Spectroelectrochemical investigation of a flavoprotein with a flavin-modified gold electrode

Mechanistic Insights into the Antibiofilm Mode of Action of Ellagic Acid

Bacterial biofilm is a major contributor to the persistence of infection and the limited efficacy of antibiotics. Antibiofilm molecules that interfere with the biofilm lifestyle offer a valuable tool in fighting bacterial pathogens. Ellagic acid (EA) is a natural polyphenol that has shown attractive antibiofilm properties. However, its precise antibiofilm mode of action remains unknown. Experimental evidence links the NADH:quinone oxidoreductase enzyme WrbA to biofilm formation, stress response, and pathogen virulence. Moreover, WrbA has demonstrated interactions with antibiofilm molecules, suggesting its role in redox and biofilm modulation. This work aims to provide mechanistic insights into the antibiofilm mode of action of EA utilizing computational studies, biophysical measurements, enzyme inhibition studies on WrbA, and biofilm and reactive oxygen species assays exploiting a WrbA-deprived mutant strain of Escherichia coli. Our research efforts led us to propose that the antibiofilm mode of action of EA stems from its ability to perturb the bacterial redox homeostasis driven by WrbA. These findings shed new light on the antibiofilm properties of EA and could lead to the development of more effective treatments for biofilm-related infections.

Proteomic and physiological analyses reveal the role of exogenous spermidine on cucumber roots in response to Ca(NO3)2 stress

The mechanism of exogenous Spd-induced Ca(NO₃)₂ stress tolerance in cucumber was studied by proteomics and physiological analyses. Protein-protein interaction network revealed 13 key proteins involved in Spd-induced Ca(NO₃)₂ stress resistance. Ca(NO₃)₂ stress is one of the major reasons for secondary salinization that limits cucumber plant development in greenhouse. The conferred protective role of exogenous Spd on cucumber in response to Ca(NO₃)₂ stress cues involves changes at the cellular and physiological levels. To investigate the molecular foundation of exogenous Spd in Ca(NO₃)₂ stress tolerance, a proteomic approach was performed in our work. After a 9 days period of Ca(NO₃)₂ stress and/or exogenous Spd, 71 differential protein spots were confidently identified. The resulting proteins were enriched in seven different categories of biological processes, including protein metabolism, carbohydrate and energy metabolism, ROS homeostasis and stress defense, cell wall related, transcription, others and unknown. Protein metabolism (31.2%), carbohydrate and energy metabolism (15.6%), ROS homeostasis and stress defense (32.5%) were the three largest functional categories in cucumber root and most of them were significantly increased by exogenous Spd. The Spd-responsive protein interaction network revealed 13 key proteins, whose accumulation changes could be critical for Spd-induced resistance; all 13 proteins were upregulated by Spd at transcriptional and protein levels in response to Ca(NO₃)₂ stress. Furthermore, accumulation of antioxidant enzymes, non-enzymatic antioxidant and polyamines, along with reduction of H₂O₂ and MDA, were detected after exogenous Spd application during Ca(NO₃)₂ stress. The results of these proteomic and physiological analyses in cucumber root may facilitate a better understanding of the underlying mechanism of Ca(NO₃)₂ stress tolerance mediated by exogenous Spd.

Immobilized aptamer on gold electrode senses trace amount of aflatoxin M1

An electrochemical aptasensor for detection of trace amounts of aflatoxin M1 was developed. This required immobilization of aptamer on screen printed gold electrode comprising of working electrode, counter electrode and reference electrode and was achieved by sequentially layering dithiodipropionic acid, streptavidin and biotinylated-tetraethylene glycol-aptamer. Immobilization of aptamer was monitored by cyclic voltammetry. Peak current in square wave voltammogram was inversely related to logarithmic concentration of aflatoxin M1. Dynamic range of sensor was 1-105 ppt aflatoxin M1. Sensor can be regenerated by treating electrode with 10% sodium dodecyl sulfate or 40 mM tris-HCl (pH 8.0) containing 10 mM ethylenediaminetetraacetic acid and 0.02% tween-20.

Nanomechanical properties of protein-DNA layers with different oligonucleotide tethers

The length and flexibility of the oligonucleotide tethers strongly affect the viscoelastic properties of the resulting protein–DNA layers.

