Sensing nitrite through a pseudoazurin-nitrite reductase electron transfer relay

A molecular dynamics and quantum mechanical investigation of intermolecular interaction and electron-transfer mechanism between copper-containing nitrite reductase and redox partner pseudoazurin

Much of biological electron transfer occurs between proteins. These molecular processes usually involve molecular recognition and intermolecular electron transfer (inter-ET). The inter-ET reaction between copper-containing nitrite reductase (CuNiR) and partner protein pseudoazurin (PAz) is the first step in denitrification, which is affected by intermolecular association. However, the transient interaction between CuNiR and PAz and the indistinct inter-ET pathway pose challenges for people to understand the biological functions of the CuNiR-PAz complex. Thus, molecular dynamics simulation and quantum mechanical calculation were used to investigate the question in this study. The interaction of the interface residues was determined through hydrogen bonds, root-mean-square deviation, root-mean-square fluctuation, the dynamics cross-correlation matrix, and molecular mechanics Poisson-Boltzmann surface area of molecular dynamics simulations. The interactions among the residues Glu89, Gly200, Asp205, Asn91, Glu204, Thr92, and Met141 on CuNiR and the residues Lys109, Ala15, Lys10, Asn9, Ile110, Met84, and Met16 on PAz are responsible for the stabilization of the complex. The binding free energy is up to -25.33 kcal mol^-1. We compared the wild-type and mutant (M84A) interfacial optimized complex models at the CAM-B3LYP level with Grimme dispersion corrections (GD3) to confirm Met84 as a relay station for promoting the inter-ET. Additionally, to test whether Met84 may combine with the adjacent Met141 to form a special two-center, three-electron (S∴S)⁺ structure to promote the inter-ET, QM/MM was further performed to discuss the possibility of generating an electron stepping stone. Our study will promote a deep understanding of the stable protein-protein interaction, and the identified inter-residue interaction will be theoretical guidance for enhancing the catalytic activity of CuNiR in denitrification.

Electrocatalysis by Heme Enzymes—Applications in Biosensing

Heme proteins take part in a number of fundamental biological processes, including oxygen transport and storage, electron transfer, catalysis and signal transduction. The redox chemistry of the heme iron and the biochemical diversity of heme proteins have led to the development of a plethora of biotechnological applications. This work focuses on biosensing devices based on heme proteins, in which they are electronically coupled to an electrode and their activity is determined through the measurement of catalytic currents in the presence of substrate, i.e., the target analyte of the biosensor. After an overview of the main concepts of amperometric biosensors, we address transduction schemes, protein immobilization strategies, and the performance of devices that explore reactions of heme biocatalysts, including peroxidase, cytochrome P450, catalase, nitrite reductase, cytochrome c oxidase, cytochrome c and derived microperoxidases, hemoglobin, and myoglobin. We further discuss how structural information about immobilized heme proteins can lead to rational design of biosensing devices, ensuring insights into their efficiency and long-term stability.

Disposable biogenic amine biosensors for histamine determination in fish

This study presents the development of disposable biosensors employed in the determination of histamine in fish samples. Screen printed carbon electrodes (SPCEs) were first modified with a mixture of titanium dioxide nanoparticles (TiO₂), carboxylated multiwalled carbon nanotubes (c-MWCNTs), hexaammineruthenium(iii) chloride (RU) and chitosan (CS). Diamine oxidase (DAO) or monoamine oxidase (MAO) enzymes were further immobilized onto the TiO₂-c-MWCNT-RU-CS/SPCEs via 1-ethyl-3-(dimethylaminopropyl) carbodiimide hydrochloride (EDC) and hydroxysuccinimide (NHS) chemistry for the fabrication of the biosensors. The morphological and electrochemical properties of the proposed biosensors were studied using scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, cyclic voltammetry (CV), chronoamperometry and electrochemical impedance spectroscopy (EIS). A performance comparison of two biosensors indicated that the one based on DAO had a linear concentration range from 9.9 × 10^-6 to 1.1 × 10^-3 M and the other based on MAO, from 5.6 × 10^-5 to 1.1 × 10^-3 M for histamine. The sensitivity of the DAO based biosensor was almost 1.5 times higher than that of the MAO based biosensor. The proposed biosensors were successfully employed to determine histamine in fish samples and the recoveries were between 100.0% and 104.6%.

