A nitrite biosensor based on a maltose binding protein nitrite reductase fusion immobilized on an electropolymerized film of a pyrrole-derived bipyridinium

Comparative analysis of amino acid composition in the active site of nirk gene encoding copper-containing nitrite reductase (CuNiR) in bacterial spp

The nirk gene encoding the copper-containing nitrite reductase (CuNiR), a key catalytic enzyme in the environmental denitrification process that helps to produce nitric oxide from nitrite. The molecular mechanism of denitrification process is definitely complex and in this case a theoretical investigation has been conducted to know the sequence information and amino acid composition of the active site of CuNiR enzyme using various Bioinformatics tools. 10 Fasta formatted sequences were retrieved from the NCBI database and the domain and disordered regions identification and phylogenetic analyses were done on these sequences. The comparative modeling of protein was performed through Modeller 9v14 program and visualized by PyMOL tools. Validated protein models were deposited in the Protein Model Database (PMDB) (PMDB id: PM0080150 to PM0080159). Active sites of nirk encoding CuNiR enzyme were identified by Castp server. The PROCHECK showed significant scores for four protein models in the most favored regions of the Ramachandran plot. Active sites and cavities prediction exhibited that the amino acid, namely Glycine, Alanine, Histidine, Aspartic acid, Glutamic acid, Threonine, and Glutamine were common in four predicted protein models. The present in silico study anticipates that active site analyses result will pave the way for further research on the complex denitrification mechanism of the selected species in the experimental laboratory.

A novel nitrite biosensor based on single-layer graphene nanoplatelet-protein composite film

A novel nitrite biosensor was developed through a sensing platform consisted of single-layer graphene nanoplatelet (SLGnP)-protein composite film. SLGnP with the virtues of excellent biocompatibility, conductivity and high sensitivity to the local perturbations can provide a biocompatible microenvironment for protein immobilization and a suitable electron transfer distance between electroactive centers of heme protein and electrode surface. A pair of well-defined and quasi-reversible cyclic voltammetric peaks that reflected the direct electrochemistry for ferric/ferrous couple of myoglobin (Mb) was achieved at the composite film modified electrode. Field emission scanning electron microscopy (FESEM) and ultraviolet visible spectra (UV-vis) were utilized to characterize the composite film. The results demonstrated that the morphology of the composite film was unique and the protein in the composite film retained its secondary structure similar to the native state. The composite film also displayed excellent electrocatalytic ability for the reduction of nitric oxide, which was applied to determine nitrite indirectly. It exhibited good electrochemical response to nitrite with a linear range from 0.05 to 2.5 mM and a detection limit of 0.01 mM.

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 nitrite biosensor based on the immobilization of cytochrome c on multi-walled carbon nanotubes-PAMAM-chitosan nanocomposite modified glass carbon electrode

A novel nitrite biosensor was successfully prepared via immobilizing Cytochrome c (Cyt c) onto the multi-walled carbon nanotubes-poly(amidoamine) (PAMAM)-chitosan (MWNT-PAMAM-Chit) nanocomposite modified glass carbon electrode (GCE). Ultraviolet and visible (UV-vis) absorption spectrum, cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were used to examine the native conformation and bioactivity of the immobilized Cyt c, and the electrochemical properties of the modified electrodes, respectively. The results indicate that the immobilized Cyt c retained its native characters, and the MWNT-PAMAM-Chit nanocomposite is a good platform for the immobilization of Cyt c as well as an excellent promoter for the electron transfer between Cyt c and electrode. The high reactive Cyt c pi-cation, which can oxidize NO(2)(-) into NO(3)(-) in the solution, is generated at higher potential (>0.7 V) based on the further oxidation of Cyt c. The nitrite biosensor showed a fast response to nitrite (about 5 s) in two concentration intervals, one was from 0.1 to 29 microM, and the other from 29 to 254 microM. The low detection limit of 0.01 microM was obtained.

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.

Electrochemical characterization of biosensor based on nitrite reductase and methyl viologen co-immobilized glassy carbon electrode

