Artykuły w czasopismach: „NADH molecules”

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Wos, M. L., i P. C. Pollard. "Cellular nicotinamide adenine dinucleotide (NADH) as an indicator of bacterial metabolic activity dynamics in activated sludge". Water Science and Technology 60, nr 3 (1.07.2009): 783–91. http://dx.doi.org/10.2166/wst.2009.393.

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In this study, native fluorescent nicotinamide adenine dinucleotide (NADH) was used as a direct indicator of bacterial metabolic activity in activated sludge. Specific NADH concentration was dynamic and varied between 106–108 molecules per bacterial cell. Low concentrations (106–107 NADH molecules cell−1) indicate efficient bacterial metabolic activity while high concentrations (107–108 NADH molecules cell−1) indicate inefficient bacterial metabolic activity. Specific [NADH] did not correlate to changes in dissolved organic carbon, but increases correlated to decreases in oxygen uptake rates. Perhaps a lack of oxygen as the terminal electron acceptor prevented efficient reoxidization of NADH to NAD+, which resulted in an accumulation of NADH within the cells. Also, significant amounts of NADH were released and accumulated into the extracellular medium of metabolically active E. coli cells in log phase. Such overflow metabolism may be the product of favourable conditions. Thus, the flux of both specific intracellular and extracellular [NADH] indicates the dynamics of bacterial metabolic activity in activated sludge.

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Tsai, Hsieh-Chin, Cheng-Hung Hsieh, Ching-Wen Hsu, Yau-Heiu Hsu i Lee-Feng Chien. "Cloning and Organelle Expression of Bamboo Mitochondrial Complex I Subunits Nad1, Nad2, Nad4, and Nad5 in the Yeast Saccharomyces cerevisiae". International Journal of Molecular Sciences 23, nr 7 (6.04.2022): 4054. http://dx.doi.org/10.3390/ijms23074054.

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Mitochondrial respiratory complex I catalyzes electron transfer from NADH to ubiquinone and pumps protons from the matrix into the intermembrane space. In particular, the complex I subunits Nad1, Nad2, Nad4, and Nad5, which are encoded by the nad1, nad2, nad4, and nad5 genes, reside at the mitochondrial inner membrane and possibly function as proton (H+) and ion translocators. To understand the individual functional roles of the Nad1, Nad2, Nad4, and Nad5 subunits in bamboo, each cDNA of these four genes was cloned into the pYES2 vector and expressed in the mitochondria of the yeast Saccharomyces cerevisiae. The mitochondrial targeting peptide mt gene (encoding MT) and the egfp marker gene (encoding enhanced green fluorescent protein, EGFP) were fused at the 5′-terminal and 3′-terminal ends, respectively. The constructed plasmids were then transformed into yeast. RNA transcripts and fusion protein expression were observed in the yeast transformants. Mitochondrial localizations of the MT-Nad1-EGFP, MT-Nad2-EGFP, MT-Nad4-EGFP, and MT-Nad5-EGFP fusion proteins were confirmed by fluorescence microscopy. The ectopically expressed bamboo subunits Nad1, Nad2, Nad4, and Nad5 may function in ion translocation, which was confirmed by growth phenotype assays with the addition of different concentrations of K+, Na+, or H+.

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Qi, Xiangying, Kaiqi Wang, Liping Yang, Zhenshan Deng i Zhihong Sun. "The complete mitogenome sequence of the coral lily (Lilium pumilum) and the Lanzhou lily (Lilium davidii) in China". Open Life Sciences 15, nr 1 (31.12.2020): 1060–67. http://dx.doi.org/10.1515/biol-2020-0102.

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AbstractBackgroundThe mitogenomes of higher plants are conserved. This study was performed to complete the mitogenome of two China Lilium species (Lilium pumilum Redouté and Lilium davidii var. unicolor (Hoog) cotton).MethodsGenomic DNA was separately extracted from the leaves of L. pumilum and L. davidii in triplicate and used for sequencing. The mitogenome of Allium cepa was used as a reference. Genome assembly, annotation and phylogenetic tree were analyzed.ResultsThe mitogenome of L. pumilum and L. davidii was 988,986 bp and 924,401 bp in length, respectively. There were 22 core protein-coding genes (including atp1, atp4, atp6, atp9, ccmB, ccmC, ccmFc, ccmFN1, ccmFN2, cob, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7 and nad9), one open reading frame and one ribosomal protein-coding gene (rps12) in the mitogenomes. Compared with the A. cepa mitogenome, the coding sequence of the 24 genes and intergenic spacers in L. pumilum and L. davidii mitogenome contained 1,621 and 1,617 variable sites, respectively. In the phylogenetic tree, L. pumilum and L. davidii were distinct from A. cepa (NC_030100).ConclusionsL. pumilum and L. davidii mitogenomes have far distances from other plants. This study provided additional information on the species resources of China Lilium.

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Cronholm, T. "Hydrogen transfer between ethanol molecules during oxidoreduction in vivo". Biochemical Journal 229, nr 2 (15.07.1985): 315–22. http://dx.doi.org/10.1042/bj2290315.

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Rates of exchange catalysed by alcohol dehydrogenase were determined in vivo in order to find rate-limiting steps in ethanol metabolism. Mixtures of [1,1-2H2]- and [2,2,2-2H3]ethanol were injected in rats with bile fistulas. The concentrations in bile of ethanols having different numbers of 2H atoms were determined by g.l.c.-m.s. after the addition of [2H6]ethanol as internal standard and formation of the 3,5-dinitrobenzoates. Extensive formation of [2H4]ethanol indicated that acetaldehyde formed from [2,2,2-2H3]ethanol was reduced to ethanol and that NADH used in this reduction was partly derived from oxidation of [1,1-2H2]ethanol. The rate of acetaldehyde reduction, the degree of labelling of bound NADH and the isotope effect on ethanol oxidation were calculated by fitting models to the found concentrations of ethanols labelled with 1-42H atoms. Control experiments with only [2,2,2-2H3]ethanol showed that there was no loss of the C-2 hydrogens by exchange. The isotope effect on ethanol oxidation appeared to be about 3. Experiments with (1S)-[1-2H]- and [2,2,2-2H3]ethanol indicated that the isotope effect on acetaldehyde oxidation was much smaller. The results indicated that both the rate of reduction of acetaldehyde and the rate of association of NADH with alcohol dehydrogenase were nearly as high as or higher than the net ethanol oxidation. Thus, the rate of ethanol oxidation in vivo is determined by the rates of acetaldehyde oxidation, the rate of dissociation of NADH from alcohol dehydrogenase, and by the rate of reoxidation of cytosolic NADH. In cyanamide-treated rats, the elimination of ethanol was slow but the rates in the oxidoreduction were high, indicating more complete rate-limitation by the oxidation of acetaldehyde.

