Rate constants in two dimensions of electron transfer between pyruvate oxidase, a membrane enzyme, and ubiquinone (coenzyme Q8), its water-insoluble electron carrier

Hybrid bilayer membranes as platforms for biomimicry and catalysis

Hybrid bilayer membrane (HBM) platforms represent an emerging nanoscale bio-inspired interface that has broad implications in energy catalysis and smart molecular devices. An HBM contains multiple modular components that include an underlying inorganic surface with a biological layer appended on top. The inorganic interface serves as a support with robust mechanical properties that can also be decorated with functional moieties, sensing units and catalytic active sites. The biological layer contains lipids and membrane-bound entities that facilitate or alter the activity and selectivity of the embedded functional motifs. With their structural complexity and functional flexibility, HBMs have been demonstrated to enhance catalytic turnover frequency and regulate product selectivity of the O₂ and CO₂ reduction reactions, which have applications in fuel cells and electrolysers. HBMs can also steer the mechanistic pathways of proton-coupled electron transfer (PCET) reactions of quinones and metal complexes by tuning electron and proton delivery rates. Beyond energy catalysis, HBMs have been equipped with enzyme mimics and membrane-bound redox agents to recapitulate natural energy transport chains. With channels and carriers incorporated, HBM sensors can quantify transmembrane events. This Review serves to summarize the major accomplishments achieved using HBMs in the past decade.

Hybrid bilayer membranes on metallurgical polished aluminum

In this work we describe the functionalization of metallurgically polished aluminum surfaces yielding biomimetic electrodes suitable for probing protein/phospholipid interactions. The functionalization involves two simple steps: silanization of the aluminum and subsequent fusion of multilamellar vesicles which leads to the formation of a hybrid bilayer lipid membrane (hBLM). The vesicle fusion was followed in real-time by fast Fourier transform electrochemical impedance spectroscopy (FFT EIS). The impedance-derived complex capacitance of the hBLMs was approximately 0.61 µF cm⁻², a value typical for intact phospholipid bilayers. We found that the hBLMs can be readily disrupted if exposed to > 400 nM solutions of the pore-forming peptide melittin. However, the presence of cholesterol at 40% (mol) in hBLMs exhibited an inhibitory effect on the membrane-damaging capacity of the peptide. The melittin-membrane interaction was concentration dependent decreasing with concentration. The hBLMs on Al surface can be regenerated multiple times, retaining their dielectric and functional properties essentially intact.

Electrochemical Biosensors Based on Membrane-Bound Enzymes in Biomimetic Configurations

In nature, many enzymes are attached or inserted into the cell membrane, having hydrophobic subunits or lipid chains for this purpose. Their reconstitution on electrodes maintaining their natural structural characteristics allows for optimizing their electrocatalytic properties and stability. Different biomimetic strategies have been developed for modifying electrodes surfaces to accommodate membrane-bound enzymes, including the formation of self-assembled monolayers of hydrophobic compounds, lipid bilayers, or liposomes deposition. An overview of the different strategies used for the formation of biomimetic membranes, the reconstitution of membrane enzymes on electrodes, and their applications as biosensors is presented.

Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates

Organohalide respiration is an environmentally important but poorly characterized type of anaerobic respiration. We compared the global proteome of the versatile organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans grown with different electron acceptors (fumarate, nitrate, or tetrachloroethene [PCE]). The most significant differences in protein abundance were found for gene products of the organohalide respiration region. This genomic region encodes the corrinoid and FeS cluster containing PCE reductive dehalogenase PceA and other proteins putatively involved in PCE metabolism such as those involved in corrinoid biosynthesis. The latter gene products as well as PceA and a putative quinol dehydrogenase were almost exclusively detected in cells grown with PCE. This finding suggests an electron flow from the electron donor such as formate or pyruvate via the quinone pool and a quinol dehydrogenase to PceA and the terminal electron acceptor PCE. Two putative accessory proteins, an IscU-like protein and a peroxidase-like protein, were detected with PCE only and might be involved in PceA maturation. The proteome of cells grown with pyruvate instead of formate as electron donor indicates a route of electrons from reduced ferredoxin via an Epsilonproteobacterial complex I and the quinone pool to PCE.

