Hemoglobin-mediated nitric oxide signaling

The rate that hemoglobin reacts with nitric oxide (NO) is limited by how fast NO can diffuse into the heme pocket. The reaction is as fast as any ligand/protein reaction can be and the result, when hemoglobin is in its oxygenated form, is formation of nitrate in what is known as the dioxygenation reaction. As nitrate, at the concentrations made through the dioxygenation reaction, is biologically inert, the only role hemoglobin was once thought to play in NO signaling was to inhibit it. However, there are now several mechanisms that have been discovered by which hemoglobin may preserve, control, and even create NO activity. These mechanisms involve compartmentalization of reacting species and conversion of NO from or into other species such as nitrosothiols or nitrite which could transport NO activity. Despite the tremendous amount of work devoted to this field, major questions concerning precise mechanisms of NO activity preservation as well as if and how Hb creates NO activity remain unanswered.     

Rapeseed oil methyl esters preparation using heterogeneous catalysts

The classical method of fatty acids methyl esters (FAME) production is based on triglyceride transesterification to methyl esters. Sodium hydroxide dissolved in methanol is used as a catalyst. The purpose of this work was to examine a heterogeneous catalyst, in particular calcium compounds, to produce methyl esters of rapeseed oil. This research showed that the transesterification of rapeseed oil by methyl alcohol can be catalysed effectively by basic alkaline-earth metal compounds: calcium oxide, calcium methoxide and barium hydroxide. Calcium catalysts, due to their weak solubility in the reaction medium, are less active than sodium hydroxide. However, calcium catalysts are cheaper and lead to decreases in the number of technological stages and the amount of unwanted waste products. It was found that the transesterification reaction rate can be enhanced by ultrasound as well as by introducing an appropriate reagent into a reactor to promote methanol solubility in the rapeseed oil. Tetrahydrofuran was used as additive to accelerate the transesterification process.     

How does the push/pull effect of the axial ligand influence the catalytic properties of Compound I of catalase and cytochrome P450?

Density functional theory (DFT) calculations on the chemoselective epoxidation versus hydroxylation reactions of propene by oxoiron porphyrin models mimicking the active sites of catalase, cytochrome P450 (P450) and horseradish peroxidase Compound I (CpdI) are presented. The catalase reactions are concerted and proceed via two-state reactivity patterns on competing doublet and quartet spin state surfaces, but the lowest barrier is the one leading to epoxide products on the doublet spin surface. The results are compared with earlier DFT studies of models of cytochrome P450, horseradish peroxide (HRP), taurine/alpha-ketoglutarate dioxygenase and some synthetic oxoiron catalysts. The catalase barriers are midway in between those obtained for HRP and P450 models, so that tyrosinate ligated heme systems should be able to catalyze C-H hydroxylation and C=C epoxidation reactions. We show that for heme systems the barrier height of epoxidation linearly correlates with the electron affinity of Compound I as expected from the electron transfer mechanism of the rate determining step. Our studies show that the axial ligand does not influence the chemoselectivity of a reaction but that it does regulate the barrier heights and rate constants. Finally, we estimated the effect of the axial ligand on the oxoiron group and derived that it contributes from a field effect due to the charge of the ligand and a quantum mechanical effect as a result of orbital mixing. In catalase, the major component is the field effect, while the quantum mechanical effect is negligible. This is in contrast to P450 CpdI, where both effects are of similar order of magnitude.     

The reaction of nitrogen monoxide with the haemocyanins of the crayfish Astacus leptodactylus and the snail Helix pomatia.

The rate of the reaction of Astacus leptodactylus methaemocyanin with NO follows the Henderson-Hasselbalch equation with a pKa of 5.85, suggesting that one imidazole ligand of Cu was exchanged for NO. The reaction is blocked by F- as a bridging ligand. The same imidazole residue might be responsible for the decomposition of nitrosylhaemocyanin, [Cu1NO+CuII], with an unlocated binding site for NO, into methaemocyanin and NO, as the rate increase with pH. NO could react preferentially with CuA of Helix pomatia methaemocyanin, CuA'IICuBII, as it possibly has only two histidine ligands instead of the three of CuA in Astacus haemocyanin. This difference might explain the higher formation rate and the much greater stability of Helix nitrosylhaemocyanin. The fast reaction is governed by a pKa of 6.80, probably of a bridging mu-aquo ligand. With F- or a mu-hydroxo bridging ligand a low reaction rate was still observed, in contrast with Astacus methaemocyanin. Helix nitrosylhaemocyanin was transformed by N3- into methaemocyanin with the liberation of N2 and N2O. This methaemocyanin could almost quantitatively be regenerated with H2O2. Helix nitrosylhaemocyanin was only partially regenerated by a direct treatment with H2O2 and almost quantitatively by HONH2 in a similar fairly fast reaction, followed by a much slower one.     