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Jeong, Kang Hwa, Hyun Jin Lee, Young Woo Park i Jae Young Lee. "Structural Basis of Redox-Sensing Transcriptional Repressor Rex with Cofactor NAD+ and Operator DNA". International Journal of Molecular Sciences 23, nr 3 (29.01.2022): 1578. http://dx.doi.org/10.3390/ijms23031578.

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The transcriptional repressor Rex plays important roles in regulating the expression of respiratory genes by sensing the reduction–oxidation (redox) state according to the intracellular NAD+/NADH balance. Previously, we reported on crystal structures of apo, NAD+-bound, and NADH-bound forms of Rex from Thermotoga maritima to analyze the structural basis of transcriptional regulation depending on either NAD+ or NADH binding. In this study, the crystal structure of Rex in ternary complex with NAD+ and operator DNA revealed that the N-terminal domain of Rex, including the helix-turn-helix motif, forms extensive contacts with DNA in addition to DNA sequence specificity. Structural comparison of the Rex in apo, NAD+-bound, NADH-bound, and ternary complex forms provides a comprehensive picture of transcriptional regulation in the Rex. These data demonstrate that the conformational change in Rex when binding with the reduced NADH or oxidized NAD+ determines operator DNA binding. The movement of the N-terminal domains toward the operator DNA was blocked upon binding of NADH ligand molecules. The structural results provide insights into the molecular mechanism of Rex binding with operator DNA and cofactor NAD+/NADH, which is conserved among Rex family repressors. Structural analysis of Rex from T. maritima also supports the previous hypothesis about the NAD+/NADH-specific transcriptional regulation mechanism of Rex homologues.

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Kolappan, Subramaniapillai, David L. Shen, Renee Mosi, Jianyu Sun, Ernest J. McEachern, David J. Vocadlo i Lisa Craig. "Structures of lactate dehydrogenase A (LDHA) in apo, ternary and inhibitor-bound forms". Acta Crystallographica Section D Biological Crystallography 71, nr 2 (23.01.2015): 185–95. http://dx.doi.org/10.1107/s1399004714024791.

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Lactate dehydrogenase (LDH) is an essential metabolic enzyme that catalyzes the interconversion of pyruvate and lactate using NADH/NAD+as a co-substrate. Many cancer cells exhibit a glycolytic phenotype known as the Warburg effect, in which elevated LDH levels enhance the conversion of glucose to lactate, making LDH an attractive therapeutic target for oncology. Two known inhibitors of the human muscle LDH isoform, LDHA, designated1and2, were selected, and their IC50values were determined to be 14.4 ± 3.77 and 2.20 ± 0.15 µM, respectively. The X-ray crystal structures of LDHA in complex with each inhibitor were determined; both inhibitors bind to a site overlapping with the NADH-binding site. Further, an apo LDHA crystal structure solved in a new space group is reported, as well as a complex with both NADH and the substrate analogue oxalate bound in seven of the eight molecules and an oxalate only bound in the eighth molecule in the asymmetric unit. In this latter structure, a kanamycin molecule is located in the inhibitor-binding site, thereby blocking NADH binding. These structures provide insights into LDHA enzyme mechanism and inhibition and a framework for structure-assisted drug design that may contribute to new cancer therapies.

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Kim, Youngnyun, L. O. Ingram i K. T. Shanmugam. "Dihydrolipoamide Dehydrogenase Mutation Alters the NADH Sensitivity of Pyruvate Dehydrogenase Complex of Escherichia coli K-12". Journal of Bacteriology 190, nr 11 (28.03.2008): 3851–58. http://dx.doi.org/10.1128/jb.00104-08.

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ABSTRACT Under anaerobic growth conditions, an active pyruvate dehydrogenase (PDH) is expected to create a redox imbalance in wild-type Escherichia coli due to increased production of NADH (>2 NADH molecules/glucose molecule) that could lead to growth inhibition. However, the additional NADH produced by PDH can be used for conversion of acetyl coenzyme A into reduced fermentation products, like alcohols, during metabolic engineering of the bacterium. E. coli mutants that produced ethanol as the main fermentation product were recently isolated as derivatives of an ldhA pflB double mutant. In all six mutants tested, the mutation was in the lpd gene encoding dihydrolipoamide dehydrogenase (LPD), a component of PDH. Three of the LPD mutants carried an H322Y mutation (lpd102), while the other mutants carried an E354K mutation (lpd101). Genetic and physiological analysis revealed that the mutation in either allele supported anaerobic growth and homoethanol fermentation in an ldhA pflB double mutant. Enzyme kinetic studies revealed that the LPD(E354K) enzyme was significantly less sensitive to NADH inhibition than the native LPD. This reduced NADH sensitivity of the mutated LPD was translated into lower sensitivity of the appropriate PDH complex to NADH inhibition. The mutated forms of the PDH had a 10-fold-higher Ki for NADH than the native PDH. The lower sensitivity of PDH to NADH inhibition apparently increased PDH activity in anaerobic E. coli cultures and created the new ethanologenic fermentation pathway in this bacterium. Analogous mutations in the LPD of other bacteria may also significantly influence the growth and physiology of the organisms in a similar fashion.

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Liao, Yuqin, Ruiyun You, Min Fan, Shangyuan Feng, Dechan Lu i Yudong Lu. "Determination of NADH by Surface Enhanced Raman Scattering Using Au@MB@Ag NPs". Australian Journal of Chemistry 74, nr 10 (2021): 722. http://dx.doi.org/10.1071/ch21178.

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Nicotinamide adenine dinucleotide (NADH) is an important coenzyme involved in various metabolic processes of living cells. As an important biomarker, NADH is associated with breast cancer and Alzheimer’s disease. In this paper, silver plated gold core–shell nanoparticles containing Raman signal molecules were synthesised on the basis of bare gold. Using the Raman peak corresponding to the 4-mercaptobenzonitrile (MB) silent region C≡N vibration for quantification, while avoiding competition with the precious metal surface binding site to be measured, it can also be free from the interference of endogenous biomolecules. On the one hand, it can correct the working curve, on the other hand, it can avoid competing with the binding site. Compared with the core–shell structure prepared here, the limit of detection (LOD) for NADH was only 10−5 M for bare gold and the LOD for the core–shell structure prepared on the basis of bare gold was 3.3 × 10−7 M. In terms of correction, with Rhodamine 6G (R6G) as a Raman signalling molecule, the R2 value before SERS detection and correction is only 0.9405, and the R2 value after correction increases to 0.9853. The unique fingerprint peak of SERS was used to realise the quantitative detection of NADH, which realizes the detection of NADH in complex biological samples of serum and provides the possibility for expanding the early diagnosis of breast cancer.

