Dynamics in host-guest complexes of molecular tweezers and clips

The dynamics in the host-guest complexes of the molecular tweezers 1 a,b and clips 2 a,b with 1,2,4,5-tetracyanobenzene (TCNB, 3) and tropylium tetrafluoroborate (4) as guest molecules were analyzed by temperature-dependent 1H NMR spectroscopy. The TCNB complexes of tweezers 1 a,b were found to be particularly stable (dissociation barrier: DeltaG(++)=16.8 and 15.7 kcal mol(-1), respectively), more stable than the TCNB complexes of clips 2 a,b and the tropylium complex of tweezer 1 b (dissociation barrier: DeltaG(++)=12.4, 11.2, and 12.3 kcal mol(-1), respectively). A detailed analysis of the kinetic and thermodynamic data (especially the negative entropies of activation found for complex dissociation) suggests that in the transition state of dissociation the guest molecule is still clipped between the aromatic tips of the host molecule. The 1H NMR analysis of the TCNB complexes 3@1 b and 3@2 a at low temperatures (T<-80 degrees C) showed that 3 undergoes fast rotation inside the cavity of tweezer 1 b or clip 2 a (rotational barrier: DeltaG( not equal)=11.7 and 8.3 kcal mol(-1), respectively). This rotation of a guest molecule inside the host cavity can be considered to be the dynamic equilibration of noncovalent conformers. In the case of clip complex 3@2 a the association and rotational barriers are smaller by DeltaDeltaG(++)=3-4 kcal mol(-1) than those in tweezer complexes 3@1 a,b. This can be explained by the more open topology of the trimethylene-bridged clips compared to the tetramethylene-bridged tweezers. Finally, the bromo substituents in the newly prepared clip 2 b have a substantial effect on the kinetics and thermodynamics of complex formation. Clip 2 b forms weaker complexes with (TCNB, 3) and tetracyanoquinodimethane (TCNQ, 12) and a more stable complex with 2,4,7-trinitrofluoren-9-ylidene (TNF, 13) than the parent clip 2 a. These results can be explained by a less negative electrostatic potential surface (EPS) inside the cavity and a larger van der Waals contact surface of 2 b compared to 2 a. In the case of the highly electron-deficient guest molecules TCNB and TCNQ the attractive electrostatic interaction is predominant and hence responsible for the thermodynamic complex stability, whereas in the case of TNF with its extended pi system, dispersion forces are more important for host-guest binding.     

Electrical contacting of flavoenzymes and NAD(P)+-dependent enzymes by reconstitution and affinity interactions on phenylboronic acid monolayers associated with Au-electrodes

The preparation of integrated, electrically contacted, flavoenzyme and NAD(P)(+)-dependent enzyme-electrodes is described. The reconstitution of apo-glucose oxidase, apo-GOx, on a FAD cofactor linked to a pyrroloquinoline quinone (PQQ) phenylboronic acid monolayer yields an electrically contacted enzyme monolayer (surface coverage 2.1 x 10(-)(12) mol cm(-)(2)) exhibiting a turnover rate of 700 s(-)(1) (at 22 +/- 2 degrees C). The system is characterized by microgravimetric quartz-crystal microbalance analyses, Faradaic impedance spectroscopy, rotating disk electrode experiments, and cyclic voltammetry. The performance of the enzyme-electrode for glucose sensing is described. Similarly, the electrically contacted enzyme-electrodes of NAD(P)(+)-dependent enzymes malate dehydrogenase, MalD, and lactate dehydrogenase, LDH, are prepared by the cross-linking of affinity complexes generated between the enzymes and the NADP(+) and NAD(+) cofactors linked to a pyrroloquinoline quinone phenylboronic acid monolayer, respectively. The MalD enzyme-electrode (surface coverage 1.2 x 10(-)(12) mol cm(-)(2)) exhibits a turnover rate of 190 s(-)(1), whereas the LDH enzyme-electrode (surface coverage 7.0 x 10(-)(12) mol cm(-)(2)) reveals a turnover rate of 2.5 s(-)(1). Chronoamperometric experiments reveal that the NAD(+) cofactor is linked to the PQQ-phenylboronic acid by two different binding modes. The integration of the LDH with the two NAD(+) cofactor configurations yields enzyme assemblies differing by 1 order of magnitude in their bioelectrocatalytic activities.     