Biomimetic asymmetric hydrogenation.

Enzymes and synthetic organometallic catalysts utilize different approaches for the creation of chiral centers in prochiral substrates. While chiral organometallic catalysts realize the transfer of chirality mainly by repulsive interactions, several enzymes use preferentially stereodiscriminating hydrogen bonding. To investigate if hydrogen bonding within the catalyst-substrate assembly can also have a benefit on the rhodium diphosphine-catalyzed asymmetric hydrogenation, some model metal complexes and substrates were investigated. As 'biomimetically acting' functionalities, hydroxy groups were incorporated in the chiral ligand. Three secondary interactions could be identified by different analytical methods which influence rate and enantioselectivity of the catalytic reaction: 1) HO/Rh-interactions, 2) HO/HO-interactions within the backbone of the ligand, and 3) hydrogen bonding between HO-groups of the ligand and functional groups of an appropriate substrate. Due to the effect of the additional hydroxy groups, enantioselectivities by up to 99% ee could be induced in the hydrogenation product even with water as solvent.     

Application of immobilized hydrogenase for the detritiation of water

Detritiation of contaminated water is an essential part of nuclear power production. Most promising methods used for this process are based on catalyzed hydrogen isotope exchange reactions. It is proposed herein to replace the platinum catalysts which are currently used in industry with immobilized hydrogenase. Whole bacterial cells of Alcaligenes eutrophus immobilized in calcium alginate or κ-carrageenan gels were found to be efficient catalysts of the reaction of hydrogen–tritium (H–T) exchange in both a batch tank reactor and in a column. The dependence of the reaction rate on the amount of immobilized cells in the system, and on the concentration of the cells in the matrix, indicate that enzymatic H–T exchange is not controlled by diffusion. Immobilized A. eutrophus cells are enzymatically active over a wide range of pH, with a broad maximum from pH 6.0 to 8.0, and are quite resistant to inhibitors of hydrogenases such as O₂ and CO. Upon increasing the temperature from 4 to 37°C, the rate of hydrogenase-catalyzed H–T exchange increases by a factor of 5. From the standpoint of catalytic efficiency, 1 g of PtO₂ is approximately equivalent to 10 g of cells (wet weight). In contrast of platinum-based catalysts, bacterial hydrogenases (1) are potentially inexpensive; (2) can be readily available in bulk quantities; (3) are maximally active in liquid water.     

Procedures for the analysis of cyanogen bromide-activated Sepharose or Sephadex by quantitative determination of cyanate esters and imidocarbonates

Analytical methods have been developed for the determination of cyanate esters and imidocarbonates, the active species present on CNBr-activated polysaccharide resins. Imidocarbonates are determined by selective acid hydrolysis followed by determination of the liberated ammonia by a modification of the ninhydrin reaction. Cyanate esters are determined by a spectrophotometric procedure based on the reaction with pyridine and employing N,N'-dimethylbarbituric acid as a color-forming reagent. For the determination of the coupling capacity, a procedure is suggested which allows the amount of coupled ligand to be determined directly on the resin and without prior hydrolysis. Using those procedures it was found that the coupling capacity of activated resins toward small ligands can be predicted by determining the amounts of cyanate esters and imidocarbonates present on the resin, and that cyanate esters are predominantly responsible for coupling of ligand to activated Sepharose.     

Gold compounds for catalysis and metal-mediated transformations in biological systems

One of the challenges of modern inorganic chemistry is translating the potential of metal catalysts to living systems to achieve controlled non-natural transformations. This field poses numerous issues associated with the metal compounds biocompatibility, stability, and reactivity in complex aqueous environment. Moreover, it should be noted that although referring to ‘metal catalysis’, turnover has not yet been fully demonstrated in most of the examples within living systems. Nevertheless, transition metal catalysts offer an opportunity of modulating bioprocesses through reactions that are complementary to enzymes. In this context, gold complexes, both coordination and organometallic, have emerged as promising tools for bio-orthogonal transformations, endowed with excellent reactivity and selectivity, compatibility within aqueous reaction medium, fast kinetics of ligand exchange reactions, and mild reaction conditions. Thus, a number of examples of gold-templated reactions in a biologically relevant context will be presented and discussed here in relation to their potential applications in biological and medicinal chemistry.     

