Variation in the sequence of a mitochondrial nadh dehydrogenase i gene fragment among six natural populations of Schistosoma japonicum from China

The present study investigated the level of genetic variation among Schistosoma japonicum populations of different geographical origins from mainland China. Polymerase chain reaction-based methods were employed to determine the sequence for a subunit of the mitochondrial NADH dehydrogenase I gene for populations from Zhejiang, Anhui, Jiangxi, Hunan, Hubei and Sichuan. No variation was detectable in the NADH dehydrogenase I sequence within populations from Zhejiang and Hubei, whereas sequence variation of 0.2% was detected within populations from Anhui, Jiangxi, Hunan and Sichuan. Pairwise comparison of the sequences representing the six different populations revealed genetic differences ranging from 0 to 0.6%.     

Reversible dissociation of flavin mononucleotide from the mammalian membrane-bound NADH: ubiquinone oxidoreductase (complex I)

Conditions for the reversible dissociation of flavin mononucleotide (FMN) from the membrane-bound mitochondrial NADH:ubiquinone oxidoreductase (complex I) are described. The catalytic activities of the enzyme, i.e. rotenone-insensitive NADH:hexaammineruthenium III reductase and rotenone-sensitive NADH:quinone reductase decline when bovine heart submitochondrial particles are incubated with NADH in the presence of rotenone or cyanide at alkaline pH. FMN protects and fully restores the NADH-induced inactivation whereas riboflavin and flavin adenine dinucleotide do not. The data show that the reduction of complex I significantly weakens the binding of FMN to protein thus resulting in its dissociation when the concentration of holoenzyme is comparable with K(d ( approximately 10(-8)M at pH 10.0).     

A novel strong competitive inhibitor of complex I

Alkaline incubation of NADH results in the formation of a very potent inhibitor of complex I (NADH:ubiquinone oxidoreductase). Mass spectroscopy (molecular mass equal to 696) and absorption spectroscopy suggest that the inhibitor is derived from attachment of two oxygen atoms to the nicotinamide moiety of NADH. The inhibitor is competitive with respect to NADH with a K(i) of about 10(-8)M. The inhibitor efficiently suppresses NADH-oxidase, NADH-artificial acceptor reductase, and NADH-quinone reductase reactions catalyzed by submitochondrial particles, as well as the reactions catalyzed by either isolated complex I or the three subunit flavoprotein fragment of complex I.     

Relation of NADH/NAD to contraction in vascular smooth muscle

The relationship of NADH/NAD to O2 consumption with respect to the different phases of contraction in vascular smooth muscle in response to a maximal depolarizing concentration of KCl was investigated. The NADH bound to cellular proteins could be distinguished from free NADH in whole tissue homogenates. Evidence suggested that the NADH was bound to pyruvate dehydrogenase and perhaps to other dehydrogenases since binding paralleled the changes in the activity of pyruvate dehydrogenase with contraction. The measured changes in NADH were attributed to that within the mitochondrial compartment since the contribution of reducing equivalents within the cytoplasmic compartment was negligible. During the phase of contraction in which force was initially being generated and at which O2 consumption was the highest, there was a net increase in NADH/NAD. After stable isometric force was maintained, at which time O2 consumption had returned to slightly above the basal pre-contraction level, there was a net decrease in NADH/NAD. Previous evidence indicates the phosphorylation potential (ATP/ADP) may decrease during this phase of contraction. It is concluded that contraction of vascular smooth muscle is accompanied by a changing pool of reducing equivalents. Factors which govern O2 consumption may change during the different phases of muscle contraction.     

Contributions of active site residues to cofactor binding and catalysis of 3α-hydroxysteroid dehydrogenase/carbonyl reductase