Integrated, electrically contacted NAD(P)+-dependent enzyme-carbon nanotube electrodes for biosensors and biofuel cell applications

Integrated, electrically contacted beta-nicotinamide adenine dinucleotide- (NAD(+)) or beta-nicotinamide adenine dinucleotide phosphate- (NADP(+)) dependent enzyme electrodes were prepared on single-walled carbon nanotube (SWCNT) supports. The SWCNTs were functionalized with Nile Blue (1), and the cofactors NADP(+) and NAD(+) were linked to 1 through a phenyl boronic acid ligand. The affinity complexes of glucose dehydrogenase (GDH) with the NADP(+) cofactor or alcohol dehydrogenase (AlcDH) with the NAD(+) cofactor were crosslinked with glutaric dialdehyde and the biomolecule-functionalized SWCNT materials were deposited on glassy carbon electrodes. The integrated enzyme electrodes revealed bioelectrocatalytic activities, and they acted as amperometric electrodes for the analysis of glucose or ethanol. The bioelectrocatalytic response of the systems originated from the biocatalyzed oxidation of the respective substrates by the enzyme with the concomitant generation of NAD(P)H cofactors. The electrocatalytically mediated oxidation of NAD(P)H by 1 led to amperometric responses in the system. Similarly, an electrically contacted bilirubin oxidase (BOD)-SWCNT electrode was prepared by the deposition of BOD onto the SWCNTs and the subsequent crosslinking of the BOD units using glutaric dialdehyde. The BOD-SWCNT electrode revealed bioelectrocatalytic functions for the reduction of O(2) to H(2)O. The different electrically contacted SWCNT-based enzyme electrodes were used to construct biofuel cell elements. The electrically contacted GDH-SWCNT electrode was used as the anode for the oxidation of the glucose fuel in conjunction with the BOD-SWCNT electrode in the presence of O(2), which acted as an oxidizer in the system. The power output of the cell was 23 muW cm(-2). Similarly, the AlcDH-SWCNT electrode was used as the anode for the oxidation of ethanol, which was acting as the fuel, with the BOD-SWCNT electrode as the cathode for the reduction of O(2). The power output of the system was 48 microW cm(-2).     

Protein conformational gating of enzymatic activity in xanthine oxidoreductase

In mammals, xanthine oxidoreductase can exist as xanthine dehydrogenase (XDH) and xanthine oxidase (XO). The two enzymes possess common redox active cofactors, which form an electron transfer (ET) pathway terminated by a flavin cofactor. In spite of identical protein primary structures, the redox potential difference between XDH and XO for the flavin semiquinone/hydroquinone pair (E(sq/hq)) is ~170 mV, a striking difference. The former greatly prefers NAD(+) as ultimate substrate for ET from the iron-sulfur cluster FeS-II via flavin while the latter only accepts dioxygen. In XDH (without NAD(+)), however, the redox potential of the electron donor FeS-II is 180 mV higher than that for the acceptor flavin, yielding an energetically uphill ET. On the basis of new 1.65, 2.3, 1.9, and 2.2 ? resolution crystal structures for XDH, XO, the NAD(+)- and NADH-complexed XDH, E(sq/hq) were calculated to better understand how the enzyme activates an ET from FeS-II to flavin. The majority of the E(sq/hq) difference between XDH and XO originates from a conformational change in the loop at positions 423-433 near the flavin binding site, causing the differences in stability of the semiquinone state. There was no large conformational change observed in response to NAD(+) binding at XDH. Instead, the positive charge of the NAD(+) ring, deprotonation of Asp429, and capping of the bulk surface of the flavin by the NAD(+) molecule all contribute to altering E(sq/hq) upon NAD(+) binding to XDH.     