The multi-ligand binding flavoprotein dodecin is reconstituted on top of flavin-terminated oligonucleotide monolayers. A detailed quartz crystal microbalance with a dissipation monitoring (QCM-D) study showing how the length and flexibility of the oligonucleotide tethers influence the stability and the viscoelastic properties of the resulting DNA–protein layers is presented. Relatively dense protein layers can be obtained, if the length of the tethers is in the same range as the diameter of dodecin. When significantly longer tethers are used, less dense layers are formed. When rather short tethers are used, the reaching area of individual tethers is too low to capture single apododecin molecules cooperatively, and the formation of stable and dense protein layers is not possible. On top of the DNA–dodecin layers additional flavin–DNA ligands may be captured to form sandwich-type DNA–protein–DNA layers. Differences in the binding and unbinding behavior of flavin-dsDNA and flavin-ssDNA ligands are measured by QCM-D and surface plasmon fluorescence spectroscopy (SPFS). Both type of ligands show relatively low k_on values, which might be explained by the structural rigidity of the binding pockets allowing a ligand to enter only when it approaches precisely in the right orientation. Apparently apododecin–flavin binding follows Fischer's classic lock-and-key binding model.

Flavin Derivatives with Tailored Redox Properties: Synthesis, Characterization, and Electrochemical Behavior

This study establishes structure-property relationships for four synthetic flavin molecules as bioinspired redox mediators in electro- and photocatalysis applications. The studied flavin compounds were disubstituted with polar substituents at the N1 and N3 positions (alloxazine) or at the N3 and N10 positions (isoalloxazines). The electrochemical behavior of one such synthetic flavin analogue was examined in detail in aqueous solutions of varying pH in the range from 1 to 10. Cyclic voltammetry, used in conjunction with hydrodynamic (rotating disk electrode) voltammetry, showed quasi-reversible behavior consistent with freely diffusing molecules and an overall global 2e(-) , 2H(+) proton-coupled electron transfer scheme. UV/Vis spectroelectrochemical data was also employed to study the pH-dependent electrochemical behavior of this derivative. Substituent effects on the redox behavior were compared and contrasted for all the four compounds, and visualized within a scatter plot framework to afford comparison with prior knowledge on mostly natural flavins in aqueous media. Finally, a preliminary assessment of one of the synthetic flavins was performed of its electrocatalytic activity toward dioxygen reduction as a prelude to further (quantitative) studies of both freely diffusing and tethered molecules on various electrode surfaces.

Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA

Quantum mechanical calculations using the Marcus equation are applied to compare the electron-transfer probability for two distinct crystal structures of the Escherichia coli protein WrbA, an FMN-dependent

NAD(P)H

quinone oxidoreductase, with the bound substrate benzoquinone. The calculations indicate that the position of benzoquinone in a new structure reported here and solved at 1.33 Å resolution is more likely to be relevant for the physiological reaction of WrbA than a previously reported crystal structure in which benzoquinone is shifted by ∼5 Å. Because the true electron-acceptor substrate for WrbA is not yet known, the present results can serve to constrain computational docking attempts with potential substrates that may aid in identifying the natural substrate(s) and physiological role(s) of this enzyme. The approach used here highlights a role for quantum mechanical calculations in the interpretation of protein crystal structures.

Tuning the reactivity of nanostructured indium tin oxide electrodes toward chemisorption

This contribution highlights correlation between the surface concentration of a chemisorbed organophosphorous probe (flavin mononucleotide) and the relative hydroxyl surface coverage of nanostructured ITO electrodes, which can be tuned during post-deposition reductive annealing.