3α-Hydroxysteroid dehydrogenase/carbonyl reductase reversely catalyzes the oxidation of androsterone with NAD⁺ to form androstanedione and NADH. In this study, we investigated the function of active site residues N86, Y155, and K159 in NADH binding and catalysis in the reduction of androstanedione, using site-directed mutagenesis, steady-state kinetics, fluorescence quenching, and anisotropy measurements. The N86A, Y155F, and K159A mutant enzymes decreased the catalytic constant by 37- to 220-fold and increased the dissociation constant by 3- to 75-fold, respectively. Binding of NADH with wild-type and mutant enzymes caused different levels of fluorescence resonance energy transfer, implying a different orientation of nicotinamide ring versus W173. In addition, the enzyme-bound NADH decreased the fluorescence anisotropy value in the order WT > N86A > Y155F > K159A, indicating an increase in the mobility of the bound NADH for the mutants. Data suggest that hydrogen bonding with the hydroxyl group of nicotinamide ribose by K159 and Y155 is important to maintain the orientation of NADH and contributes greatly to the transition-state binding energy to facilitate the catalysis. N86 is important for stabilizing the position of K159. Substitution of alanine for N86 has a minor effect on NADH binding through K159, resulting in a slight increase in the mobility of the bound NADH and decreases in affinity and catalytic constant.     

Inhibition of Lactate Production in Rat Brain Extracts and Synaptosomes by 3-[4-(Reduced 3-Pyridine Aldehyde-Adenine Dinucleotide)]-Pyruvate

In basic solutions, pyruvate enolizes and reacts (through its 3-carbon) with the 4-carbon of the nicotinamide ring of NAD+, yielding an NAD-pyruvate adduct in which the nicotinamide ring is in the reduced form. This adduct is a strong inhibitor of lactate dehydrogenase, presumably because it binds simultaneously to the NADH and pyruvate sites. The potency of the inhibition, however, is muted by the adduct's tendency to cyclize to a lactam. We prepared solutions of the pyruvate adduct of NAD+ and of NAD+ analogues in which the -C(O)NH2 of NAD+ was replaced with -C(S)NH2, -C(O)CH3, and -C(O)H. Of the four, only the last analogue, 3-[4-(reduced 3-pyridine aldehyde-adenine dinucleotide)]-pyruvate (RAP) cannot cyclize and it was found to be the most potent inhibitor of beef heart and rat brain lactate dehydrogenases. The inhibitor binds very tightly to the NADH site (Ki approximately 1 nM for the A form). Even at high concentrations (20 microM), RAP had little or no effect on rat brain glyceraldehyde-3-phosphate, pyruvate, alpha-ketoglutarate, isocitrate, soluble and mitochondrial malate, and glutamate dehydrogenases. The glycolytic enzymes, hexokinase and phosphofructokinase, were similarly unaffected. RAP strongly inhibited lactate production from glucose in rat brain extracts but was less effective in inhibiting lactate production from glucose in synaptosomes.     

Aniline hydroxylase activities of haemoglobin: Kinetics and mechanism

The mechanism of the aniline hydroxylase activity of methaemoglobin in a monooxygenase system consisting of NADH as electron donor, riboflavin, FAD, FMN or methylene blue as electron carrier and methaemoglobin as the terminal oxidase has been studied. Hydrogen peroxide is produced from oxygen in a methaemoglobin-independent process. 4-Aminophenol is subsequently produced peroxidatively by an NADH-dependent process; NADH prevents a further oxidation of 4-aminophenol in the presence of haemoglobin. In the absence of electron carrier, NADH slowly reduces haemoglobin and then oxyhaemoglobin reacts with aniline to give 4-aminophenol. In the absence of electron donor and electron carrier, oxyhaemoglobin and aniline give rise to the reversible production of 4-aminophenol.     

Reconstituted mitochondrial transhydrogenase is a transmembrane protein

Bovine heart mitochondrial transhydrogenase, a redox-linked proton pump, can be functionally and asymmetrically inserted into liposomes by a cholate-dialysis procedure such that the active site faces the external medium. N-(4-Azido-2-nitrophenyl)-2-aminoethylsulfonate (NAP-taurine), a membrane-impermeant photoprobe, when encapsulated in the vesicles, covalently modified the enzyme and inhibited transhydrogenation between NADPH and the 3-acetylpyridine analog of NAD+ (AcPyAD+) in a light-dependent manner. External AcPyAD+ increased the rate of inactivation several fold, whereas NADPH, NADP+, and NADH were without effect. Labeling of the enzyme by intravesicular [35S]NAP-taurine was enhanced by AcPyAD+ and NADP+, decreased by NADH, and not significantly affected by NADPH. These results indicate that transhydrogenase spans the membrane and that substrate binding alters the conformation of that domain of the enzyme protruding from the inner surface of the membrane.     