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Tedokon, M., K. Suzuki, Y. Kayamori, S. Fujita i Y. Katayama. "Enzymatic Assay of Inorganic Phosphate with Use of Sucrose Phosphorylase and Phosphoglucomutase". Clinical Chemistry 38, nr 4 (1.04.1992): 512–15. http://dx.doi.org/10.1093/clinchem/38.4.512.

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Abstract We developed a new enzymatic method for the assay of inorganic phosphate (Pi) by using sucrose phosphorylase (SP; EC 2.4.1.7) and phosphoglucomutase (PGM; EC 5.4.2.2). Pi is transferred to sucrose by SP, producing alpha-D-glucose 1-phosphate (G1P) and alpha-D-fructose. G1P is transphosphorylated by PGM in the presence of alpha-D-glucose 1,6-bisphosphate to form alpha-D-glucose 6-phosphate, which is oxidized by NAD+ and glucose-6-phosphate dehydrogenase (EC 1.1.1.49) to form 6-phosphogluconate (6PG) and NADH. Finally, the oxidation of 6PG by NAD+, catalyzed by 6-phosphogluconic dehydrogenase (EC 1.1.1.44), yields D-ribulose 5-phosphate and NADH. Thus two molecules of NADH are formed for each molecule of Pi, and the reaction is monitored at 340 nm. The Km values of SP for Pi and sucrose were 4.44 and 5.31 mmol/L, respectively. The best buffer was 1,4-piperazinediethanesulfonic acid (PIPES) at 50 mmol/L and pH 6-7. Implementing this method with a Cobas-Bio centrifugal analyzer allowed us to measure Pi accurately and precisely.

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Ruiz, Lorena, Miguel Gueimonde, Patricia Ruas-Madiedo, Angela Ribbera, Clara G. de los Reyes-Gavilán, Marco Ventura, Abelardo Margolles i Borja Sánchez. "Molecular Clues To Understand the Aerotolerance Phenotype of Bifidobacterium animalis subsp. lactis". Applied and Environmental Microbiology 78, nr 3 (18.11.2011): 644–50. http://dx.doi.org/10.1128/aem.05455-11.

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ABSTRACTOxygen is one of the abiotic factors negatively affecting the survival ofBifidobacteriumstrains used as probiotics, mainly due to the induction of lethal oxidative damage. Aerobic conditions are present during the process of manufacture and storage of functional foods, and aerotolerance is a desired trait for bifidobacteria intended for use in industry. In the present study, the molecular response ofBifidobacterium animalissubsp.lactisIPLA4549 to aerobic conditions is presented. Molecular targets affected by oxygen were studied using two-dimensional electrophoresis (2DE) and quantitative reverse transcriptase (qRT) PCR. Globally, oxygen stress induced a shift in the glycolytic pathway toward the production of acetic acid with a concomitant increase in ATP formation. Several changes in the expression of genes coding for enzymes involved in redox reactions were detected, although the redox ratio remained unaltered. Interestingly, cells grown under aerobic conditions were characterized by higher activity of coproporphyrinogen III oxidase, which can directly detoxify molecular oxygen, and by higher NADH oxidase specific activity, which can oxidize NADH using hydrogen peroxide. In turn, this is in agreement with the glycolytic shift toward acetate production, in that more NADH molecules may be available due to the lower level of lactic acid formation. These findings further our ability to elucidate the mechanisms by whichB. animaliscopes with an oxygen-containing atmosphere.

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Wang, Pinpin, Kai Liu, Huanqing Ma, Hao Nian, Yawen Li, Qingfang Li, Lin Cheng i Liping Cao. "Synthesis and aqueous anion recognition of an imidazolium-based nonacationic cup". Chemical Communications 57, nr 98 (2021): 13377–80. http://dx.doi.org/10.1039/d1cc05603d.

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An imidazolium-based nonacationic cup exhibited anionic recognition for nucleoside molecules such as ATP and NADH via C–H⋯A− ionic hydrogen bonds, hydrophobic effects, and electrostatic interactions in aqueous solution.

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Singh, Ruchi, Rajesh K. Yadav, Ravindra K. Shukla, Satyam Singh, Atul P. Singh, Dilip K. Dwivedi, Ahmad Umar i Navneet K. Gupta. "Highly Selective Nitrogen-Doped Graphene Quantum Dots/Eriochrome Cyanine Composite Photocatalyst for NADH Regeneration and Coupling of Benzylamine in Aerobic Condition under Solar Light". Catalysts 13, nr 1 (14.01.2023): 199. http://dx.doi.org/10.3390/catal13010199.

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Photocatalysis is an ecofriendly and sustainable pathway for utilizing solar energy to convert organic molecules. In this context, using solar light responsive graphene-based materials for C–N bond activation and coenzyme regeneration (nicotinamide adenine dinucleotide hydrogen; NADH) is one of the utmost important and challenging tasks in this century. Herein, we report the synthesis of nitrogen-doped graphene quantum dots (NGQDs)-eriochrome cyanine (EC) solar light active highly efficient “NGQDs@EC” composite photocatalyst for the conversion of 4-chloro benzylamine into 4-chloro benzylamine, accompanied by the regeneration of NADH from NAD+, respectively. The NGQDs@EC composite photocatalyst system is utilized in a highly efficient and stereospecific solar light responsive manner, leading to the conversion of imine (98.5%) and NADH regeneration (55%) in comparison to NGQDs. The present research work highlights the improvements in the use of NGQDs@EC composite photocatalyst for stereospecific NADH regeneration and conversion of imine under solar light.

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Maeda, K., K. Truscott, X. L. Liu i R. K. Scopes. "A thermostable NADH oxidase from anaerobic extreme thermophiles". Biochemical Journal 284, nr 2 (1.06.1992): 551–55. http://dx.doi.org/10.1042/bj2840551.

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A high-abundance NADH-oxidizing enzyme (NADH: acceptor oxidoreductase, EC 1.6.99.3) has been identified and isolated from a range of anaerobic extreme thermophiles, including strains of Clostridium thermohydrosulfuricum and Thermoanaerobium brockii. By use of a pseudo-affinity salt-promoted adsorbent, a nearly pure sample was obtained in one step; remaining impurities were separated by ion-exchange. The fully active purified enzyme contains FAD (two molecules per subunit of 75-78 kDa) and iron-sulphur, and is hexameric in its most active form. The reaction with oxygen is a one- or two-electron transfer to produce superoxide radical and H2O2; other acceptors include tetrazolium salts, dichlorophenol-indophenol, menadione and ferricyanide. The role of the enzyme is not clear; it was found not to be NAD:ferredoxin oxidoreductase, which is a major NADH-utilizing enzyme in these organisms.