Reconstitution of respiratory complex I on a biomimetic membrane supported on gold electrodes

For the first time, respiratory complex I has been reconstituted on an electrode preserving its structure and activity. Respiratory complex I is a membrane-bound enzyme that has an essential function in cellular energy production. It couples NADH:quinone oxidoreduction to translocation of ions across the cellular (in prokaryotes) or mitochondrial membranes. Therefore, complex I contributes to the establishment and maintenance of the transmembrane difference of electrochemical potential required for adenosine triphosphate synthesis, transport, and motility. Our new strategy has been applied for reconstituting the bacterial complex I from Rhodothermus marinus onto a biomimetic membrane supported on gold electrodes modified with a thiol self-assembled monolayer (SAM). Atomic force microscopy and faradaic impedance measurements give evidence of the biomimetic construction, whereas electrochemical measurements show its functionality. Both electron transfer and proton translocation by respiratory complex I were monitored, simulating in vivo conditions.

The metabolic potential of Escherichia coli BL21 in defined and rich medium

BACKGROUND

The proteome reflects the available cellular machinery to deal with nutrients and environmental challenges. The most common E. coli strain BL21 growing in different, commonly employed media was evaluated using a detailed quantitative proteome analysis.

RESULTS

The presence of preformed biomass precursor molecules in rich media such as Luria Bertani supported rapid growth concomitant to acetate formation and apparently unbalanced abundances of central metabolic pathway enzymes, e.g. high levels of lower glycolytic pathway enzymes as well as pyruvate dehydrogenase, and low levels of TCA cycle and high levels of the acetate forming enzymes Pta and AckA. The proteome of cells growing exponentially in glucose-supplemented mineral salt medium was dominated by enzymes of amino acid synthesis pathways, contained more balanced abundances of central metabolic pathway enzymes, and a lower portion of ribosomal and other translational proteins. Entry into stationary phase led to a reconstruction of the bacterial proteome by increasing e.g. the portion of proteins required for scavenging rare nutrients and general cell protection. This proteomic reconstruction during entry into stationary phase was more noticeable in cells growing in rich medium as they have a greater reservoir of recyclable proteins from the translational machinery.

CONCLUSIONS

The proteomic comparison of cells growing exponentially in different media reflected the antagonistic and competitive regulation of central metabolic pathways through the global transcriptional regulators Cra, Crp, and ArcA. For example, the proteome of cells growing exponentially in rich medium was consistent with a dominating role of phosphorylated ArcA most likely a result from limitations in reoxidizing reduced quinones in the respiratory chain under these growth conditions. The proteomic alterations of exponentially growing cells into stationary phase cells were consistent with stringent-like and stationary phase responses and a dominating control through DksA-ppGpp and RpoS.

Ubiquinone-10 in gold-immobilized lipid membrane structures acts as a sensor for acetylcholine and other tetraalkylammonium cations

It is reported that the reduction of ubiquinone incorporated into supported lipid bilayers and into immobilized liposome layers on gold electrodes is kinetically and thermodynamically enhanced by the presence of acetylcholine and tetrabutylammonium (TBA(+)) in solution. The reduction peak and the mid-peak potentials of the redox reactions, determined by cyclic voltammetry, are displaced towards more positive potentials by approximately 500 and 250mV, respectively, in the case of TBA(+); and by approximately 750 and 530mV, respectively, in the case of acetylcholine. The intensity of the signal varies with the cation concentration, allowing for quantitative determinations in the millimolar range. It is proposed that the enhanced reduction of ubiquinone arises from the formation of tetraalkylammonium cation-ubiquinone radical anion ion-pairs. Electrochemical quartz crystal microbalance with dissipation monitoring (EQCM-D) measurements confirmed that the potential shift and the intensity of the redox signal are coupled with the adsorption of the tetraalkylammonium cations on the lipid membrane. The Langmuir adsorption equilibrium constant (K) of TBA(+) on lipid membranes at physiological pH is determined. In supported lipid bilayers K=440.7±160M(-1), while in an immobilized liposome layer K=35.53±3.53M(-1).

Reversible redox of NADH and NAD+ at a hybrid lipid bilayer membrane using ubiquinone

Here, we report the reversible interconversion between NADH and NAD(+) at a low overpotential, which is in part mediated by ubiquinone embedded in a biomimetic membrane to mimic the initial stages of respiration. This system can be used as a platform to examine biologically relevant electroactive molecules embedded in a natural membrane environment and provide new insights into the mechanism of biological redox cycling.