NAD(P)H dehydrogenases on the inner surface of the inner mitochondrial membrane studied using inside-out submitochondrial particles

Submitochondrial particles (SMP) were isolated from potato ( Solanum tuberosum L. cv. Bintje) tubers. The SMP were 91% inside-out and they were able to form a membrane potential, as monitored by oxonol VI, with succinate, NADH and NADPH. The pH dependence and kinetics of NADH and NADPH oxidation by these SMP was studied using three different electron acceptors – O₂, duroquinone and ferricyanide. In addition, the SMP were solubilized, fractionated by non-denaturing polyacrylamide gel electrophoresis, and the gels were stained for NAD(P)H dehydrogenase activity and specificity at different pH using Nitro Blue Tetrazolium. From the results we conclude that there are at least two distinct NAD(P)H dehydrogenases on the inner surface of the inner membrane: (1) Complex 1 which oxidizes NADH and deamino-NADH in a rotenone-sensitive manner, (O₂ as acceptor) with optimum activity at pH 8 and a very low K_m(NADH) of 3 μ M . It also oxidizes NADPH and deamino-NADPH in a rotenone-sensitive manner, but with a pH optimum at pH 5.8 and a very high K_m(NADPH) of more than 1 m M . This complex is found as a broad, diffuse band at the top of the gels. (2) A second dehydrogenase which oxidizes NADH in a rotenone-insensitive manner with optimum activity at pH 6.2 and a higher K_m(NADH) of 14 μ M . It also oxidizes NADPH in a rotenone-insensitive manner with an activity optimum at pH 6.8 and low K_m(NADPH) of 25 μ M . This dehydrogenase does not oxidize deamino-NAD(P)H. One of the sharp bands around the middle of the native gels may be caused by this dehydrogenase indicating that it has a relatively low molecular mass compared to Complex I. Several other NAD(P)H dehydrogenase bands were observed on the gels which we cannot yet assign.     

The ND2 subunit is labeled by a photoaffinity analogue of asimicin, a potent complex I inhibitor

NADH:ubiquinone oxidoreductase (complex I) is the entry enzyme of mitochondrial oxidative phosphorylation. To obtain the structural information on inhibitor/quinone binding sites, we synthesized [³H]benzophenone-asimicin ([³H]BPA), a photoaffinity analogue of asimicin, which belongs to the acetogenin family known as the most potent complex I inhibitor. We found that [³H]BPA was photo-crosslinked to ND2, ND1 and ND5 subunits, by the three dimensional separation (blue-native/doubled SDS-PAGE) of [³H]BPA-treated bovine heart submitochondrial particles. The cross-linking was blocked by rotenone. This is the first finding that ND2 was photo-crosslinked with a potent complex I inhibitor, suggesting its involvement in the inhibitor/quinone-binding.     

低温冷藏提高家蚕滞育卵NAD含量和胞质苹果酸脱氢酶活性

为了调查5℃低温处理是否改变家蚕Bombyx mori卵滞育NAD代谢, 本研究利用HPLC和分光光度法测定了经25℃和5℃分别处理的滞育卵中NADH 含量、 NAD⁺含量、 乳酸脱氢酶（LDH）活性和胞质苹果酸脱氢酶（cMDH）活性。结果表明： 5℃处理的NAD（NADH + NAD⁺）含量和cMDH活性分别增加了106%和53%, 并且显著高于25℃处理（P< 0.01）; 但是两种处理的NADH/NAD⁺比值和LDH活性没有显著差异（P> 0.05）。据此推测, 5℃低温处理加强了家蚕滞育卵NAD⁺合成和再生能力。     

Interaction of reduced nicotinamide adenine dinucleotide with an antifreeze protein from Dendroides canadensis: mechanistic implication of antifreeze activity enhancement