Two-dimensional infrared spectroscopy of azido-nicotinamide adenine dinucleotide in water

Mid-IR active analogs of enzyme cofactors have the potential to be important spectroscopic reporters of enzyme active site dynamics. Azido-nicotinamide adenine dinucleotide (NAD(+)), which has been recently synthesized in our laboratory, is a mid-IR active analog of NAD(+), a ubiquitous redox cofactor in biology. In this study, we measure the frequency-frequency time correlation function for the antisymmetric stretching vibration of the azido group of azido-NAD(+) in water. Our results are consistent with previous studies of pseudohalides in water. We conclude that azido-NAD(+) is sensitive to local environmental fluctuations, which, in water, are dominated by hydrogen-bond dynamics of the water molecules around the probe. Our results demonstrate the potential of azido-NAD(+) as a vibrational probe and illustrate the potential of substituted NAD(+)-analogs as reporters of local structural dynamics that could be used for studies of protein dynamics in NAD-dependent enzymes.     

Molecular clips based on diphenylglycoluril and benzocrown ethers: promising complexing agents for the alkali metal cations

The interaction of new molecular clips containing diphenylglycoluril and benzocrown ethers moieties with alkali metals ions was studied. Stability constants were determined by spectrophotometric titrations with chloride salts in methanol. Complex stability and cation binding selectivity were shown to be dependent on the size of the crown ether moiety. The “sandwich-type” 1:1 (clip to cation) complexes and the “classical” 1:2 complexes were found. Their ratio varies depending on the molecular clips nature and on the cation type. It was found an unexpected selectivity of the molecular clip with benzo-15-crown-5 moieties toward K⁺ and Rb⁺ cations. The molecular structure of the clip complex with benzo-15-crown-5 fragments and sodium picrate was determined by X-ray crystallography. The crystal structure and solution-state structure were proven to be similar.     

Diphtheria toxin catalyzed hydrolysis of NAD(+): molecular dynamics study of enzyme-bound substrate, transition state, and inhibitor.

The mechanism of the diphtheria toxin-catalyzed hydrolysis of NAD(+) was investigated by quantum chemical calculations and molecular dynamics simulations. Several effects that could explain the 6000-fold rate acceleration (Delta Delta G(++) approximately 5 kcal/mol) by the enzyme were considered. First, the carboxamide arm of the enzyme-bound NAD(+) adopts a trans conformation while the most stable conformation is cis. The most stable conformation for the nicotinamide product has the amide carbonyl trans. The activation energy for the cleavage of the ribosidic bond is reduced by 2 kcal/mol due to the relaxation of this ground state conformational stress in the transition state. Second, molecular dynamics simulations to the nanosecond time range revealed that the carboxylate of Glu148 forms a hydrogen bond to the substrate's 2' hydroxyl group in E.S (approximately 17% of the time) and E.TS (approximately 57% of the time) complexes. This interaction is not seen in crystal structures. The ApUp inhibitor is held more tightly by the enzyme than the transition state and the substrate. Analysis of correlated motions reveals differences in the pattern of anticorrelated motions for protein backbone atoms when the transition state occupies the active site as compared to the E.NAD(+) complex.     

Amperometric biosensor for ethanol based on immobilization of alcohol dehydrogenase on a nickel hexacyanoferrate modified microband gold electrode

Alcohol dehydrogenase (ADH) has been immobilized on a nickel hexacyanoferrate modified microband gold electrode surface by a glutaraldehyde/bovine serum albumin (BSA) cross-linking procedure to provide a new amperometric sensor for the assay of ethanol. The resulting enzyme electrode exhibits excellent electrocatalysis for the oxidation of reduced nicotinamide-adenine dinucleotide (NADH). The amperometric determination is based on the electrochemical detection of NADH which is generated in the enzymatic reaction of ethanol with NAD(+) under catalysis of ADH. The influence of various experimental conditions was examined for the determination of the optimum analytical performance. The sensor responds rapidly to ethanol with a detection limit of (5.0 +/- 0.3) x 10(-7) mol 1(-1). The response current increases linearly with ethanol concentration up to 5 mmol 1(-1). The sensor remains relatively stable for about 1 week.     