Molecular dynamics comparison of E. coli WrbA apoprotein and holoprotein

WrbA is a novel multimeric flavodoxin-like protein of unknown function. A recent high-resolution X-ray crystal structure of E. coli WrbA holoprotein revealed a methionine sulfoxide residue with full occupancy in the FMN-binding site, a finding that was confirmed by mass spectrometry. In an effort to evaluate whether methionine sulfoxide may have a role in WrbA function, the present analyses were undertaken using molecular dynamics simulations in combination with further mass spectrometry of the protein. Methionine sulfoxide formation upon reconstitution of purified apoWrbA with oxidized FMN is fast as judged by kinetic mass spectrometry, being complete in ∼5 h and resulting in complete conversion at the active-site methionine with minor extents of conversion at heterogeneous second sites. Analysis of methionine oxidation states during purification of holoWrbA from bacterial cells reveals that methionine is not oxidized prior to reconstitution, indicating that methionine sulfoxide is unlikely to be relevant to the function of WrbA in vivo. Although the simulation results, the first reported for WrbA, led to no hypotheses about the role of methionine sulfoxide that could be tested experimentally, they elucidated the origins of the two major differences between apo- and holoWrbA crystal structures, an alteration of inter-subunit distance and a rotational shift within the tetrameric assembly.

1.2 Å resolution crystal structure of Escherichia coli WrbA holoprotein

The Escherichia coli protein WrbA, an FMN-dependent NAD(P)H:quinone oxidoreductase, was crystallized under new conditions in the presence of FAD or the native cofactor FMN. Slow-growing deep yellow crystals formed with FAD display the tetragonal bipyramidal shape typical for WrbA and diffract to 1.2 Å resolution, the highest yet reported. Faster-growing deep yellow crystals formed with FMN display an atypical shape, but diffract to only ∼1.6 Å resolution and are not analysed further here. The 1.2 Å resolution structure detailed here revealed only FMN in the active site and no electron density that can accommodate the missing parts of FAD. The very high resolution supports the modelling of the FMN isoalloxazine with a small but distinct propeller twist, apparently the first experimental observation of this predicted conformation, which appears to be enforced by the protein through a network of hydrogen bonds. Comparison of the electron density of the twisted isoalloxazine ring with the results of QM/MM simulations is compatible with the oxidized redox state. The very high resolution also supports the unique refinement of Met10 as the sulfoxide, confirmed by mass spectrometry. Bond lengths, intramolecular distances, and the pattern of hydrogen-bond donors and acceptors suggest the cofactor may interact with Met10. Slow incorporation of FMN, which is present as a trace contaminant in stocks of FAD, into growing crystals may be responsible for the near-atomic resolution, but a direct effect of the conformation of FMN and/or Met10 sulfoxide cannot be ruled out.

Biphasic kinetic behavior of E. coli WrbA, an FMN-dependent NAD(P)H:quinone oxidoreductase

The E. coli protein WrbA is an FMN-dependent NAD(P)H:quinone oxidoreductase that has been implicated in oxidative defense. Three subunits of the tetrameric enzyme contribute to each of four identical, cavernous active sites that appear to accommodate NAD(P)H or various quinones, but not simultaneously, suggesting an obligate tetramer with a ping-pong mechanism in which NAD departs before oxidized quinone binds. The present work was undertaken to evaluate these suggestions and to characterize the kinetic behavior of WrbA. Steady-state kinetics results reveal that WrbA conforms to a ping-pong mechanism with respect to the constancy of the apparent Vmax to Km ratio with substrate concentration. However, the competitive/non-competitive patterns of product inhibition, though consistent with the general class of bi-substrate reactions, do not exclude a minor contribution from additional forms of the enzyme. NMR results support the presence of additional enzyme forms. Docking and energy calculations find that electron-transfer-competent binding sites for NADH and benzoquinone present severe steric overlap, consistent with the ping-pong mechanism. Unexpectedly, plots of initial velocity as a function of either NADH or benzoquinone concentration present one or two Michaelis-Menten phases depending on the temperature at which the enzyme is held prior to assay. The effect of temperature is reversible, suggesting an intramolecular conformational process. WrbA shares these and other details of its kinetic behavior with mammalian DT-diaphorase, an FAD-dependent NAD(P)H:quinone oxidoreductase. An extensive literature review reveals several other enzymes with two-plateau kinetic plots, but in no case has a molecular explanation been elucidated. Preliminary sedimentation velocity analysis of WrbA indicates a large shift in size of the multimer with temperature, suggesting that subunit assembly coupled to substrate binding may underlie the two-plateau behavior. An additional aim of this report is to bring under wider attention the apparently widespread phenomenon of two-plateau Michaelis-Menten plots.