Oriented immobilization of a membrane-bound hydrogenase onto an electrode for direct electron transfer

The interaction of redox enzymes with electrodes is of great interest for studying the catalytic mechanisms of redox enzymes and for bioelectronic applications. Efficient electron transport between the biocatalysts and the electrodes has achieved more success with soluble enzymes than with membrane enzymes because of the higher structural complexity and instability of the latter proteins. In this work, we report a strategy for immobilizing a membrane-bound enzyme onto gold electrodes with a controlled orientation in its fully active conformation. The immobilized redox enzyme is the Ni-Fe-Se hydrogenase from Desulfovibrio vulgaris Hildenborough, which catalyzes H(2)-oxidation reversibly and is associated with the cytoplasmic membrane by a lipidic tail. Gold surfaces modified with this enzyme and phospholipids have been studied by atomic force microscopy (AFM) and electrochemical methods. The combined study indicates that by a two-step immobilization procedure the hydrogenase can be inserted via its lipidic tail onto a phospholipidic bilayer formed over the gold surface, allowing only mediated electron transfer between the enzyme and electrode. However, a one-step immobilization procedure favors the formation of a hydrogenase monolayer over the gold surface with its lipidic tail inserted into a phospholipid bilayer formed on top of the hydrogenase molecules. This latter method has allowed for the first time efficient electron transfer between a membrane-bound enzyme in its native conformation and an electrode.

Flavin redox switching of protein functions

Flavin cofactors impart remarkable catalytic diversity to enzymes, enabling them to participate in a broad array of biological processes. The properties of flavins also provide proteins with a versatile redox sensor that can be utilized for converting physiological signals such as cellular metabolism, light, and redox status into a unique functional output. The control of protein functions by the flavin redox state is important for transcriptional regulation, cell signaling pathways, and environmental adaptation. A significant number of proteins that have flavin redox switches are found in the Per-Arnt-Sim (PAS) domain family and include flavoproteins that act as photosensors and respond to changes in cellular redox conditions. Biochemical and structural studies of PAS domain flavoproteins have revealed key insights into how flavin redox changes are propagated to the surface of the protein and translated into a new functional output such as the binding of a target protein in a signaling pathway. Mechanistic details of proteins unrelated to the PAS domain are also emerging and provide novel examples of how the flavin redox state governs protein-membrane interactions in response to appropriate stimuli. Analysis of different flavin switch proteins reveals shared mechanistic themes for the regulation of protein structure and function by flavins.

A study of cytochrome bo3 in a tethered bilayer lipid membrane

An assay has been developed in which the activity of an ubiquinol oxidase from Escherichia coli, cytochrome bo(3) (cbo(3)), is determined as a function of the hydrophobic substrate ubiquinol-10 (UQ-10) in tethered bilayer lipid membranes (tBLMs). UQ-10 was added in situ, while the enzyme activity and the UQ-10 concentration in the membrane have been determined by cyclic voltammetry. Cbo(3) is inhibited by UQ-10 at concentrations above 5-10 pmol/cm(2), while product inhibition is absent. Cyclic voltammetry has also been used to characterise the effects of three inhibitors; cyanide, inhibiting oxygen reduction; 2-n-Heptyl-4-hydroxyquinoline N-oxide (HQNO), inhibiting the quinone oxidation and Zn(II), thought to block the proton channels required for oxygen reduction and proton pumping activity. The electrochemical behaviour of cbo(3) inhibited with HQNO and Zn(II) is almost identical, suggesting that Zn(II) ions inhibit the enzyme reduction by quinol, rather than oxygen reduction. This suggests that at Zn(II) concentration below 50µM the proton release of cbo(3) is inhibited, but not the proton uptake required to reduce oxygen to water.

Electrodes modified with lipid membranes to study quinone oxidoreductases

Quinone oxidoreductases are a class of membrane enzymes that catalyse the oxidation or reduction of membrane-bound quinols/quinones. The conversion of quinone/quinol by these enzymes is difficult to study because of the hydrophobic nature of the enzymes and their substrates. We describe some biochemical properties of quinones and quinone oxidoreductases and then look in more detail at two model membranes that can be used to study quinone oxidoreductases in a native-like membrane environment with their native lipophilic quinone substrates. The results obtained with these model membranes are compared with classical enzyme assays that use water-soluble quinone analogues.