Amperometric determination of heavy metal using an HRP inhibition biosensor based on ITO nanoparticles-ruthenium (III) hexamine trichloride composite: Central composite design optimization

A novel horseradish peroxidase (HRP) enzyme inhibition biosensor based on indium tin oxide (ITO) nanoparticles, hexaammineruthenium (III) chloride (RUT), and chitosan (CH) modified glassy carbon electrode (GCE) was developed. The biosensor fabrication process was investigated using scanning electron microscopy, energy-dispersive X-ray spectroscopy, cyclic voltammetry, and electrochemical impedance spectroscopy. The amounts of ITO nanoparticles and RUT were optimized using a 2² central composite design for the optimization of electrode composition. The detection limits were determined as 8 nM, 3 nM, and 1 nM for Pb²⁺, Ni²⁺, and Cd²⁺, respectively. The inhibition calibration curves of the biosensor were found to be within the range of 0.009-0.301 µM with a sensitivity of 11.97 µA µM^-1 cm^-2 (0.85 µA µM^-1) for Pb²⁺, 0.011-0.368 µM with a sensitivity of 10.84 µA µM^-1 cm^-2 (0.77 µA µM^-1) for Ni²⁺, and 0.008-0.372 µM with a sensitivity of 10.99 µA µM^-1 cm^-2 (0.78 µA µM^-1) for Cd²⁺. The type of HRP inhibition by Pb²⁺, Ni²⁺ and Cd²⁺ was investigated by the Dixon and Cornish-Bowden plots. The effects of possible interfering species on the biosensor response were examined. The analysis of Pb²⁺, Ni²⁺, and Cd²⁺ in tap water was demonstrated using the HRP/ITO-RUT-CH/GCE with satisfactory experimental results. The proposed method agreed with the atomic absorption spectrometry results.

Electrochemical Enzyme Biosensors Revisited: Old Solutions for New Problems

Worldwide legislation is driving the development of novel and highly efficient analytical tools for assessing the composition of every material that interacts with Consumers or Nature. The biosensor technology is one of the most active R&D domains of Analytical Sciences focused on the challenge of taking analytical chemistry to the field. Electrochemical biosensors based on redox enzymes, in particular, are highly appealing due to their usual quick response, high selectivity and sensitivity, low cost and portable dimensions. This review paper aims to provide an overview of the most important advances made in the field since the proposal of the first biosensor, the well-known hand-held glucose meter. The first section addresses the current needs and challenges for novel analytical tools, followed by a brief description of the different components and configurations of biosensing devices, and the fundamentals of enzyme kinetics and amperometry. The following sections emphasize on enzyme-based amperometric biosensors and the different stages of their development.

Small electron-transfer proteins as mediators in enzymatic electrochemical biosensors

Electrochemical mediators transfer redox equivalents between the active sites of enzymes and electrodes and, in this way, initiate bioelectrocatalytic redox processes. This has been very useful in the development of the so-called second-generation biosensors, in which they transduce a catalyzed reaction into an electrical signal. Among other pre-requisites, redox mediators must be readily oxidized and/or reduced at the electrode surface and readily interact with the biorecognition component. Small chemical compounds (e.g. ferrocene derivatives, ruthenium, or osmium complexes and viologens) are frequently used for this purpose but, lately, small redox proteins (e.g. horse heart cytochrome c) have also been used as redox partners in biosensing applications. In general, docking between two complementary proteins introduces a second level of selectivity to the biosensor and enlarges the list of compounds analyzed. Moreover, electrochemical interferences are frequently minimized owing to the small overpotentials achieved. This paper provides an overview of enzyme biosensors that are mediated by electron-transfer proteins. The paper begins with a brief discussion of mediated electrochemistry in biosensing systems and proceeds with a detailed description of relevant work on the cooperative use of redox enzymes and biological electron donors and/or acceptors.

Probing redox proteins on a gold surface by single molecule fluorescence spectroscopy

The interaction between the fluorescently labeled redox protein, azurin, and a thin gold film is characterized using single-molecule fluorescence intensity and lifetime measurements. Fluorescence quenching starts at distances below 2.3 nm from the gold surface. At shorter distances the quantum yield may decrease down to fourfold for direct attachment of the protein to bare gold. Outside of the quenching range, up to fivefold enhancement of the fluorescence is observed on average with increasing roughness of the gold layer. Fluorescence-detected redox activity of individual azurin molecules, with a lifetime switching ratio of 0.4, is demonstrated for the first time close to a gold surface.

