Investigation of Direct Electron Transfer of Glucose Oxidase on a Graphene-CNT Composite Surface: A Molecular Dynamics Study Based on Electrochemical Experiments

Graphene and its variants exhibit excellent electrical properties for the construction of enzymatic interfaces. In particular, the direct electron transfer of glucose oxidase on the electrode surface is a very important issue in the development of enzyme-based bioelectrodes. However, the number of studies conducted to assess how pristine graphene forms different interfaces with other carbon materials is insufficient. Enzyme-based electrodes (formed using carbon materials) have been extensively applied because of their low manufacturing costs and easy production techniques. In this study, the characteristics of a single-walled carbon nanotube/graphene-combined enzyme interface are analyzed at the atomic level using molecular dynamics simulations. The morphology of the enzyme was visualized using an elastic network model by performing normal-mode analysis based on electrochemical and microscopic experiments. Single-carbon electrodes exhibited poorer electrical characteristics than those prepared as composites with enzymes. Furthermore, the composite interface exhibited 4.61- and 2.45-fold higher direct electron efficiencies than GOx synthesized with single-carbon nanotubes and graphene, respectively. Based on this study, we propose that pristine graphene has the potential to develop glucose oxidase interfaces and carbon-nanotube-graphene composites for easy fabrication, low cost, and efficient electrode structures for enzyme-based biofuel cells.

Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications

Nanoscale biosensors, a highly promising technique in clinical analysis, can provide sensitive yet label-free detection of biomolecules. The spatial and chemical specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for optimizing the performance of a biosensor. Due to experimental limitations at the microscopic level, integrated cross-disciplinary approaches that combine in silico design with experimental measurements have the potential to present a powerful new paradigm that tackles the issue of developing novel biosensors. In some cases, computational studies can be seen as alternative approaches to assess the microscopic working mechanisms of biosensors. Nonetheless, the complex architecture of a biosensor, associated with the collective contribution from "substrate-receptor-analyte" conjugate in a solvent, often requires extensive atomistic simulations and systems of prohibitive size which need to be addressed. In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomolecules are usually unable to correctly describe the biomolecule/surface interface. Thus, the computational studies in this field are limited to date. In this review, we aim to introduce fundamental principles that govern the absorption of biomolecules onto functionalized nanomaterials and to report state-of-the-art computational strategies to rationally design nanoscale biosensors. A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented. The insights will not only stimulate the field to rationally design functionalized nanomaterials with improved biosensing performance but also foster research on the required functionalization to improve biomolecule-surface complex formation as a whole.

Reusable System for Phenol Detection in an Aqueous Medium Based on Nanodiamonds and Extracellular Oxidase from Basidiomycete Neonothopanus nambi

A reusable system for phenol determination in an aqueous medium was obtained by adsorption of extracellular oxidase from fungus Neonothopanus nambi onto modified nanodiamonds (MND) synthesized by detonation. It was found that the enzyme strongly binds to MND and exhibits catalytic activity in the reaction of co-oxidation of phenol with 4-aminoantipyrine without the addition of hydrogen peroxide. In the presence of the MND-oxidase complex, a significantly (by an order of magnitude) higher yield of the reaction product is recorded as compared to the yield in the presence of a free enzyme; the mechanism of the revealed effect is discussed. Model experiments have demonstrated the multiple use of the MND-oxidase complex for testing phenol in aqueous samples. The immobilized enzyme exhibits functional activity during long-term (2 months) storage of the MND-oxidase complex at 4°C. The data obtained create the prerequisites for using the created system in environmental monitoring of water pollution with phenol.

Extracellular Oxidase from the Neonothopanus nambi Fungus as a Promising Enzyme for Analytical Applications

The extracellular enzyme with oxidase function was extracted from the Neonothopanus nambi luminescent fungus by using mild processing of mycelium with β-glucosidase and then isolated by gel-filtration chromatography. The extracted enzyme is found to be a FAD-containing protein, catalyzing phenol co-oxidation with 4-aminoantipyrine without addition of H₂O₂, which distinguishes it from peroxidases. This fact allowed us to assume that this enzyme may be a mixed-function oxidase. According to gel-filtration chromatography and SDS-PAGE, the oxidase has molecular weight of 60 kDa. The enzyme exhibits maximum activity at 55-70 °C and pH 5.0. Kinetic parameters K_m and V_max of the oxidase for phenol were 0.21 mM and 0.40 µM min^-1. We suggest that the extracted enzyme can be useful to develop a simplified biosensor for colorimetric detection of phenol in aqueous media, which does not require using hydrogen peroxide.