A modular system for regeneration of NAD cofactors using graphite particles modified with hydrogenase and diaphorase moieties

Pyrolytic graphite particles modified with hydrogenase and an NAD(+)/NADH cycling enzyme provide a modular heterogeneous catalyst system for regeneration of oxidised or reduced nicotinamide cofactors using H(2) and H(+) as electron source or sink. Particles can be tuned for cofactor supply under different conditions by appropriate choice of hydrogenase.     

Amperometric Methods for Oxidoreductase Enzymes Based on Liquid Chromatography with Electrochemical Detection. Alcohol Dehydrogenase

Abstract

Nicotinamide adenine dinucleotide (NAD) is an important cofactor in a number of oxidoreductase enzyme systems. The detection and quantitation of its reduced form (NADH) is the basis for a number of methods which determine both substrates and enzyme activity. Although electrochemical techniques have shown promise in this area, they have suffered from a lack of selectivity. Liquid chromatography with electrochemical detection (LCEC) provides the selectivity and the sensitivity required. The use of alcohol dehydrogenase (ADH) for blood alcohol detection is investigated as a model system.     

Biosynthesis of pipecolic acid by RapL, a lysine cyclodeaminase encoded in the rapamycin gene cluster

Rapamycin, FK506, and FK520 are immunosuppressant macrolactone natural products comprised of predominantly polyketide-based core structures. A single nonproteinogenic pipecolic acid residue is installed into the scaffold by a nonribosomal peptide synthetase that also performs the subsequent macrocyclization step at the carbonyl group of this amino acid. It has been assumed that pipecolic acid is generated from lysine by the cyclodeaminases RapL/FkbL. Herein we report the heterologous overexpression and purification of RapL and validate its ability to convert L-lysine to L-pipecolic acid by a cyclodeamination reaction that involves redox catalysis. RapL also accepts L-ornithine as a substrate, albeit with a significantly reduced catalytic efficiency. Turnover is presumed to encompass a reversible oxidation at the alpha-amine, internal cyclization, and subsequent re-reduction of the cyclic delta1-piperideine-2-carboxylate intermediate. As isolated, RapL has about 0.17 equiv of tightly bound NAD+, suggesting that the enzyme is incompletely loaded when overproduced in E. coli. In the presence of exogenous NAD+, the initial rate is elevated 8-fold with a Km of 2.3 microM for the cofactor, consistent with some release and rebinding of NAD+ during catalytic cycles. Through the use of isotopically labeled substrates, we have confirmed mechanistic details of the cyclodeaminase reaction, including loss of the alpha-amine and retention of the hydrogen atom at the alpha-carbon. In addition to the characterization of a critical enzyme in the biosynthesis of a medically important class of natural products, this work represents the first in vitro characterization of a lysine cyclodeaminase, a member of a unique group of enzymes which utilize the nicotinamide cofactor in a catalytic manner.     

Affinity partitioning of yeast and horse liver alcohol dehydrogenases in polyethylene glycol-dyes/dextran two-phase systems

Summary Affinity partition of yeast and horse liver alcohol dehydrogenases (ADH) in two-phase systems containing polyethylene glycol (PEG)-dyes is most effective using Cu(II) complexes of Light resistant yellow 2KT and Red-violet 2KT. The effects of NaCl, NAD and chelating agents (imidazole and adenine) on the partitioning of ADH's were studied. It was shown that two-phase systems containing dyes in the top and bottom phases with different affinity to yeast ADH are promising for the extraction of enzyme from crude extract.     

A Rigidoporus Vinctus Alcohol Dehydrogenase and Its Characterization

Alcohol dehydrogenases (ADHs; E.C. 1.1.1.1) are widely distributed enzymes found in many microorganisms. ADHs are oxidoreductases that catalyze the NAD(P)⁺‐dependent conversion of alcohols to aldehydes or ketones as well as the reverse reaction. The ADH cloned from Rigidoporus vinctus (RvADH) was 1035 bp that encodes a protein of 344 amino acid residues with calculated molecular mass of 38.39 kDa. This ADH is belonging to the medium‐chain family (medium‐chain dehydrogenase/reductase (MDR) and has the highly conserved GXXGXXG sequence found in the MDR family which found as the coenzyme‐binding pocket. To characterize the ADH protein, the coding region was subcloned into an expression vector pET‐20b(+) and transformed into E. coli Rosetta (DE3). The recombinant His6‐tagged ADH was overexpressed and purified by Ni²⁺‐nitrilotriacetic acid Sepharose. The purified enzyme showed one band on 12 % sodium dodecyl sulfate‐polyacrylamide gel electrophoresis. The Michaelis constant (K_M) value of the recombinant enzyme for ethanol was 0.79 mM. In substrates specificity analysis showed that RvADH had great oxidative activity toward primary alcohols. However, the less activtiy toward secondary alcohols and alcohol derivatives were compared with ethanol. Regarding the reductase activity showed low or even no activity to aldehydes and ketone.     