Nitrite reductase (NiR, nitric-oxide: ferricytochrome c oxidoreductase, EC 1.7.2.1) and methyl viologen (MV) were co-immobilized on glassy carbon electrode (GCE, d=3 mm) by polymer entrapment, and the electrode was tested as an electrochemical biosensor for amperometric determination of nitrite. The immobilization was performed by sequential loading and drying of a homogeneous mixture of poly(vinyl alcohol) (PVA), NiR and MV, followed by poly(allylamine hydrochloride) (PAH) solution, and finally hydrophilic polyurethane (HPU) dissolved in chloroform. The positively charged PAH layer could effectively keep immobilized cationic MV from diffusing through the membrane, holding mediator tightly near or on the electrode surface. The working principle of the biosensor was based on MV mediated electron transfer between electrode and immobilized NiR. The response time (t(90%)) of the biosensor was about 20 s and sensitivity was 11.8 nA/ microM (2.5 mU NiR) with linear response range of 1.5-260 microM (r(2)=0.996) and detection limit of 1.5 microM (S/N=3). Lineweaver-Burk plot showed that Michaelis-Menten constant (K(m,app)) was about 770 microM. The biosensor showed durable storage stability for 24 days (stored in ambient air at room temperature) retaining 80% of its initial activity, and showed satisfactory reproducibility (relative standard deviation (R.S.D.)=3.8%, n=9). Interference study showed that chlorate, chloride, sulfite, sulfate did not interfere with the nitrite determination, however, nitrate interfered with the determination with relative sensitivity of 38% (ratio of sensitivity for nitrate to that for nitrite). In addition to the full characterization of the biosensor, kinetic study was also conducted in solution and the homogeneous rate constant (k(2)) between NiR and MV were determined by chronoamperometry to be 5.8 x 10(5) M(-1) s(-1).

Diphenylamino group as an effective handle to conjugated donor-acceptor polymers through electropolymerization

[reaction: see text] The diphenylamino group is an effective handle for electropolymerization to give electron donor-acceptor conjugated polymers. In addition, interesting electrochromic and photoresponsive behavior of 13 has been investigated.

Crystal structure of the soluble domain of the major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria: a new class of copper-containing nitrite reductases

The major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria gonorrhoeae is essential for cell growth under oxygen limiting conditions in the presence of nitrite and is protective against killing by human sera. A phylogenic analysis indicates that AniA is a member of a new class of copper-containing nitrite reductases. Expression of the soluble domain of AniA yields a protein capable of reducing nitrite with specific activity of 160 units/mg, approximately 50 % of that measured for the nitrite reductase from the strong soil denitrifier Alcaligenes faecalis S-6. The crystal structure of the soluble domain of AniA was solved by molecular replacement and sixfold averaging to a resolution of 2.4 A. The nitrite soaked AniA crystal structure refined to 1.95 A reveals a bidentate mode of substrate binding to the type II copper. Despite low sequence identity (approximately 30 %), the core cupredoxin fold of AniA is similar to that found in copper-containing nitrite reductases from soil bacteria. The main structural differences are localized to two attenuated surface loops that map to deletions in the sequence alignment. In soil nitrite reductases, one of these surface loops is positioned near the type I copper site and contributes residues to the docking surface for proteaceous electron donors. In AniA, the attenuation of this loop results in a restructured hydrophobic binding surface that may be required to interact with a lipid anchored azurin. The second attenuated loop is positioned on the opposite side of AniA and may facilitate a more intimate interaction with the lipid membrane. A unique combination of structural effectors surrounding the type I copper site of sAnia contribute to a unusual visible absorption spectra with components observed previously in either green or blue type I copper sites.

Inorganic nitrogen metabolism in bacteria

Enzymatic reactions involving inorganic nitrogen species provide a rich variety of systems with which to study biological chemistry. In many cases, catalysis involves redox chemistry and takes place at metal centres. Recent structures and new spectroscopic data have rapidly advanced our knowledge of nitrogen cycle enzymology, particularly in the areas of nitrogen fixation, hydroxylamine oxidation and nitrite reduction. In the case of the nitrate reductases and nitric oxide reductase, models for structure and catalysis can be designed, based on new structural information that is now available for closely related enzymes. The past two years have also seen significant progress in our understanding of the enzymology of some 'new' reactions of the nitrogen cycle, for example anaerobic ammona oxidation and heterotrophic nitrification.

Electrocatalytic reduction of S-nitrosoglutathione at electrodes modified with an electropolymerized film of a pyrrole-derived viologen system and their application to cellular S-nitrosoglutathione determinations

The preparation, electrochemical characterization, and analytical applications of glassy carbon (GC) electrodes modified with electropolymerized films of the cation N,N'-di(3-pyrrol-1-yl-propyl)-4,4'-bipyridine (DPPB) are described. Electropolymerized films of DPPB on GC electrodes exhibit two one-electron redox processes centered at -0.45 and -0.85 V, respectively. S-Nitrosoglutathione (GSNO) can be electrocatalytically reduced at electrodes modified with electropolymerized films of DPPB at approximately -0.4 V vs sodium-saturated calomel electrode, which represents a dramatic diminution of about 600 mV in the overpotential in comparison with the reaction carried out at a bare GC electrode. The kinetics of the catalytic reaction have been characterized using cyclic voltammetry and rotated disk electrode techniques from which a value of (1.3 +/- 0.2) x 10(3)M-1 s-1 was obtained. Using electrodes modified with an electropolymerized film of DPPB we have carried out preliminary studies of the determination of intracellular GSNO concentrations in two strains of the bacterium Rhodobacter sphaeroides.