Atomistic simulations of gold surface functionalization for nanoscale biosensors applications

A wide class of biosensors can be built via functionalization of gold surface with proper bio conjugation element capable of interacting with the analyte in solution, and the detection can be performed either optically, mechanically or electrically. Any change in physico-chemical environment or any slight variation in mass localization near the surface of the sensor can cause differences in nature of the transduction mechanism. The optimization of such sensors may require multiple experiments to determine suitable experimental conditions for the immobilization and detection of the analyte. Here, we employ molecular modeling techniques to assist the optimization of a gold-surface biosensor. The gold surface of a quartz-crystal-microbalance sensor is functionalized using polymeric chains of poly(ethylene glycol) (PEG) of 2 KDa molecular weight, which is an inert long chain amphiphilic molecule, supporting biotin molecules (bPEG) as the ligand molecules for streptavidin analyte. The PEG linkers are immobilized onto the gold surface through sulphur chemistry. Four gold surfaces with different PEG linker density and different biotinylation ratio between bPEG and PEG, are investigated by means of state-of-the art atomistic simulations and compared with available experimental data. Results suggest that the amount of biotin molecules accessible for the binding with the protein increases upon increasing the linkers density. At the high density a 1:1 ratio of bPEG/PEG can further improve the accessibility of the biotin ligand due to a strong repulsion between linker chains and different degree of hydrophobicity between bPEG and PEG linkers. The study provides a computaional protocol to model sensors at the level of single molecular interactions, and for optimizing the physical properties of surface conjugated ligand which is crucial to enhance output of the sensor.

Effects of the Hydrophobicity of Key Residues on the Characteristics and Stability of Glucose Oxidase on a Graphene Surface

Glucose oxidase (GOx) is one of the most widely investigated enzymes in the field of bioelectrochemistry. It is mainly used for the detection of glucose in solutions and enzyme-based biofuel cells. On the basis of the combination of GOx with graphene, novel nanodevices exceeding conventional limits can be developed. To develop a hybrid enzyme-graphene nanodevice with a good performance, it is important that GOx is deposited well on the graphene surface while maintaining its structure and not impeding the oxidation activity of the GOx. In this study, we propose a method to improve the stability of GOx and secure its immobility on the graphene sheet and its glucose-binding affinity by single-point mutation of GOx using molecular dynamics simulations. We confirm that the structural stability, immobility, and substrate binding affinity of GOx can be modified by changing the hydrophobicity of a key residue. We demonstrate that biosensors or biofuel cells can be redesigned and their properties can be improved by using molecular dynamics simulation.

Structural determination of Enzyme-Graphene Nanocomposite Sensor Material

State-of-the-art ultra-sensitive blood glucose-monitoring biosensors, based on glucose oxidase (GOx) covalently linked to a single layer graphene (SLG), will be a valuable next generation diagnostic tool for personal glycemic level management. We report here our observations of sensor matrix structure obtained using a multi-physics approach towards analysis of small-angle neutron scattering (SANS) on graphene-based biosensor functionalized with GOx under different pH conditions for various hierarchical GOx assemblies within SLG. We developed a methodology to separately extract the average shape of GOx molecules within the hierarchical assemblies. The modeling is able to resolve differences in the average GOx dimer structure and shows that treatment under different pH conditions lead to differences within the GOx at the dimer contact region with SLG. The coupling of different analysis methods and modeling approaches we developed in this study provides a universal approach to obtain detailed structural quantifications, for establishing robust structure-property relationships. This is an essential step to obtain an insight into the structure and function of the GOx-SLG interface for optimizing sensor performance.

Controlling enzyme function through immobilisation on graphene, graphene derivatives and other two dimensional nanomaterials

Controlling enzyme function through immobilisation on graphene, graphene derivatives and other two dimensional nanomaterials.