Increasing the coulombic efficiency of glucose biofuel cell anodes by combination of redox enzymes

A highly efficient anode for glucose biofuel cells has been developed by a combination of pyranose dehydrogenase from Agaricus meleagris (AmPDH) and cellobiose dehydrogenase from Myriococcum thermophilum (MtCDH). These two enzymes differ in how they oxidize glucose. AmPDH oxidizes glucose at the C(2) and C(3) carbon, whereas MtCDH at the C(1) carbon. Both enzymes oxidize efficiently a number of other mono- and disaccharides. They do not react directly with oxygen and produce no H(2)O(2). Electrodes were prepared by embedding (i) only AmPDH (in order to study this enzyme separately) and (ii) a mixture of AmPDH and MtCDH in an Os redox polymer hydrogel. Single-walled carbon nanotubes (SWCNTs) were added in order to enhance the current density. The electrodes were investigated with linear sweep and cyclic voltammetry in the presence of different substrates at physiological conditions. The electrochemical measurements revealed that the product of one enzyme can serve as a substrate for the other. In addition, a kinetic pathway analysis was performed by spectrophotometric measurements leading to the conclusion that up to six electrons can be gained from one glucose molecule through a combination of AmPDH and MtCDH. Hence, the combination of redox enzymes can lead to an enzymatic biofuel cell anode with an increased coulombic efficiency far beyond the usual yields of two electrons per substrate molecule.

Influence of solvation and the structure of adsorbates on the kinetics and mechanism of dimerization-induced compositional changes of mixed monolayers on TiO(2)

Mixed monolayers of thiol-terminated (T) and methyl-terminated (Me) carboxylic acids on nanocrystalline TiO(2) films underwent dimerization-induced compositional changes. At short reaction times, the compositions of mixed monolayers were kinetically controlled and mirrored the compositions of coadsorption solutions. On time scales up to several hours, well after the establishment of saturation surface coverages, the monolayers relaxed to thermodynamically controlled compositions through the displacement of Me by T. Equilibration was driven by the formation of intermolecular disulfide bonds between thiol groups of adsorbed T, which yielded polydentate dimeric adsorbates that were bound more strongly than monomeric adsorbates to TiO(2). The rate of compositional changes increased with decreasing solvent viscosity and decreasing alkyl chain length of T, suggesting that the rate of adsorption of T to TiO(2) strongly influenced the overall kinetics under certain conditions. Steric bulk within adsorbates and the strength of surface-attachment interactions also influenced the rate of compositional changes. A kinetic model, derived on the basis of Langmuir adsorption and desorption kinetics, accounts for key aspects of the mixed-monolayer compositional changes. The rate-determining step in the overall mechanism involved either the adsorption of T or the formation of disulfide bonds, depending on the conditions under which monolayers were prepared. Our findings illustrate that dimerization and other intermolecular interactions between adsorbates may dramatically influence the composition and terminal functionalization of mixed monolayers.

Structural organization of WrbA in apo- and holoprotein crystals

Two previously reported holoprotein crystal forms of the flavodoxin-like E. coli protein WrbA, diffracting to 2.6 and 2.0 A resolution, and new crystals of WrbA apoprotein diffracting to 1.85 A, are refined and analysed comparatively through the lens of flavodoxin structures. The results indicate that differences between apo- and holoWrbA crystal structures are manifested on many levels of protein organization as well as in the FMN-binding sites. Evaluation of the influence of crystal contacts by comparison of lattice packing reveals the protein's global response to FMN binding. Structural changes upon cofactor binding are compared with the monomeric flavodoxins. Topologically non-equivalent residues undergo remarkably similar local structural changes upon FMN binding to WrbA or to flavodoxin, despite differences in multimeric organization and residue types at the binding sites. Analysis of the three crystal structures described here, together with flavodoxin structures, rationalizes functional similarities and differences of the WrbAs relative to flavodoxins, leading to a new understanding of the defining features of WrbAs. The results suggest that WrbAs are not a remote and unusual branch of the flavodoxin family as previously thought but rather a central member with unifying structural features.