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Горбунова, И. А., М. Э. Сасин i О. С. Васютинский. "Достижение субпикосекундного временного разрешения при исследовании процессов анизотропной релаксации биологических молекул". Письма в журнал технической физики 46, nr 4 (2020): 7. http://dx.doi.org/10.21883/pjtf.2020.04.49041.18062.

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A novel pump-probe method has been developed to study anisotropic relaxation and energy transfer in excited states of polyatomic molecules excited by femtosecond laser pulses. The method was used to study the rotational diffusion of NADH with a temporal resolution of about 0.6 ps. For the first time, absorption from the excited state of biological molecules pumped by laser pulses with energies of 1 nJ was detected

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Di Spiridione, Carmela, Michele Aresta i Angela Dibenedetto. "Improving the Enzymatic Cascade of Reactions for the Reduction of CO2 to CH3OH in Water: From Enzymes Immobilization Strategies to Cofactor Regeneration and Cofactor Suppression". Molecules 27, nr 15 (2.08.2022): 4913. http://dx.doi.org/10.3390/molecules27154913.

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The need to decrease the concentration of CO2 in the atmosphere has led to the search for strategies to reuse such molecule as a building block for chemicals and materials or a source of carbon for fuels. The enzymatic cascade of reactions that produce the reduction of CO2 to methanol seems to be a very attractive way of reusing CO2; however, it is still far away from a potential industrial application. In this review, a summary was made of all the advances that have been made in research on such a process, particularly on two salient points: enzyme immobilization and cofactor regeneration. A brief overview of the process is initially given, with a focus on the enzymes and the cofactor, followed by a discussion of all the advances that have been made in research, on the two salient points reported above. In particular, the enzymatic regeneration of NADH is compared to the chemical, electrochemical, and photochemical conversion of NAD+ into NADH. The enzymatic regeneration, while being the most used, has several drawbacks in the cost and life of enzymes that suggest attempting alternative solutions. The reduction in the amount of NADH used (by converting CO2 electrochemically into formate) or even the substitution of NADH with less expensive mimetic molecules is discussed in the text. Such an approach is part of the attempt made to take stock of the situation and identify the points on which work still needs to be conducted to reach an exploitation level of the entire process.

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Trisolini, Lucia, Nicola Gambacorta, Ruggiero Gorgoglione, Michele Montaruli, Luna Laera, Francesco Colella, Mariateresa Volpicella, Anna De Grassi i Ciro Leonardo Pierri. "FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function". Journal of Clinical Medicine 8, nr 12 (2.12.2019): 2117. http://dx.doi.org/10.3390/jcm8122117.

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Flavoprotein oxidoreductases are members of a large protein family of specialized dehydrogenases, which include type II NADH dehydrogenase, pyridine nucleotide-disulphide oxidoreductases, ferredoxin-NAD+ reductases, NADH oxidases, and NADH peroxidases, playing a crucial role in the metabolism of several prokaryotes and eukaryotes. Although several studies have been performed on single members or protein subgroups of flavoprotein oxidoreductases, a comprehensive analysis on structure–function relationships among the different members and subgroups of this great dehydrogenase family is still missing. Here, we present a structural comparative analysis showing that the investigated flavoprotein oxidoreductases have a highly similar overall structure, although the investigated dehydrogenases are quite different in functional annotations and global amino acid composition. The different functional annotation is ascribed to their participation in species-specific metabolic pathways based on the same biochemical reaction, i.e., the oxidation of specific cofactors, like NADH and FADH2. Notably, the performed comparative analysis sheds light on conserved sequence features that reflect very similar oxidation mechanisms, conserved among flavoprotein oxidoreductases belonging to phylogenetically distant species, as the bacterial type II NADH dehydrogenases and the mammalian apoptosis-inducing factor protein, until now retained as unique protein entities in Bacteria/Fungi or Animals, respectively. Furthermore, the presented computational analyses will allow consideration of FAD/NADH oxidoreductases as a possible target of new small molecules to be used as modulators of mitochondrial respiration for patients affected by rare diseases or cancer showing mitochondrial dysfunction, or antibiotics for treating bacterial/fungal/protista infections.

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El-Sayed, Ivan, Xiaohua Huang, Fima Macheret, Joseph Oren Humstoe, Randall Kramer i Mostafa El-Sayed. "Effect of Plasmonic Gold Nanoparticles on Benign and Malignant Cellular Autofluorescence: A Novel Probe for Fluorescence Based Detection of Cancer". Technology in Cancer Research & Treatment 6, nr 5 (październik 2007): 403–12. http://dx.doi.org/10.1177/153303460700600505.

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Due to the strong surface fields of noble metal nanoparticles, absorption and scattering of electromagnetic radiation is greatly enhanced. Noble metallic nanoparticles represent potential novel optical probes for simultaneous molecular imaging and photothermal cancer therapy using the enhanced scattering and absorption of light. Further, gold nanoparticles can affect molecular fluorescence via chemical, electronic, or photonic interactions. Live cells generate fluorescence due to intracellular and extracellular molecules. Differences in the biochemical composition between healthy and malignant cells can be exploited in vivo to help identify cancer spectroscopically. The interaction of gold nanoparticles with cellular autofluorescence has not yet been characterized. We hypothesized that gold nanoparticles delivered to live cells in vitro would alter cellular autofluorescence and may be useful as a novel class of contrast agent for fluorescence based detection of cancer. The fluorescence of two fluorophores that are responsible for tissue autofluorescence, NADH and collagen, and of two oral squamous carcinoma cell lines and one immortalized benign epithelial cell line were measured in vitro. Gold nanoparticles of different shapes, both spheres and rods, quenched the fluorescence of the soluble NADH and collagen. Reduction of NADH fluorescence was due to oxidation of NADH to NAD+ catalyzed by gold nanoparticles (results we previously published). Reduction of collagen fluorescence appears due to photonic absorption of light. Furthermore, a mean quenching of 12/8% (p<0.00050) of the tissue autofluorescence of cell suspensions was achieved in this model when nanospheres were incubated with the live cells. Gold nanospheres significantly decrease cellular autofluorescence of live cells under physiological conditions when excited at 280nm. This is the first report to our knowledge to suggest the potential of developing targeted gold nanoparticles optical probes as contrast agents for fluorescence based diagnoses of cancer.