Identification of a stable flavin-thiolate adduct in heterotetrameric sarcosine oxidase

Heterotetrameric sarcosine oxidase (TSOX) is a complex bifunctional flavoenzyme that contains two flavins. Most of the FMN in recombinant TSOX is present as a covalent adduct with an endogenous ligand. Enzyme denaturation disrupts the adduct, accompanied by release of a stoichiometric amount of sulfide. Enzyme containing>or=90% unmodified FMN is prepared by displacement of the endogenous ligand with sulfite, a less tightly bound competing ligand. Reaction of adduct-depleted TSOX with sodium sulfide produces a stable complex that resembles the endogenous TSOX adduct and known 4a-S-cysteinyl flavin adducts. The results provide definitive evidence for sulfide as the endogenous TSOX ligand and strongly suggest that the modified FMN is a 4a-sulfide adduct. A comparable reaction with sodium sulfide is not detected with other flavoprotein oxidases. A model of the postulated TSOX adduct suggests that it is stabilized by nearby residues that may be important in the electron transferase/oxidase function of the coenzyme.     

Microscopic description of voltage effects on ion-driven cotransport systems

A microscopic model for the analysis of voltage effects on ion-driven cotransport systems is described. The model is based on the notion that the voltage dependence of a given rate constant is directly related to the amount of charge which is translocated in the corresponding reaction step. Charge translocation may result from the movement of an ion along the transport pathway, from the displacement of charged ligand groups of the ion-binding site, or from reorientation of polar residues of the protein in the course of a conformational transition. The voltage dependence of overall transport rate is described by a set of dimensionless coefficients reflecting the dielectric distances over which charge is displaced in the elementary reaction steps. The dielectric coefficients may be evaluated from the shape of the experimental flux-voltage curve if sufficient information on the rate constants of the reaction cycle is available. Examples of flux-voltage curves which are obtained by numerical simulation of the transport model are given for a number of limiting cases.     

Mechanism of the cobalt-catalyzed carbonylation of ethyl diazoacetate

Carbonyl cobalt complexes serve as catalysts or catalyst precursors for the facile and selective transformation of primary diazoalkanes into the corresponding ketene. The mechanism of this carbonylation reaction has been elucidated in the case of ethyl diazoacetate as model diazoalkane using octacarbonyl dicobalt as the catalyst precursor. Dinuclear cobalt complexes having ethoxycarbonylcarbene ligand(s) in bridging position(s) have been identified as active intermediary of the catalytic cycles and their relevant chemical properties have been explored. Key step of the carbonylation is the formation of the highly reactive ethoxycarbonylketene by intramolecular coupling of a carbonyl ligand with the ethoxycarbonylcarbene ligand. DFT calculations reveal that the ketene formation takes place via a rapid coupling of the carbene ligand with one terminal CO followed by coordination of an external carbon monoxide and by a facile intramolecular rearrangement and ketene elimination. The ethoxycarbonylketene can be in situ trapped by OH, NH, or CH acid compounds or by N-substituted imines. In the presence of ethanol diethyl malonate is the only product of the catalytic carbonylation of ethyl diazoacetate. On the bases of the kinetics of the composing steps of the catalytic cycles, localization of the rate-determining step(s) under various reaction conditions has been made.     

Mathematical modeling of precipitation and dissolution reactions in microbiological systems

We expand the biogeochemical model CCBATCH to include a precipitation/dissolution sub-model that contains kinetic and equilibrium options. This advancement extends CCBATCH's usefulness to situations in which microbial reactions cause or are affected by formation or dissolution of a solid phase. The kinetic option employs a rate expression that explicitly includes the intrinsic kinetics for reaction ormass-transport control, the differencefrom thermodynamic equilibrium, and the aqueous concentration of the rate-limiting metal or ligand. The equilibrium feature can be used alone, and it also serves as check that the kinetic rate never is too fast and ``overshoots' equilibrium. The features of the expanded CCBATCH are illustrated by an example in which the precipitation of Fe(OH)_{3 (s)} allows the biodegradation of citric acid, even though complexes are strong and not bioavailable. Precipitation releases citrate ligand, and biodegradation of the citrate increases the pH.     