Synthesis and complexation of molecular clips based on diphenylglycoluril and dibenzocrown ethers with alkali metal cations and paraquat

A new synthetic route to the molecular clip with diphenylglycoluril and dibenzo-18-crown-6 using protection-deprotection protocol is proposed. Yield of desired compound has increased from 10-15% to 41%. Starting from 4,5-dibromobenzene-1,2-diol 4,5-dibromodibenzo-18-crown-6 and then tetrabromo-substituted molecular clip were obtained. The target molecular clip was obtained by bromine cleavage by hydrogenolysis. Stability constants were determined by spectrophotometric titration with alkali metal cations and paraquat. Quantum-chemical calculations confirm the assumption of additional stabilization of complex with K⁺ by π–π stacking between the terminal aromatic fragments with formation of a “pseudocryptand” type structure. The structures of complexes of the molecular clips with paraquat were determined by X-ray crystallography.     

Drastic difference in the photo-driven hydrogenation reactions of ruthenium complexes containing NAD model ligands

Successful control of photo-driven NAD(+)/NADH type hydrogenation reactions in ruthenium complexes has been accomplished by using a new NAD(+) model ligand with modulated distortion of the ligand taking advantage of the substituent effect.     

A Modular Phosphorylated Glycoluril-Derived Molecular Tweezer for Potent Binding of Aliphatic Diamines

A molecular tweezer based on a glycoluril-derived framework bearing four phosphate groups was synthesized and shown to be capable of binding organic amines in aqueous solution. This work reports the K_a values for 30 complexes of this molecular tweezer and amine guests, determined by means of ¹H NMR titrations. Both the hydrophobic cavity and the phosphate groups contribute to the binding. Bulkier molecules and molecules bearing negatively charged groups like carboxylates in amino acids bind less tightly due to a steric clash and coulombic repulsion. The narrow cavity and the strong ionic interactions of the phosphate groups with ammonium guests favor binding of aliphatic diamines. These binding properties clearly distinguish this system from structurally related molecular clips and tweezers.     

Coenzyme Regeneration in Hexanol Oxidation Catalyzed by Alcohol Dehydrogenase

The enzymatic ways of coenzyme regeneration include the addition of a second enzyme to the system or the addition of the co-substrate. In the present study, both methods of enzymatic coenzyme (NAD⁺) regeneration were studied and compared in the reaction of hexanol oxidation catalyzed by alcohol dehydrogenase (ADH). As a source of ADH, commercial isolated enzyme and the whole baker??s yeast cells were used. First, coenzyme regeneration was employed in the reaction of acetaldehyde reduction catalyzed by the same enzyme that catalyzed the main reaction, and then NAD⁺ regeneration was applied in the reaction of pyruvate reduction catalyzed by l-lactate dehydrogenase (l-LDH). Hexanal was obtained as the product of hexanol oxidation catalyzed by isolated ADH while hexaonic acid was detected as a product of the same reaction catalyzed by baker??s yeast cells. All of the used biocatalysts were kinetically characterized. The mass reactions were described by the mathematical models. All models were validated in the batch reactor. One hundred percent hexanol conversion was obtained using permeabilized yeast cells using both methods of cofactor regeneration. By using isolated enzyme ADH, the higher conversion was achieved in a system with cofactor regeneration catalyzed by l-LDH.     