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Kmita, H., O. Stobienia i J. Michejda. "The access of metabolites into yeast mitochondria in the presence and absence of the voltage dependent anion selective channel (YVDAC1)." Acta Biochimica Polonica 46, nr 4 (31.12.1999): 991–1000. http://dx.doi.org/10.18388/abp.1999_4124.

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Since yeast Saccharomyces cerevisiae mutants depleted of the voltage dependent anion selective channel (YVDAC1) are still able to grow on a non-fermentable carbon source, a functional transport system in the outer mitochondrial membrane must exist to support the access of metabolites into mitochondria. It was assumed that the properties of the system could be inferred from the differences in the results observed between wild type and mutant mitochondria since no crucial differences in this respect between the two types of mitoplasts were observed. YVDAC1-depleted mitochondria displayed a highly reduced permeability of the outer membrane, which was reflected in increased values of K0.5(NADH) for respiration and K0.5(ADP) for triggering phosphorylating state as well as in delayed action of carboxyatractylate (CATR) in inhibition of phosphorylating state. The parameters were chosen to express the accessibility of the applied species to the intermembrane space. The passage of the molecules through the outer membrane depleted of YVDAC1 could be partially improved in the presence of bivalent cations (Mg2+, Ca2+), as in their presence lower values of the calculated parameters were obtained. The restrictions imposed on the transport of molecules through the YVDAC1-depleted outer membrane resulted in a competition between them for the access to the intermembrane space as measured by changes in parameters observed for a given species in the presence of another one. The competition was stronger in the absence of Mg2+ and depended on charge and size of transported molecules, as the strongest competitor was CATR and the weakest one--NADH. Thus, it can be concluded that the transport system functioning in the absence of YVDAC1 is modulated by bivalent cations and charge as well as size of transported molecules. Since an increased level of respiration due to the dissipation of delta psi causes an increase of K0.5(NADH) in both wild type and YVDAC1-depleted mitochondria it is concluded that a common property of YVDAC1 and the system functioning in YVDAC1-depleted mitochondria seems to be the dependence of the capacity on the level of mitochondrial respiration.

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Zhao, Li-Jun, Ruo-Can Qian, Wei Ma, He Tian i Yi-Tao Long. "Electrocatalytic Efficiency Analysis of Catechol Molecules for NADH Oxidation during Nanoparticle Collision". Analytical Chemistry 88, nr 17 (9.08.2016): 8375–79. http://dx.doi.org/10.1021/acs.analchem.6b02365.

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Harbut, Michael B., Baiyuan Yang, Renhe Liu, Takahiro Yano, Catherine Vilchèze, Bo Cheng, Jonathan Lockner i in. "Small Molecules Targeting Mycobacterium tuberculosis Type II NADH Dehydrogenase Exhibit Antimycobacterial Activity". Angewandte Chemie 130, nr 13 (22.02.2018): 3536–40. http://dx.doi.org/10.1002/ange.201800260.

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Harbut, Michael B., Baiyuan Yang, Renhe Liu, Takahiro Yano, Catherine Vilchèze, Bo Cheng, Jonathan Lockner i in. "Small Molecules Targeting Mycobacterium tuberculosis Type II NADH Dehydrogenase Exhibit Antimycobacterial Activity". Angewandte Chemie International Edition 57, nr 13 (22.02.2018): 3478–82. http://dx.doi.org/10.1002/anie.201800260.

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Cho, Eun Jeong, Ashwini K. Devkota, Gabriel Stancu, Ramakrishna Edupunganti, Garth Powis i Kevin N. Dalby. "A Fluorescence-Based High-Throughput Assay for the Identification of Anticancer Reagents Targeting Fructose-1,6-Bisphosphate Aldolase". SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, nr 1 (18.08.2017): 1–10. http://dx.doi.org/10.1177/2472555217726325.

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A high rate of glycolysis, which supplies energy and materials for anabolism, is observed in a wide range of tumor cells, making it a potential pathway to control cancer growth. ALDOA is a multifunctional enzyme in the glycolytic pathway and also promotes HIF-1α, which is of importance in hypoxic solid tumors. The current method for assaying ALDOA activity involves monitoring the consumption of NADH in vitro using absorbance or intrinsic fluorescence via a coupled enzymatic reaction. Here, we report the development of a homogeneous biochemical assay that can overcome limitations of current methods, in particular for the application of high-throughput drug screening. The assay utilizes the commercially available Elite NADH Assay Kit, which incorporates an enzymatic reaction to measure the level of NADH using a fluorescent probe. Assay optimization and validation are discussed. Its feasibility for high-throughput screening (HTS) was demonstrated by screening 65,000 compounds for the identification of small molecules that inhibit ALDOA. Through a validation screen and dose–response evaluation, four inhibitors with IC50 below 10 µM were identified. In conclusion, we demonstrate that a traditional ALDOA assay can be transformed readily into a fluorescence-based assay utilizing a commercial NADH detection kit that is rapid, sensitive, inexpensive, and HTS friendly.

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Shidhi, Pattayampadam Ramakrishnan, Vadakkemukadiyil Chellappan Biju, Sasi Anu, Chandrasekharan Laila Vipin, Kumar Raveendran Deelip i Sukumaran Nair Achuthsankar. "Genome Characterization, Comparison and Phylogenetic Analysis of Complete Mitochondrial Genome of Evolvulus alsinoides Reveals Highly Rearranged Gene Order in Solanales". Life 11, nr 8 (30.07.2021): 769. http://dx.doi.org/10.3390/life11080769.

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Mitogenome sequencing provides an understanding of the evolutionary mechanism of mitogenome formation, mechanisms driving plant gene order, genome structure, and migration sequences. Data on the mitochondrial genome for family Convolvulaceae members is lacking. E. alsinoides, also known as shankhpushpi, is an important medicinal plant under the family Convolvulaceae, widely used in the Ayurvedic system of medicine. We identified the mitogenome of E. alsinoides using the Illumina mate-pair sequencing platform, and annotated using bioinformatics approaches in the present study. The mitogenome of E. alsinoides was 344184 bp in length and comprised 46 unique coding genes, including 31 protein-coding genes (PCGs), 12 tRNA genes, and 3 rRNA genes. The secondary structure of tRNAs shows that all the tRNAs can be folded into canonical clover-leaf secondary structures, except three trnW, trnG, and trnC. Measurement of the skewness of the nucleotide composition showed that the AT and GC skew is positive, indicating higher A’s and G’s in the mitogenome of E. alsinoides. The Ka/Ks ratios of 11 protein-coding genes (atp1, ccmC, cob, cox1, rps19, rps12, nad3, nad9, atp9, rpl5, nad4L) were <1, indicating that these genes were under purifying selection. Synteny and gene order analysis were performed to identify homologous genes among the related species. Synteny blocks representing nine genes (nad9, nad2, ccmFc, nad1, nad4, nad5, matR, cox1, nad7) were observed in all the species of Solanales. Gene order comparison showed that a high level of gene rearrangement has occurred among all the species of Solanales. The mitogenome data obtained in the present study could be used as the Convolvulaceae family representative for future studies, as there is no complex taxonomic history associated with this plant.