Antifreeze proteins (AFPs) found in many organisms can noncolligatively lower the freezing point of water without altering the melting point. The difference between the depressed freezing point and the melting point, termed thermal hysteresis (TH), is usually a measure of the antifreeze activity of AFPs. Certain low molecular mass molecules and proteins can further enhance the antifreeze activity of AFPs. Interaction between an enhancer and arginine is known to play an important role in enhancing the antifreeze activity of an AFP from the beetle Dendroides canadensis (DAFP-1). Here, we examined the enhancement effects of several prevalent phosphate-containing coenzymes on the antifreeze activity of DAFP-1. β-Nicotinamide adenine dinucleotide (reduced) (NADH) is identified as the most efficient enhancer of DAFP-1, which increases the antifreeze activity of DAFP-1 by around 10 times. Examination of the enhancement abilities of a series of NADH analogs and various molecular fragments of NADH reveals that the modifications of nicotinamide generate a series of highly efficient enhancers, though none as effective as NADH itself, and the whole molecular structure of NADH is necessary for its highly efficient enhancement effect. We also demonstrated a 1:1 binding between DAFP-1 and NADH. The binding was characterized by high-performance liquid chromatography (HPLC) using the gel filtration method of Hummel and Dreyer. The data analysis suggests binding between DAFP-1 and NADH with a dissociation constant in the micromolar range. Interactions between DAFP-1 and NADH are discussed along with molecular mechanisms of enhancer action.     

Kinetics of Thermal Inactivation of Lactate Dehydrogenase from Rabbit Muscle

The kinetics of thermal inactivation of rabbit muscle lactate dehydrogenase at different temperatures has been studied using the kinetic method for the substrate reaction during irreversible inhibition of enzyme activity previously described by Tsou [Adv. Enzymol. Relat. Areas Mol. Biol. (1988), 61, 381–436]. The results show that thermal inactivation of the enzyme is an irreversible reaction. Microscopic rate constants were determined for thermal inactivation of the free enzyme and the enzyme–substrate complex. The inactivation rate constant of the free enzyme is much larger than the rate constant of the enzyme–substrate complex. The results suggest that the presence of the substrate has a certain protective effect against thermal inactivation of the enzyme.     

The proton pumping stoichiometry of purified mitochondrial complex I reconstituted into proteoliposomes

NADH:ubiquinone oxidoreductase (complex I) is the largest and most complicated enzyme of aerobic electron transfer. The mechanism how it uses redox energy to pump protons across the bioenergetic membrane is still not understood. Here we determined the pumping stoichiometry of mitochondrial complex I from the strictly aerobic yeast Yarrowia lipolytica. With intact mitochondria, the measured value of indicated that four protons are pumped per NADH oxidized. For purified complex I reconstituted into proteoliposomes we measured a very similar pumping stoichiometry of . This is the first demonstration that the proton pump of complex I stayed fully functional after purification of the enzyme.     

Carboxyl pK(a) values, ion pairs, hydrogen bonding, and the pH-dependence of folding the hyperthermophile proteins Sac7d and Sso7d

Sac7d and Sso7d are homologous, hyperthermophile proteins with a high density of charged surface residues and potential ion pairs. To determine the relative importance of specific amino acid side-chains in defining the stability and function of these Archaeal chromatin proteins, pK(a) values were measured for the acidic residues in both proteins using (13)C NMR chemical shifts. The stability of Sso7d enabled titrations to pH 1 under low-salt conditions. Two aspartate residues in Sso7d (D16 and D35) and a single glutamate residue (G54) showed significantly perturbed pK(a) values in low salt, indicating that the observed pH-dependence of stability was primarily due to these three residues. The pH-dependence of backbone amide NMR resonances demonstrated that perturbation of all three pK(a) values was primarily the result of side-chain to backbone amide hydrogen bonds. Few of the significantly perturbed acidic pK(a) values in Sac7d and Sso7d could be attributed to primarily ion pair or electrostatic interactions. A smaller perturbation of E48 (E47 in Sac7d) was ascribed to an ion pair interaction that may be important in defining the DNA binding surface. The small number (three) of significantly altered pK(a) values was in good agreement with a linkage analysis of the temperature, pH, and salt-dependence of folding. The linkage of the ionization of two or more side-chains to protein folding led to apparent cooperativity in the pH-dependence of folding, although each group titrated independently with a Hill coefficient near unity. These results demonstrate that the acid pH-dependence of protein stability in these hyperthermophile proteins is due to independent titration of acidic residues with pK(a) values perturbed primarily by hydrogen bonding of the side-chain to the backbone. This work demonstrates the need for caution in using structural data alone to argue the importance of ion pairs in stabilizing hyperthermophile proteins.     