Redox properties of LOV domains: chemical versus photochemical reduction, and influence on the photocycle

LOV (light-oxygen-voltage-sensitive) domains comprise the light-sensitive parts of many blue light photoreceptor proteins. Photoexcitation of the chromophore flavin mononucleotide (FMN) in these LOV domains leads to formation of a covalent adduct between FMN and a cysteine residue. So far, the electronically excited singlet and triplet states of FMN have been identified as the only intermediates in the photocycles of LOV domains from several organisms. Since many flavoproteins are redox-active, however, the photocycles of LOV domains might involve other redox states of FMN, and might be controlled by the external redox potential. Here we report on the redox properties of the LOV1 domain from phototropin of the green alga Chlamydomonas reinhardtii. By equilibrium-redox spectropotentiometry a redox potential [E(fq/fhq) (flavoquinone/flavohydroquinone)] of -290 mV vs. the normal hydrogen electrode (NHE) was determined for the wild-type domain (LOV1-wt). A similar value of -280 mV was found for the mutant LOV1-C57G, in which the photoreactive cysteine is replaced by glycine. The recovery kinetics (photoadduct-->ground state) in the photocycle of LOV1-wt are not influenced by a redox potential in the range between +500 and -260 mV versus NHE. No flavosemiquinone could be generated by chemical reduction with sodium dithionite. However, photoreduction of LOV1-C57G with EDTA leads exclusively to the flavosemiquinone. This semiquinone is stable against disproportionation, and the photoreduction is not mediated by free FMN.

Crystal structure of the NADH:quinone oxidoreductase WrbA from Escherichia coli

The flavoprotein WrbA, originally described as a tryptophan (W) repressor-binding protein in Escherichia coli, has recently been shown to exhibit the enzymatic activity of a NADH:quinone oxidoreductase. This finding points toward a possible role in stress response and in the maintenance of a supply of reduced quinone. We have determined the three-dimensional structure of the WrbA holoprotein from E. coli at high resolution (1.66 A), and we observed a characteristic, tetrameric quaternary structure highly similar to the one found in the WrbA homologs of Deinococcus radiodurans and Pseudomonas aeruginosa. A similar tetramer was originally observed in an iron-sulfur flavoprotein involved in the reduction of reactive oxygen species. Together with other, recently characterized proteins such as YhdA or YLR011wp (Lot6p), these tetrameric flavoproteins may constitute a large family with diverse functions in redox catalysis. WrbA binds substrates at an active site that provides an ideal stacking environment for aromatic moieties, while providing a pocket that is structured to stabilize the ADP part of an NADH molecule in its immediate vicinity. Structures of WrbA in complex with benzoquinone and NADH suggest a sequential binding mechanism for both molecules in the catalytic cycle.

Square Wave Voltcoulometry: A Tool for the Study of Strongly adsorbed Redox Molecules

A new multipotential pulse technique called square wave voltcoulometry (SWVC), based on the analysis of the difference of converted charge signals obtained between two successive half-cycles when a square wave potential is applied, is developed to study charge-transfer processes taking place in electroactive monolayers. The use of SWVC presents the advantage of giving rise to a peak-shaped response, which evolves to a charge plateau at high square wave pulse amplitudes, from which the total surface excess and the formal potential can be immediately measured for quasi-reversible and reversible processes. This characteristic represents its main advantage versus other multipotential step techniques, which lead to a negligible current under reversible conditions. The formal potential of the electroactive systems can be measured from the peak potential of the SWVC curves, even for quasi-reversible behavior. Moreover, the non-faradic effects on the response can be easily evaluated and avoided as is demonstrated in this paper. Experimental verification of the theoretical predictions is given for reversible and quasi-reversible systems.

Crystallization and preliminary diffraction analysis of Escherichia coli WrbA in complex with its cofactor flavin mononucleotide

The flavoprotein WrbA from Escherichia coli is considered to be the prototype of a new family of multimeric flavodoxin-like proteins that are implicated in cell protection against oxidative stress. The present study is aimed at structural characterization of the E. coli protein with respect to its recently revealed oxidoreductase activity. Crystals of WrbA holoprotein in complex with the oxidized flavin cofactor (FMN) were obtained using standard vapour-diffusion techniques. Deep yellow tetragonal crystals obtained from differing crystallization conditions display different space groups and unit-cell parameters. X-ray crystal structures of the WrbA holoprotein have been determined to resolutions of 2.0 and 2.6 A.