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Fu, Yan-Hua, Zhen Wang, Kai Wang, Guang-Bin Shen i Xiao-Qing Zhu. "Evaluation and comparison of antioxidant abilities of five bioactive molecules with C–H and O–H bonds in thermodynamics and kinetics". RSC Advances 12, nr 42 (2022): 27389–95. http://dx.doi.org/10.1039/d2ra04839f.

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In this work, the antioxidant abilities of NADH coenzyme analogue BNAH, F420 reduction prototype analogue F420H, vitamin C analogue iAscH−, caffeic acid, and (+)-catechin in acetonitrile in chemical reactions were studied and discussed.

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25

Andrade, Susana L. A., Eric V. Patridge, James G. Ferry i Oliver Einsle. "Crystal Structure of the NADH:Quinone Oxidoreductase WrbA from Escherichia coli". Journal of Bacteriology 189, nr 24 (19.10.2007): 9101–7. http://dx.doi.org/10.1128/jb.01336-07.

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

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26

Cafaro, Valeria, Viviana Izzo, Roberta Scognamiglio, Eugenio Notomista, Paola Capasso, Annarita Casbarra, Piero Pucci i Alberto Di Donato. "Phenol Hydroxylase and Toluene/o-Xylene Monooxygenase from Pseudomonas stutzeri OX1: Interplay between Two Enzymes". Applied and Environmental Microbiology 70, nr 4 (kwiecień 2004): 2211–19. http://dx.doi.org/10.1128/aem.70.4.2211-2219.2004.

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ABSTRACT Degradation of aromatic hydrocarbons by aerobic bacteria is generally divided into an upper pathway, which produces dihydroxylated aromatic intermediates by the action of monooxygenases, and a lower pathway, which processes these intermediates down to molecules that enter the citric acid cycle. Bacterial multicomponent monooxygenases (BMMs) are a family of enzymes divided into six distinct groups. Most bacterial genomes code for only one BMM, but a few cases (3 out of 31) of genomes coding for more than a single monooxygenase have been found. One such case is the genome of Pseudomonas stutzeri OX1, in which two different monooxygenases have been found, phenol hydroxylase (PH) and toluene/o-xylene monooxygenase (ToMO). We have already demonstrated that ToMO is an oligomeric protein whose subunits transfer electrons from NADH to oxygen, which is eventually incorporated into the aromatic substrate. However, no molecular data are available on the structure and on the mechanism of action of PH. To understand the metabolic significance of the association of two similar enzymatic activities in the same microorganism, we expressed and characterized this novel phenol hydroxylase. Our data indicate that the PH P component of PH transfers electrons from NADH to a subcomplex endowed with hydroxylase activity. Moreover, a regulatory function can be suggested for subunit PH M. Data on the specificity and the kinetic constants of ToMO and PH strongly support the hypothesis that coupling between the two enzymatic systems optimizes the use of nonhydroxylated aromatic molecules by the draining effect of PH on the product(s) of oxidation catalyzed by ToMO, thus avoiding phenol accumulation.

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27

Zabolotny, M. A., Yu M. Barabash, N. P. Kulish, O. P. Dmitrenko i M. O. Kuzmenko. "Conformational states of NADH molecules in a hydrated shell under weak electromagnetic irradiation". Biophysics 60, nr 1 (styczeń 2015): 35–42. http://dx.doi.org/10.1134/s0006350915010261.

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Bloem, Audrey, Isabelle Sanchez, Sylvie Dequin i Carole Camarasa. "Metabolic Impact of Redox Cofactor Perturbations on the Formation of Aroma Compounds in Saccharomyces cerevisiae". Applied and Environmental Microbiology 82, nr 1 (16.10.2015): 174–83. http://dx.doi.org/10.1128/aem.02429-15.

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ABSTRACTRedox homeostasis is a fundamental requirement for the maintenance of metabolism, energy generation, and growth inSaccharomyces cerevisiae. The redox cofactors NADH and NADPH are among the most highly connected metabolites in metabolic networks. Changes in their concentrations may induce widespread changes in metabolism. Redox imbalances were achieved with a dedicated biological tool overexpressing native NADH-dependent or engineered NADPH-dependent 2,3-butanediol dehydrogenase, in the presence of acetoin. We report that targeted perturbation of the balance of cofactors (NAD+/NADH or, to a lesser extent, NADP+/NADPH) significantly affected the production of volatile compounds. In most cases, variations in the redox state of yeasts modified the formation of all compounds from the same biochemical pathway (isobutanol, isoamyl alcohol, and their derivatives) or chemical class (ethyl esters), irrespective of the cofactors. These coordinated responses were found to be closely linked to the impact of redox status on the availability of intermediates of central carbon metabolism. This was the case for α-keto acids and acetyl coenzyme A (acetyl-CoA), which are precursors for the synthesis of many volatile compounds. We also demonstrated that changes in the availability of NADH selectively affected the synthesis of some volatile molecules (e.g., methionol, phenylethanol, and propanoic acid), reflecting the specific cofactor requirements of the dehydrogenases involved in their formation. Our findings indicate that both the availability of precursors from central carbon metabolism and the accessibility of reduced cofactors contribute to cell redox status modulation of volatile compound formation.

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29

Hòa, Lê Thanh, Nguyễn Thị Khuê, Nguyễn Thị Bích Nga, Đỗ Thị Roan, Đỗ Trung Dũng, Lê Thị Kim Xuyến i Đoàn Thị Thanh Hương. "Genetic characterization of mitochondrial genome of the small intestinal fluke, Haplorchis taichui (Trematoda: Heterophyidae), Vietnamese sample". Vietnam Journal of Biotechnology 14, nr 2 (30.06.2016): 215–24. http://dx.doi.org/10.15625/1811-4989/14/2/9333.