Nitrite biosensing via selective enzymes--a long but promising route

The last decades have witnessed a steady increase of the social and political awareness for the need of monitoring and controlling environmental and industrial processes. In the case of nitrite ion, due to its potential toxicity for human health, the European Union has recently implemented a number of rules to restrict its level in drinking waters and food products. Although several analytical protocols have been proposed for nitrite quantification, none of them enable a reliable and quick analysis of complex samples. An alternative approach relies on the construction of biosensing devices using stable enzymes, with both high activity and specificity for nitrite. In this paper we review the current state-of-the-art in the field of electrochemical and optical biosensors using nitrite reducing enzymes as biorecognition elements and discuss the opportunities and challenges in this emerging market.

A nitrite biosensor based on co-immobilization of nitrite reductase and viologen-modified chitosan on a glassy carbon electrode

An electrochemical nitrite biosensor based on co-immobilization of copper-containing nitrite reductase (Cu-NiR, from Rhodopseudomonas sphaeroides forma sp. denitrificans) and viologen-modified chitosan (CHIT-V) on a glassy carbon electrode (GCE) is presented. Electron transfer (ET) between a conventional GCE and immobilized Cu-NiR was mediated by the co-immobilized CHIT-V. Redox-active viologen was covalently linked to a chitosan backbone, and the thus produced CHIT-V was co-immobilized with Cu-NiR on the GCE surface by drop-coating of hydrophilic polyurethane (HPU). The electrode responded to nitrite with a limit of detection (LOD) of 40 nM (S/N = 3). The sensitivity, linear response range, and response time (t(90%)) were 14.9 nA/μM, 0.04-11 μM (r(2) = 0.999) and 15 s, respectively. The corresponding Lineweaver-Burk plot showed that the apparent Michaelis-Menten constant (K(M) (app)) was 65 μM. Storage stability of the biosensor (retaining 80% of initial activity) was 65 days under ambient air and room temperature storage conditions. Reproducibility of the sensor showed a relative standard deviation (RSD) of 2.8% (n = 5) for detection of 1 μM of nitrite. An interference study showed that anions commonly found in water samples such as chlorate, chloride, sulfate and sulfite did not interfere with the nitrite detection. However, nitrate interfered with a relative sensitivity of 64% and this interference effect was due to the intrinsic character of the NiR employed in this study.

A Random-sequential Mechanism for Nitrite Binding and Active Site Reduction in Copper-containing Nitrite Reductase

The homotrimeric copper-containing nitrite reductase (NiR) contains one type-1 and one type-2 copper center per monomer. Electrons enter through the type-1 site and are shuttled to the type-2 site where nitrite is reduced to nitric oxide. To investigate the catalytic mechanism of NiR the effects of pH and nitrite on the turnover rate in the presence of three different electron donors at saturating concentrations were measured. The activity of NiR was also measured electrochemically by exploiting direct electron transfer to the enzyme immobilized on a graphite rotating disk electrode. In all cases, the steady-state kinetics fitted excellently to a random-sequential mechanism in which electron transfer from the type-1 to the type-2 site is rate-limiting. At low [NO(-)(2)] reduction of the type-2 site precedes nitrite binding, at high [NO(-)(2)] the reverse occurs. Below pH 6.5, the catalytic activity diminished at higher nitrite concentrations, in agreement with electron transfer being slower to the nitrite-bound type-2 site than to the water-bound type-2 site. Above pH 6.5, substrate activation is observed, in agreement with electron transfer to the nitrite-bound type-2 site being faster than electron transfer to the hydroxyl-bound type-2 site. To study the effect of slower electron transfer between the type-1 and type-2 site, NiR M150T was used. It has a type-1 site with a 125-mV higher midpoint potential and a 0.3-eV higher reorganization energy leading to an approximately 50-fold slower intramolecular electron transfer to the type-2 site. The results confirm that NiR employs a random-sequential mechanism.

Biosensors and bioelectrochemistry

This review describes recent developments in the field of biosensors and bioelectrochemistry. Nanoparticles have been used to improve sensor performance and to develop biosensors based on new detection principles. Their use has extended into all areas of biosensor and bioelectrochemistry research. Other active areas of biosensor development include DNA sensing, immunosensing, direct electron transfer between an electrode and a redox protein or enzyme, and in vivo sensors.

Interfacial sensing: surface assembled molecular receptors

The controlled surface assembly of biological or appropriately designed synthetic host systems on optically or electrochemically-active surfaces has advanced considerably during the past decade. Recent activities, from the authors laboratory and elsewhere, and possible future directions are discussed herein.