a sensitivity of 1.1 μAmM−1 cm−2, a detection limit of 0.025 mM, and 0.082 mM as glucose quantification limit. The studies reveal stable, repeatable, and reproducible biosensors response. The results indicate that the novel poly-ferulic acid membrane synthesized by electropolymerization is a promising method for glucose oxidase immobilization towards the development of glucose biosensors. The developed glucose biosensors exhibit a broader linear glucose response than other polymer-based glucose biosensors.

Gold nanoparticles-coated eggshell membrane with immobilized glucose oxidase for fabrication of glucose biosensor

2011 ◽  
Vol 152 (1) ◽  
pp. 49-55 ◽  
Author(s):  
Baozhan Zheng ◽  
Shunping Xie ◽  
Lei Qian ◽  
Hongyan Yuan ◽  
Dan Xiao ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Glucose Oxidase ◽  
Glucose Biosensor ◽  
Eggshell Membrane ◽  
Immobilized Glucose Oxidase

A Glucose Biosensor Based on Immobilization of Glucose Oxidase in Chitosan Network Matrix

2005 ◽  
Vol 23 (3) ◽  
pp. 275-279 ◽  
Author(s):  
Yao Hui ◽  
Li Nan ◽  
Xu Jing-Zhong ◽  
Zhu Jun-Jie
Keyword(s):  
Glucose Oxidase ◽  
Glucose Biosensor

Voltammetric glucose biosensor based on glucose oxidase encapsulation in a chitosan-kappa-carrageenan polyelectrolyte complex

2019 ◽  
Vol 95 ◽  
pp. 152-159 ◽  
Author(s):  
Ilhem Rassas ◽  
Mohamed Braiek ◽  
Anne Bonhomme ◽  
Francois Bessueille ◽  
Guy Rafin ◽  
...  
Keyword(s):  
Glucose Oxidase ◽  
Polyelectrolyte Complex ◽  
Glucose Biosensor ◽  
Kappa Carrageenan

scholarly journals Natural Compound Modulates the Cervical Cancer Microenvironment—A Pharmacophore Guided Molecular Modelling Approaches

2018 ◽  
Vol 7 (12) ◽  
pp. 551 ◽  
Author(s):  
Shailima Rampogu ◽  
Doneti Ravinder ◽  
Smita Pawar ◽  
Keun Lee
Keyword(s):  
Cervical Cancer ◽  
Md Simulations ◽  
Data Bank ◽  
Docking Studies ◽  
New Drugs ◽  
Binding Modes ◽  
Cervical Cancer Cells ◽  
Causative Agents ◽  
Nitric Oxide Synthase 2 ◽  
Oxide Synthase

Cervical cancer is regarded as one of the major burdens noticed in women next to breast cancer. Although, human papilloma viruses (HPVs) are regarded as the principal causative agents, they require certain other factors such as oestrogen hormone to induce cervical cancer. Aromatase is an enzyme that converts androgens into oestrogens and hindering this enzyme could subsequently hamper the formation of oestrogen thereby alleviating the disease. Accordingly, in the current investigation, a structure based pharmacophore was generated considering two proteins bearing the Protein Data Bank (PDB) codes 3EQM (pharm 1) and 3S7S (pharm 2), respectively. The two models were employed as the 3D query to screen the in-house built natural compounds database. The obtained 51 compounds were escalated to molecular docking studies to decipher on the binding affinities and to predict the quintessential binding modes which were affirmed by molecular dynamics (MD) simulations. The compound has induced dose-dependent down regulation of PP2B, Nitric oxide synthase-2 (NOS2), and Interleukin 6 (IL-6) genes in the HeLa cells and has modulated the expression of apoptotic genes such as Bax, Bcl2, and caspases-3 at different concentrations. These results guide us to comprehend that the identified aromatase inhibitor was effective against the cervical cancer cells and additionally could server as scaffolds in designing new drugs.

Amperometric glucose biosensor based on silver nanowires and glucose oxidase

2013 ◽  
Vol 176 ◽  
pp. 9-14 ◽  
Author(s):  
Lisha Wang ◽  
Xia Gao ◽  
Lingyan Jin ◽  
Qi Wu ◽  
Zhichun Chen ◽  
...  
Keyword(s):  
Glucose Oxidase ◽  
Silver Nanowires ◽  
Glucose Biosensor

scholarly journals Electrodeposition–Assisted Assembled Multilayer Films of Gold Nanoparticles and Glucose Oxidase onto Polypyrrole-Reduced Graphene Oxide Matrix and Their Electrocatalytic Activity toward Glucose

Nanomaterials ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 993 ◽  
Author(s):  
Baoyan Wu ◽  
Shihua Hou ◽  
Yongyong Xue ◽  
Zhan Chen
Keyword(s):  
Gold Nanoparticles ◽  
Graphene Oxide ◽  
Glucose Oxidase ◽  
Reduced Graphene Oxide ◽  
Self Assembly ◽  
Electrocatalytic Activity ◽  
Multilayer Films ◽  
Glucose Biosensor ◽  
Future Design ◽  
Reduced Graphene

The study reports a facile and eco-friendly approach for nanomaterial synthesis and enzyme immobilization. A corresponding glucose biosensor was fabricated by immobilizing the gold nanoparticles (AuNPs) and glucose oxidase (GOD) multilayer films onto the polypyrrole (PPy)/reduced graphene oxide (RGO) modified glassy carbon electrode (GCE) via the electrodeposition and self-assembly. PPy and graphene oxide were first coated on the surface of a bare GCE by the electrodeposition. Then, AuNPs and GOD were alternately immobilized onto PPy-RGO/GCE electrode using the electrodeposition of AuNPs and self-assembly of GOD to obtain AuNPs-GOD multilayer films. The resulting PPy-RGO-(AuNPs-GOD)n/GCE biosensors were used to characterize and assess their electrocatalytic activity toward glucose using cyclic voltammetry and amperometry. The response current increased with the increased number of AuNPs-GOD layers, and the biosensor based on four layers of AuNPs-GOD showed the best performance. The PPy-RGO-(AuNPs-GOD)4/GCE electrode can detect glucose in a linear range from 0.2 mM to 8 mM with a good sensitivity of 0.89 μA/mM, and a detection limit of 5.6 μM (S/N = 3). This study presents a promising eco-friendly biosensor platform with advantages of electrodeposition and self-assembly, and would be helpful for the future design of more complex electrochemical detection systems.

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