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The small intestinal fluke, Haplorchis taichui Nishigori, 1924, belonging to genus Haplorchis (family Heterophyidae, class Trematoda, phylum Platyhelminthes), is a zoonotic pathogen causing disease in humans and animals. Complete mitochondrial genome (mtDNA) of H. taichui (strain HTAQT, collected from Quang Tri) was obtained and characterized for structural genomics providing valuable data for studies on epidemiology, species identification, diagnosis, classification, molecular phylogenetic relationships and prevention of the disease. The entire nucleotide mtDNA sequence of H. taichui (HTAQT) is 15.119 bp in length, containing 36 genes, including 12 protein-coding genes (cox1, cox2, cox3, nad1, nad2, nad3, nad4L, nad4, nad5, nad6, atp6 and cob); 2 ribosomal RNA genes, rrnL (16S) and rrnS (12S); 22 transfer RNA genes (tRNA or trn), and a non-coding region (NR), divided into two sub-regions of short non-coding (short, SNR) and long non-coding (long, LNR). LNR region, 1.692 bp in length, located between the position of trnG (transfer RNA-Glycine) and trnE (Glutamic acid), contains 6 tandem repeats (TR), arranged as TR1A, TR2A, TR1B, TR2B, TR3A, TR3B, respectively. Each protein coding gene (overall, 12 genes), ribosomal rRNA (2 genes) and tRNA (22 genes) were analyzed, in particular, protein-coding genes were defined in length, start and stop codons, and rRNA and tRNA genes for secondary structure.

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Schneckenburger, H., P. Gessler i I. Pavenstädt-Grupp. "Measurements of mitochondrial deficiencies in living cells by microspectrofluorometry." Journal of Histochemistry & Cytochemistry 40, nr 10 (październik 1992): 1573–78. http://dx.doi.org/10.1177/40.10.1527376.

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Microspectrofluorometric methods were developed for detection of mitochondrial metabolites and marker molecules in living cells. After excitation in the near UV and blue spectral ranges, respiratory-deficient strains of Saccharomyces cerevisiae showed higher levels of intrinsic fluorescence than corresponding wild types. This may be attributed to an increased emission by NADH and flavin molecules of the mutants. After incubation with the mitochondrial marker rhodamine 123, there was a strong indication that an energy transfer from flavin to rhodamine molecules occurred, which was more pronounced for the respiratory-deficient yeast strains. Skin fibroblasts obtained from patients with mitochondrial diseases showed approximately the same levels of autofluorescence and energy transfer but higher variances than a control cell line. These higher variances may result from a coexistence of intact and defective mitochondria.

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Chen, Siqi, Yuanbing Wang, Kongfu Zhu i Hong Yu. "Mitogenomics, Phylogeny and Morphology Reveal Ophiocordyceps pingbianensis Sp. Nov., an Entomopathogenic Fungus from China". Life 11, nr 7 (14.07.2021): 686. http://dx.doi.org/10.3390/life11070686.

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The new entomopathogenic fungus Ophiocordyceps pingbianensis, collected from Southeast China, was described by mitogenomic, morphological, and phylogenetic evidence. The systematic position of O. pingbianensis was determined by phylogenetic analyses based on six nuclear gene (ITS, tef1-α, nrSSU, nrLSU, rpb1 and rpb2) and 14 mitochondrial protein-coding gene (PCGs) (cox1, cox2, cox3, atp6, atp8, atp9, cob, nad1, nad2, nad3, nad4, nad5, nad6 and nad4L) data. Phylogenetic analyses reveal that O. pingbianensis was belonged to the Hirsutella nodulosa clade in the genus Ophiocordyceps of Ophiocordycipiaceae. This fungus exhibits distinctive characteristics which differed from other related Ophiocordyceps species with slender and geminate stromata, monophialidic conidiogenous cells with an inflated awl-shaped base, a twisty and warty phialide neck and a fusiform or oval conidia, as well as being found on a tiger beetle of Coleoptera buried in moss at the cave. The complete mitochondrial genome of O. pingbianensis was a circular DNA molecule 80,359 bp in length, containing 15 PCGs, 24 open reading frames genes (ORFs), 25 transfer RNA genes (tRNAs) and 27 introns. Ophiocordyceps pingbianensis, containing 27 introns, has the second largest mitogenome in Ophiocordycipiaceae and was next to O. sinensis. To our knowledge, this is the first report of the mitogenome from a new entomopathogenic fungus, and thus provides an important foundation for future studies on taxonomy, genetics and evolutionary biology of Ophiocordycipiaceae.

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Heslop, Kareem A., Pieter Burger, Monika Gooz, Amandine Rovini, Thomas Benton, Catherine Mills, Patrick Woster i Eduardo N. Maldonado. "Small molecules targeting the VDAC-NADH binding pocket modulate mitochondrial metabolism in cancer cells". Biophysical Journal 121, nr 3 (luty 2022): 316a. http://dx.doi.org/10.1016/j.bpj.2021.11.1175.

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Nowall, Wilbur B., i Werner G. Kuhr. "Electrocatalytic Surface for the Oxidation of NADH and Other Anionic Molecules of Biological Significance". Analytical Chemistry 67, nr 19 (październik 1995): 3583–88. http://dx.doi.org/10.1021/ac00115a031.

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Valentini, Federica, Silvia Orlanducci, M. L. Terranova i Giuseppe Palleschi. "Fabrication Routes of Microsized Electrochemical Biosensors Based on Single-Walled Carbon Nanotubes". Materials Science Forum 539-543 (marzec 2007): 1098–103. http://dx.doi.org/10.4028/www.scientific.net/msf.539-543.1098.

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In this work two different synthesis processes for Single-Wall Carbon Nanotubes deposition (such as the Hot Filament-Chemical Vapor Deposition, HF-CVD, and the electrophoretic deposition, EPD) on microwire surfaces, were described. Then, the morphological and structural characterization of SWNT-modified microwires were performed by Scanning Electron Microscopy (FE-SEM) and Raman Spectroscopy, respectively. Finally, the nanostrcutured microelectrodes were electrochemically characterized using NADH, NAD+, epinephrine, and ascorbic acid (AA), useful biological molecules to develop electrochemical sensors and biosensors.

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35

Yoshioka, Shota, Sota Nimura, Masayuki Naruto i Susumu Saito. "Reaction of H2 with mitochondria-relevant metabolites using a multifunctional molecular catalyst". Science Advances 6, nr 43 (październik 2020): eabc0274. http://dx.doi.org/10.1126/sciadv.abc0274.