The ACCEL Model for Accelerating the Detoxification Kinetics of Hydrocarbons Requiring Initial Monooxygenation Reactions

The two-tank accelerator/aerator modification of activated sludge significantly increases the biodegradation of hydrocarbons requiring initial monooxygenation reactions, such as phenol and 2,4-dichlorophenol (DCP). The small accelerator tank has a controlled low dissolved oxygen (DO) concentration that can enrich the biomass in NADH + H⁺. It also has a very high specific growth rate (μ_acc) that up-regulates the biomass’s content of the monooxygenase enzyme. Here, we develop and test the ACCEL model, which quantifies all key phenomena taking place when the accelerator/aerator system is used to enhance biodegradation of hydrocarbons requiring initial monooxygenations. Monooxygenation kinetics follow a multiplicative relationship in which the organic substrates (phenol or DCP) and DO have separate Monod terms, while the biomass’s content of NADH + H⁺ has a first-order term. The monooxygenase enzyme has different affinities (K values) for phenol and DCP. The biomass’s NADH + H⁺ content is based on a proportioning of NAD(H) according to the relative rates of NADH + H⁺ sources and sinks. Biomass synthesis occurs simultaneously through utilization of acetate, phenol, and DCP, but each has its own true yield. The ACCEL model accurately simulates all trends for one-tank and two-tank experiments in which acetate, phenol, and DCP are biodegraded together. In particular, DCP removal is affected most by DO_acc and the retention-time ratio, Θ_acc/Θ_total. Adding an accelerator tank dramatically increases DCP removal, and the best DCP removal occurs for 0.2 < DO_acc < 0.5 mg/l and 0.08 < Θ_acc/Θ_total < 0.2. The rates of phenol and DCP utilization follow the multiplicative relationship with a maximum specific rate coefficient proportional to μ_acc. Finally, μ_acc increases rapidly for Θ_acc/Θ_total < 0.25, acetate removal in the accelerator fuels the high μ_acc, and the biomass’s NADH + H⁺ content increases very dramatically for DO_acc < 0.25 mg/l.     

A detailed analysis of the mechanisms controlling the acceleration of 2,4-DCP monooxygenation in the two-tank suspended growth process

The mechanisms underlying the observed acceleration of monooxygenationreactions in two-tank accelerator/aerator suspended growth system are evaluatedin detail. The accelerator tank is characterized by a very high electron flow throughreduced nicotinamide adenine dinucleotide (NADH + H⁺), particularly when the retention-time ratio is small. Only a small fraction of the electron flow wasdiverted to oxygenation reactions, and the major sinks of NADH + H⁺ were respiration and biomass synthesis. The main producer of NADH + H⁺ is oxidation of acetate, a rapidly degraded electron-donor substrate. The half-maximum-rate concentration for oxygen used in respiration was 0.03 mg/L, while the half-maximum-rate concentration for oxygen used as a cosubstrate in monooxygenation was 0.18 mg/L. Thus, monooxygenations were more sensitive to oxygen limitation than was respiration. The NADH + H⁺ concentration had a direct effect on the monooxygenation kinetics. Therate coefficients for both monooxygenation reactions were directly proportional to thespecific growth rate in the accelerator, which supports that the accelerator tank causedan up-regulation of the monooxygenase content. Because the rate coefficients in theaerator tank were much larger than in the one-tank system, even though the specificgrowth rates were nearly the same, monooxygenases may have carried over from theaccelerator tank to the aerator tank. Its higher concentration of 2,4-dichlorophenol(2,4-DCP) and the higher specific growth rate were the main reasons why the accelerator had faster kinetics for 2,4-DCP utilization than did the aerator tank. The apparently higher levels of monooxygenase in both tanks of the two-tank system also appears be a primary reason why its performance was substantially superior to that of the one-tank system in terms of 2,4-DCP removal.     