Stochastic problems in information transfer across the plasma membrane

The surfaces of many cells are viscous fluids; consequently, most membrane proteins are able to diffuse laterally, in a more or less random fashion, with diffusion coefficients typically of order 10⁻¹⁰ cm²/sec. If a molecule (ligand) in solution outside the cell and a protein molecule on the surface (receptor) each have two or more sites at which they can interact with one another, large, branched receptor-ligand networks can form on the cell surface by virtue of the chemical interactions that surface fluidity permits. Evidence from a variety of systems indicates that such receptor clustering plays a role in the sequence of events leading to cellular activity. This paper describes a number of mathematical problems that arise in the analysis of experiments in which clustering occurs. I begin by reviewing methods for finding the time evolution of the cluster size distribution function in terms of reaction rate constants. The methods solve an essentially infinite system of coupled nonlinear differential equations. Next, the rate constants are analyzed, the Brownian motion problems that arise in attempting to understand ligand recognition are described and relevant experimental systems are discussed. Finally the notion of ligand as a signal amplifier is introduced—an idea that emerges naturally from the requirement that receptors be clustered for a finite amount of time before a signal can be transmitted.     

Cytochrome P-450-dependent 14 alpha-demethylation of lanosterol in Candida albicans.

Analysis of receptor-ligand binding characteristics can be greatly hampered by the presence of non-specific binding, defined as low-affinity binding to non-receptor domains which is not saturable within the range of ligand concentrations used. Conventional binding analyses, e.g. according to the methods described by Scatchard or Klotz, relate the amount of specific receptor-ligand binding to the concentration of free ligand, and therefore require assumptions on the amount of non-specific binding. In this paper a method is described for determining the parameters of specific receptor-ligand interaction which does not require any assumption or separate determination of the amount of non-specific binding. If the concentration of labelled free ligand is constant, a plot of Fu/(B0*-B*) versus Fu yields a linear relationship, in the case of a single receptor class, in which Fu is the concentration of unlabelled free ligand, B0* is the total amount of labelled bound ligand in the absence of unlabelled ligand and B* is the total amount of labelled bound ligand in the presence of an unlabelled ligand concentration Fu; all of these data are readily obtained from binding studies. This linear relationship holds irrespective of the amount of non-specific binding, and the values for receptor density, ligand dissociation constant and a constant for non-specific binding can be readily obtained from it. If the concentration of labelled free ligand is not a constant for all data points, data are first converted according to a straightforward normalization procedure to permit the use of this relationship. The presence of multiple receptor classes with dissociation constants in the range of the ligand concentrations used results in a negative deviation from this linearity, and therefore the presence of multiple receptor classes can be discriminated unequivocally from non-specific binding. Both theoretical and practical advantages of the present method are described. The method, which will be referred to as the linear subtraction method, is illustrated using the binding of tumour promoters and polypeptide growth factors to their specific cellular receptors.     

Effects of thermodynamic nonideality in ligand binding studies

Effects of thermodynamic nonideality are considered in relation to the quantitative characterization of the interaction between a small ligand. S, and a macromolecular acceptor. A, by two types of experimental procedure. The first involves determination of the concentration of ligand in dialysis equilibrium with the acceptor/ligand mixture, and the second, measurement of the concentration of unbound ligand in the reaction mixture by ultrafiltration or the rate of dialysis method. For each situation explicit expressions are formulated for the appropriate binding function with allowance for composition-dependent nonideality effects expressed in terms of molar volume, charge-charge interaction and covolume contributions. The magnitudes of these effects are explored with the aid of experimental studies on the binding of tryptophan and of methyl orange to bovine serum albumin. It is concluded for experiments conducted utilizing either equilibrium dialysis or frontal gel chromatography that, provided a correction is made for any Donnan redistribution of ligand, theoretically predicted acceptor-concentration dependence is likely to be negligible and that use of the conventional binding equation written for an ideal system is appropriate to the analysis of the results. Use of ultrafiltration or the rate of dialysis method requires examination of the assumption that the activity coefficient ratio y(A)y(s)/y(AS) for the reaction mixture approximates unity; but again reassurance is provided that nonideality manifested as a dependence of the binding function on acceptor concentration is unlikely to be significant.     