Molecular clips based on propanediurea: exceptionally high binding affinities for resorcinol guests

A series of new receptor molecules derived from 2,4,6,8-tetraazabicyclo[3.3.1]nonane-3,7-dione (propanediurea) is described. These molecules possess a cavity which is defined by two nearly parallel aromatic side walls positioned on top of a bis-urea framework. The resulting "U-shaped" clip molecules are ideal hosts for the complexation of flat aromatic guest molecules. The affinity of these new propanediurea based molecular clips for dihydroxybenzene derivatives is exceptionally high, with association constants up to K(a) = 2 400 000 L mol(-)(1). Comparison of the binding mechanism of a variety of clip and half clip hosts, in conjunction with NMR, IR, and X-ray studies, has enabled the reason for this high binding to be elucidated. It is shown that subtle sub-angstrom changes in the geometry of the clip molecules have a great impact on their binding properties.     

Mutation of Tyr-218 to Phe in <Emphasis Type="Italic">Thermoanaerobacter ethanolicus</Emphasis> Secondary Alcohol Dehydrogenase: Effects on Bioelectronic Interface Performance

Bioelectronic interfaces that facilitate electron transfer between the electrode and a dehydrogenase enzyme have potential applications in biosensors, biocatalytic reactors, and biological fuel cells. The secondary alcohol dehydrogenase (2° ADH) from Thermoanaerobacter ethanolicus is especially well suited for the development of such bioelectronic interfaces because of its thermostability and facile production and purification. However, the natural cofactor for the enzyme, β-nicotinamide adenine dinucleotide phosphate (NADP⁺), is more expensive and less stable than β-nicotinamide adenine dinucleotide (NAD⁺). PCR-based, site-directed mutagenesis was performed on 2° ADH in an attempt to adjust the cofactor specificity toward NAD⁺ by mutating Tyr²¹⁸ to Phe (Y218F 2° ADH). This mutation increased the K _m(app) for NADP⁺ 200-fold while decreasing the K _m(app) for NAD⁺ 2.5-fold. The mutant enzyme was incorporated into a bioelectronic interface that established electrical communication between the enzyme, the NAD⁺, the electron mediator toluidine blue O (TBO), and a gold electrode. Cyclic voltammetry, impedance spectroscopy, gas chromatography, mass spectrometry, constant potential amperometry, and chronoamperometry were used to characterize the mutant and wild-type enzyme incorporated in the bioelectronic interface. The Y218F 2° ADH exhibited a fourfold increase in the turnover ratio compared to the wild type in the presence of NAD⁺. The electrochemical and kinetic measurements support the prediction that the Rossmann fold of the enzyme binds to the phosphate moiety of the cofactor. During the 45 min of continuous operation, NAD⁺ was electrically recycled 6.7 × 10⁴ times, suggesting that the Y218F 2° ADH-modified bioelectronic interface is stable.     

Electrical communication between electrode and dehydrogenase by a ferrocene-labeled high molecular-weight cofactor derivative: application to a reagentless biosensor

A ferrocene-labeled high molecular weight cofactor derivative (PEI-Fc-NAD) was prepared by attaching both ferrocene and nicotinamide adenine dinucleotide (NAD⁺) to a water soluble polyelectrolyte, polyethylenimine (PEI). Approximately 9.8% and 2.9% of all the primary amino groups of PEI were coupled with ferrocene and the bioactive cofactor, respectively. The cyclic voltammograms of PEI-Fc-NAD exhibited a one-electron transfer process, and the difference between the anodic and cathodic peak potential was found to be 80 mV. The PEI-Fc-NAD was used together with NAD-dependent dehydrogenase to construct a reagentless biosensor. An NAD-dependent alcohol dehydrogenase (ADH) was selected as the model enzyme, and both ADH and PEI-Fc-NAD were retained onto the sensing area of gold electrodes by a dialysis membrane or immobilized by layer-by-layer adsorption method. In both cases, the modified electrodes showed current response to ethanol without the addition of native NAD⁺ to the system, which suggested that the electrical communication between ADH and the electrode was achieved through PEI-Fc-NAD. In summary, PEI-Fc-NAD provides a new way for immobilization of mediator and cofactor, and exhibits the potential as a platform for constructing reagentless NAD-dependent dehydrogenase biosensors.