Characterization of cytochrome bo3 activity in a native-like surface-tethered membrane

We have developed a simple native-like surface-tethered membrane system to investigate the activity of cbo(3) (cytochrome bo(3)), a terminal oxidase in Escherichia coli. The tethered membranes consist of E. coli inner-membrane extracts mixed with additional E. coli lipids containing various amounts of the cbo(3) substrate UQ-10 (ubiquinol-10). Tethered membranes are formed by self-assembly from vesicles on to gold electrodes functionalized with cholesterol derivatives. cbo(3) activity was monitored using CV (cyclic voltammetry) with electron transfer to cbo(3) mediated by UQ-10. The apparent K(m) for oxygen with this system is 1.1+/-0.4 microM, in good agreement with values reported in the literature for whole-cell experiments and for purified cbo(3). Increasing the concentration of lipophilic UQ-10 in the membrane leads to an increase in cbo(3) activity. The activity of cbo(3) with long-chain ubiquinones appears to be different from previous reports using short-chain substrate analogues such as UQ-1 in that typical Michaelis-Menten kinetics are not observed using UQ-10. This native-like membrane model thus provides new insights into the interaction of transmembrane enzymes with hydrophobic substrates which contrasts with studies using hydrophilic UQ analogues.

Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli

The thiamin- and flavin-dependent peripheral membrane enzyme pyruvate oxidase from E. coli catalyzes the oxidative decarboxylation of the central metabolite pyruvate to CO(2) and acetate. Concomitant reduction of the enzyme-bound flavin triggers membrane binding of the C terminus and shuttling of 2 electrons to ubiquinone 8, a membrane-bound mobile carrier of the electron transport chain. Binding to the membrane in vivo or limited proteolysis in vitro stimulate the catalytic proficiency by 2 orders of magnitude. The molecular mechanisms by which membrane binding and activation are governed have remained enigmatic. Here, we present the X-ray crystal structures of the full-length enzyme and a proteolytically activated truncation variant lacking the last 23 C-terminal residues inferred as important in membrane binding. In conjunction with spectroscopic results, the structural data pinpoint a conformational rearrangement upon activation that exposes the autoinhibitory C terminus, thereby freeing the active site. In the activated enzyme, Phe-465 swings into the active site and wires both cofactors for efficient electron transfer. The isolated C terminus, which has no intrinsic helix propensity, folds into a helical structure in the presence of micelles.

Crystallization and preliminary X-ray diffraction analysis of full-length and proteolytically activated pyruvate oxidase from Escherichia coli

The thiamine diphosphate- and flavin-dependent peripheral membrane enzyme pyruvate oxidase from Escherichia coli (EcPOX) has been crystallized in the full-length form and as a proteolytically activated C-terminal truncation variant which lacks the last 23 amino acids (Delta23 EcPOX). Crystals were grown by the hanging-drop vapour-diffusion method using either protamine sulfate (full-length EcPOX) or 2-methyl-2,4-pentanediol (Delta23 EcPOX) as precipitants. Native data sets were collected at a X-ray home source to a resolution of 2.9 A. The two forms of EcPOX crystallize in different space groups. Whereas full-length EcPOX crystallizes in the tetragonal space group P4(3)2(1)2 with two monomers per asymmetric unit, the crystals of Delta23 EcPOX belong to the orthorhombic space group P2(1)2(1)2(1) and contain 12 monomers per asymmetric unit.

Dynamic simulation of an in vitro multi-enzyme system

Parameters often are tuned with metabolite concentration time series data to build a dynamic model of metabolism. However, such tuning may reduce the extrapolation ability (generalization capability) of the model. In this study, we determined detailed kinetic parameters of three purified Escherichia coli glycolytic enzymes using the initial velocity method for individual enzymes; i.e., the parameters were determined independently from metabolite concentration time series data. The metabolite concentration time series calculated by the model using the parameters matched the experimental data obtained in an actual multi-enzyme system consisting of the three purified E. coli glycolytic enzymes. Thus, the results indicate that kinetic parameters can be determined without using an undesirable tuning process.

Self-assembly of solid-supported membranes using a triggered fusion of phospholipid-enriched proteoliposomes prepared from the inner mitochondrial membrane

A general procedure for the formation ofsolid-supported artificial membranes containing transmembrane proteins is reported. The main objective was to directly use the pool of proteins of the native biomembrane (here the inner membrane from mitochondria of human carcinogenic hepatic cells) and to avoid purification steps with detergent. Proteoliposomes of phospholipid-enriched inner membranes from mitochondria were tethered and fused onto a tailored surface via a streptavidin link. The failure of some preliminary experiments on membrane formation was attributed to strong nonspecific interactions between the solid surface and the protuberant hydrophilic parts of the transmembrane complexes. The correct loading of uniform membranes was performed after optimization of a tailored surface, covered with a grafted short-chain poly(ethylene glycol), so that nonspecific interactions are reduced. Step-by-step assembly of the structure and triggered fusion of the immobilized proteoliposomes were monitored by surface plasmon resonance and fluorescence photobleaching recovery, respectively. The long-range lateral diffusion coefficient (at 22 degrees C) for a fluorescent lipid varies from 2.5 x 10(-8) cm2 s(-1) for a tethered lipid bilayer without protein to 10(-9) cm2 s(-1) for a tethered membrane containing the transmembrane proteins of the respiratory chain at a protein area fraction of about 15%. The decrease in the diffusion coefficient in the tethered membrane with increase in protein area fraction was too pronounced to be fully explained by the theoretical models of obstructed lateral diffusion. Covalent tethering links with the solid are certainly involved in the decrease of the overall lateral mobility of the components in the supported membrane at the highest protein-to-lipid ratios.