Labeling study of avidin by modular method for affinity labeling (MoAL)

We studied the specific labeling of avidin with biotinylated modular ligand catalysts via MoAL, which we recently established. The labeling yield was found to depend on the linker length connecting the catalytic site to biotin in the modular ligand catalyst 1, and the maximum yield was obtained with 1d possessing octamethylene linker. The labeling reaction reached a maximum rate with only 4 equiv of the ligand catalyst. Presumably, all the subunits of avidin with homotetrameric structure formed a stable complex with 4 equiv of the catalyst because of the extremely high affinity. The ligand catalyst bound to avidin first catalyzed N-triazinylation of the ε-amino group of Lys111, and the resulting regenerated catalyst then catalyzed the reaction of Asp108 and CDMT.     

Real-time kinetic analysis of hCG–monoclonal antibody interaction using radiolabeled hCG probe: presence of two forms of Ag–mAb complex as revealed by solid phase dissociation studies

Real-time kinetics of ligand–ligate interaction has predominantly been studied by either fluorescence or surface plasmon resonance based methods. Almost all such studies are based on association between the ligand and the ligate. This paper reports our analysis of dissociation data of monoclonal antibody-antigen (hCG) system using radio-iodinated hCG as a probe and nitrocellulose as a solid support to immobilize mAb. The data was analyzed quantitatively for a one-step and a two-step model. The data fits well into the two-step model. We also found that a fraction of what is bound is non-dissociable (tight-binding portion (TBP)). The TBP was neither an artifact of immobilization nor does it interfere with analysis. It was present when the reaction was carried out in homogeneous solution in liquid phase. The rate constants obtained from the two methods were comparable. The work reported here shows that real-time kinetics of other ligand–ligate interaction can be studied using nitrocellulose as a solid support.     

The forward rate of binding of surface-tethered reactants: effect of relative motion between two surfaces

The reaction of molecules confined to two dimensions is of interest in cell adhesion, specifically for the reaction between cell surface receptors and substrate-bound ligand. We have developed a model to describe the overall rate of reaction of species that are bound to surfaces under relative motion, such that the Peclet number is order one or greater. The encounter rate between reactive species is calculated from solution of the two-dimensional convection-diffusion equation. The probability that each encounter will lead to binding depends on the intrinsic rate of reaction and the encounter duration. The encounter duration is obtained from the theory of first passage times. We find that the binding rate increases with relative velocity between the two surfaces, then reaches a plateau. This plateau indicates that the increase in the encounter rate is counterbalanced by the decrease in the encounter duration as the relative velocity increases. The binding rate is fully described by two dimensionless parameters, the Peclet number and the Damk?hler number. We use this model to explain data from the cell adhesion literature by incorporating these rate laws into "adhesive dynamics" simulations to model the binding of a cell to a surface under flow. Leukocytes are known to display a "shear threshold effect" when binding selectin-coated surfaces under shear flow, defined as an increase in bind rate with shear; this effect, as calculated here, is due to an increase in collisions between receptor and ligand with increasing shear. The model can be used to explain other published data on the effect of wall shear rate on the binding of cells to surfaces, specifically the mild decrease in binding within a fixed area with increasing shear rate.     

Importance of surface properties of affinity resin for capturing a target protein,Cyclooxygenase-1

We have prepared affinity resins based on two kinds of solid phases, including a commercially available solid phase, to re-realize the importance of surface properties of affinity resins such as controlled ligand density as well as existential surroundings of the ligand. Affinity resins were prepared using non-steroidal anti-inflammatory drugs, such as Ketoprofen, Ibuprofen, and Aspirin, having different activities as ligands. The ligand density was controlled through two different strategies: one strategy was that the solid phases having different amino group densities (20, 60, 100, 125 μmol/ml) were utilized then, Ketoprofen was fully immobilized through condensation reaction to amino groups; another strategy was that a solid phase having amino group density (125 μmol/ml) was utilized then, each ligand was immobilized with controlled immobilization rate. In addition, a typical hydrophobic group, stearoyl group (C₁₈ group), was immobilized on the affinity resin with controlled ligand immobilization rate to change the existential surroundings of the ligand. Affinity tests were performed for Cyclooxgenase-1 (COX-1) as it was the target protein in this work. The amount of captured COX-1 was evaluated utilizing each affinity resin. It was suggested that the density of surface ligand tends to relate to the amount of captured COX-1 on our solid phase-based affinity resins; however, several exceptions occurred according to the surface properties of affinity resins in the case of commercial one.