Hydrogen sulfide is a reversible inhibitor of the NADH oxidase activity of synaptic plasma membranes

Hydrogen sulfide is now accepted as a neuromodulator, which can be involved in neuronal defence against oxidative stress insults in the brain. In this work we show that concentrations of H₂S within the physiological range reported in the brain produce a reversible inhibition of the NADH oxidase activity and coupled superoxide anion production by synaptic plasma membranes from rat brain. At physiological pH 7 the concentration of H₂S needed for 50% inhibition of the NADH oxidase activity is 5 ± 1 μM, which is within the low range of the reported physiological H₂S concentrations. Thus, the NADH oxidase activity of the neuronal plasma membrane can act as a sensor of local H₂S depletion in neurones. H₂S inhibition of the NADH oxidase activity of the neuronal plasma membrane can be accounted for direct reduction by H₂S of cytochrome b₅. However, H₂S fails to afford a significant protection against the inhibition of this activity by peroxynitrite. In conclusion, our results point out that H₂S is more potent as inhibitor of reactive oxygen species formation than as a sacrificial antioxidant.     

Towards catalyst compartimentation in combined chemo- and biocatalytic processes: Immobilization of alcohol dehydrogenases for the diastereoselective reduction of a β-hydroxy ketone obtained from an organocatalytic aldol reaction

The alcohol dehydrogenases (ADHs) from Lactobacillus kefir and Rhodococcus sp., which earlier turned out to be suitable for a chemoenzymatic one-pot synthesis with organocatalysts, were immobilized with their cofactors on a commercially available superabsorber based on a literature known protocol. The use of the immobilized ADH from L. kefir in the reduction of acetophenone as a model substrate led to high conversion (>95%) in the first reaction cycle, followed by a slight decrease of conversion in the second reaction cycle. A comparable result was obtained when no cofactor was added although a water rich reaction media was used. The immobilized ADHs also turned out to be suitable catalysts for the diastereoselective reduction of an organocatalytically prepared enantiomerically enriched aldol adduct, leading to high conversion, diastereomeric ratio and enantioselectivity for the resulting 1,3-diols. However, at a lower catalyst and cofactor amount being still sufficient for biotransformations with “free” enzymes the immobilized ADH only showed high conversion and >99% ee for the first reaction cycle whereas a strong decrease of conversion was observed already in the second reaction cycle, thus indicating a significant leaching effect of catalyst and/or cofactor.     

Identification of a collapsed intermediate with non-native long-range interactions on the folding pathway of a pair of Fyn SH3 domain mutants by NMR relaxation dispersion spectroscopy

Recent 15N and 13C spin-relaxation dispersion studies of fast-folding mutants of the Fyn SH3 domain have established that folding proceeds through a low-populated on-pathway intermediate (I) where the central beta-sheet is at least partially formed, but without interactions between the NH2- and COOH-terminal beta-strands that exist in the folded state (F). Initial studies focused on mutants where Gly48 is replaced; in an effort to establish whether this intermediate is a general feature of Fyn SH3 folding a series of 15N relaxation experiments monitoring the folding of Fyn SH3 mutants N53P/V55L and A39V/N53P/V55L are reported here. For these mutants as well, folding proceeds through an on-pathway intermediate with similar features to those observed for G48M and G48V Fyn SH3 domains. However, the 15N chemical shifts extracted for the intermediate indicate pronounced non-native contacts between the NH2 and COOH-terminal regions not observed previously. The kinetic parameters extracted for the folding of A39V/N53P/V55L Fyn SH3 from the three-state folding model F<-->I<-->U are in good agreement with folding and unfolding rates extrapolated to zero denaturant obtained from stopped-flow experiments analyzed in terms of a simplified two-state folding reaction. The folding of the triple mutant was studied over a wide range of temperatures, establishing that there is no difference in heat capacities between F and I states. This confirms a compact folding intermediate structure, which is supported by the 15N chemical shifts of the I state extracted from the dispersion data. The temperature-dependent relaxation data simplifies data analysis because at low temperatures (< 25 degrees C) the unfolded state (U) is negligibly populated relative to I and F. A comparison between parameters extracted at low temperatures where the F<-->I exchange model is appropriate with those from the more complex, three-state model at higher temperatures has been used to validate the protocol for analysis of three-site exchange relaxation data.