Direct electrochemical interaction between a modified gold electrode and a bacterial membrane extract

A novel electrochemical approach is described for redox-active membrane proteins. A total membrane extract (in the form of vesicles) of Bacillus subtilis is tethered onto gold surfaces modified with cholesterol based thiols. The membrane vesicles remain intact on the surface and do not rupture or fuse to form a planar bilayer. Oxidation/reduction signals are obtained of the natural co-enzyme, menaquinone-7, located in the membrane. The membrane protein, succinate menaquinone oxidoreductase (SQR), remains in the vesicles and is able to reduce fumarate using menaquinone as mediator. The catalysis of the reverse reaction (oxidation of succinate), which is the natural catalytic function of SQR, is almost absent with menaquinone. However, adding the co-enzyme ubiquinone, which has a reduction potential that is about 0.2 V higher, restores the succinate oxidation activity.

Pyruvate:quinone oxidoreductase from Corynebacterium glutamicum: purification and biochemical characterization

Pyruvate:quinone oxidoreductase catalyzes the oxidative decarboxylation of pyruvate to acetate and CO2 with a quinone as the physiological electron acceptor. So far, this enzyme activity has been found only in Escherichia coli. Using 2,6-dichloroindophenol as an artificial electron acceptor, we detected pyruvate:quinone oxidoreductase activity in cell extracts of the amino acid producer Corynebacterium glutamicum. The activity was highest (0.055 +/- 0.005 U/mg of protein) in cells grown on complex medium and about threefold lower when the cells were grown on medium containing glucose, pyruvate, or acetate as the carbon source. From wild-type C. glutamicum, the pyruvate:quinone oxidoreductase was purified about 180-fold to homogeneity in four steps and subjected to biochemical analysis. The enzyme is a flavoprotein, has a molecular mass of about 232 kDa, and consists of four identical subunits of about 62 kDa. It was activated by Triton X-100, phosphatidylglycerol, and dipalmitoyl-phosphatidylglycerol, and the substrates were pyruvate (kcat=37.8 +/- 3 s(-1); Km=30 +/- 3 mM) and 2-oxobutyrate (kcat=33.2 +/- 3 s(-1); Km=90 +/- 8 mM). Thiamine pyrophosphate (Km=1 microM) and certain divalent metal ions such as Mg2+ (Km=29 microM), Mn2+ (Km=2 microM), and Co2+ (Km=11 microM) served as cofactors. In addition to several dyes (2,6-dichloroindophenol, p-iodonitrotetrazolium violet, and nitroblue tetrazolium), menadione (Km=106 microM) was efficiently reduced by the purified pyruvate:quinone oxidoreductase, indicating that a naphthoquinone may be the physiological electron acceptor of this enzyme in C. glutamicum.

Polymer-cushioned lipid bilayers in porous alumina

Using small-angle neutron scattering (SANS) and cyclic voltammetry (CV), we show that model biological membranes can be deposited on a polymer cushion confined in highly regular porous alumina. The thicknesses of the dilute polymer cushion chemically bound to the alumina and of the supported bilayer are obtained for two polyethylene glycol cushions (PEG(5000) and PEG(20000)) and for a cushion made of chains bearing a lipid anchor at their free end (DSPE-PEG(3400)). The bilayers are studied well below and well above the chain melting temperature of the lipid mixture (DMPC/DMPE: 80/20), using a coenzyme (Ubiquinone, UQ(10)) as a redox probe for the voltammetry experiments. Analysis of the SANS form factor of the bilayers shows that the bilayer thickness can be extracted in this particular geometry. Using PEG chains grafted at a low surface density (D < 2R(g)), the thickness of the complete molecular construction is obtained by CV, which shows (after subtracting the bilayer thickness) that the polymer cushion thickness can be varied from 50 to 150 Angstroms. The values obtained with three different chain lengths, are in perfect agreement with the radius derived from the Flory theory.

Survey of the year 2001 commercial optical biosensor literature

We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.