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The Krebs cycle is the fuel/energy source for cellular activity and therefore of paramount importance for oxygen-based life. The cycle occurs in the mitochondrial matrix, where it produces and transfers electrons to generate energy-rich NADH and FADH2, as well as C4-, C5-, and C6-polycarboxylic acids as energy-poor metabolites. These metabolites are biorenewable resources that represent potential sustainable carbon feedstocks, provided that carbon-hydrogen bonds are restored to these molecules. In the present study, these polycarboxylic acids and other mitochondria-relevant metabolites underwent dehydration (alcohol-to-olefin and/or dehydrative cyclization) and reduction (hydrogenation and hydrogenolysis) to diols or triols upon reaction with H2, catalyzed by sterically confined iridium–bipyridyl complexes. The investigation of these single–metal site catalysts provides valuable molecular insights into the development of molecular technologies for the reduction and dehydration of highly functionalized carbon resources.

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Mikšanová, Markéta, Jiří Hudeček, Jan Páca i Marie Stiborová. "To the Mechanism of Horseradish Peroxidase-Mediated Degradation of a Recalcitrant Dye Remazol Brilliant Blue R". Collection of Czechoslovak Chemical Communications 66, nr 4 (2001): 663–75. http://dx.doi.org/10.1135/cccc20010663.

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Thein vitroenzymatic metabolism of a recalcitrant dye Remazol Brilliant Blue R (RBBR) was investigated using horseradish peroxidase (HRP). At optimum pH (4.5), the apparent Michaelis constant (KM) value for the oxidation of RBBR catalyzed by HRP is 14.8 μmol l-1. HRP-mediated conversion of RBBR proceedsviaa conventional peroxidase reaction, by a sequential one-electron oxidation of two molecules of RBBR by the peroxidase Compounds I and II. The oxidation is inhibited by radical trapping agents (nicotinamide adenine dinucleotide reduced (NADH), ascorbate, glutathione). This confirms that the peroxidase-mediated oxidation of RBBR proceedsviaradical mechanism. Gel permeation profile of the RBBR oxidation products shows that the pattern of molecular weight distribution was shifted to the higher molecular weight region indicating formation of RBBR oligomers. In addition to HRP, the RBBR dye is also oxidized by another peroxidase, the mammalian lactoperoxidase.

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Allali, Naoual, Veronika Urbanova, Mathieu Etienne, Xavier Devaux, Martine Mallet, Brigitte Vigolo, Jean-Joseph Adjizian i in. "Accurate control of the covalent functionalization of single-walled carbon nanotubes for the electro-enzymatically controlled oxidation of biomolecules". Beilstein Journal of Nanotechnology 9 (26.10.2018): 2750–62. http://dx.doi.org/10.3762/bjnano.9.257.

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Single-walled carbon nanotubes (SWCNTs) were functionalized by ferrocene through ethyleneglycol chains of different lengths (FcETGn) and the functionalized SWCNTs (f-SWCNTs) were characterized by different complementary analytical techniques. In particular, high-resolution scanning electron transmission microscopy (HRSTEM) and electron energy loss spectroscopy (EELS) analyses support that the outer tubes of the carbon-nanotube bundles were covalently grafted with FcETGn groups. This result confirms that the electrocatalytic effect observed during the oxidation of the reduced form of nicotinamide adenine dinucleotide (NADH) co-factor by the f-SWCNTs is due to the presence of grafted ferrocene derivatives playing the role of a mediator. This work clearly proves that residual impurities present in our SWCNT sample (below 5 wt. %) play no role in the electrocatalytic oxidation of NADH. Moreover, molecular dynamic simulations confirm the essential role of the PEG linker in the efficiency of the bioelectrochemical device in water, due to the favorable interaction between the ETG units and water molecules that prevents π-stacking of the ferrocene unit on the surface of the CNTs. This system can be applied to biosensing, as exemplified for glucose detection. The well-controlled and well-characterized functionalization of essentially clean SWCNTs enabled us to establish the maximum level of impurity content, below which the f-SWCNT intrinsic electrochemical activity is not jeopardized.

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Matic, Sandra, Daniela A. Geisler, Ian M. Møller, Susanne Widell i Allan G. Rasmusson. "Alamethicin permeabilizes the plasma membrane and mitochondria but not the tonoplast in tobacco (Nicotiana tabacum L. cv Bright Yellow) suspension cells". Biochemical Journal 389, nr 3 (26.07.2005): 695–704. http://dx.doi.org/10.1042/bj20050433.

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The ion channel-forming peptide AlaM (alamethicin) is known to permeabilize isolated mitochondria as well as animal cells. When intact tobacco (Nicotiana tabacum L.) Bright Yellow-2 cells were treated with AlaM, the cells became permeable for low-molecular-mass molecules as shown by induced leakage of NAD(P)+. After the addition of cofactors and substrates, activities of cytosolic as well as mitochondrial respiratory enzymes could be directly determined inside the permeabilized cells. However, at an AlaM concentration at which the cytoplasmic enzymes were maximally accessible, the vacuole remained intact, as indicated by an unaffected tonoplast proton gradient. Low-flux permeabilization of plasma membranes and mitochondria at moderate AlaM concentrations was reversible and did not affect cell vigour. Higher AlaM concentrations induced cell death. After the addition of catalase that removes the H2O2 necessary for NADH oxidation by apoplastic peroxidases, mitochondrial oxygen consumption could be measured in permeabilized cells. Inhibitor-sensitive oxidation of the respiratory substrates succinate, malate and NADH was observed after the addition of the appropriate coenzymes (ATP, NAD+). The capacities of different pathways in the respiratory electron-transport chain could thus be determined directly. We conclude that AlaM permeabilization provides a very useful tool for monitoring metabolic pathways or individual enzymes in their native proteinaceous environment with controlled cofactor concentrations. Possible uses and limitations of this method for plant cell research are discussed.

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Heslop, Kareem A., Pieter Burger, Christiana Kappler, Ashish K. Solanki, Monika Gooz, Yuri K. Peterson, Catherine Mills i in. "Small molecules targeting the NADH-binding pocket of VDAC modulate mitochondrial metabolism in hepatocarcinoma cells". Biomedicine & Pharmacotherapy 150 (czerwiec 2022): 112928. http://dx.doi.org/10.1016/j.biopha.2022.112928.

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Yu, Steve S. F., Kelvin H. C. Chen, Mandy Y. H. Tseng, Yane-Shih Wang, Chiu-Feng Tseng, Yu-Ju Chen, Ded-Shih Huang i Sunney I. Chan. "Production of High-Quality Particulate Methane Monooxygenase in High Yields from Methylococcus capsulatus (Bath) with a Hollow-Fiber Membrane Bioreactor". Journal of Bacteriology 185, nr 20 (15.10.2003): 5915–24. http://dx.doi.org/10.1128/jb.185.20.5915-5924.2003.

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ABSTRACT In order to obtain particulate methane monooxygenase (pMMO)-enriched membranes from Methylococcus capsulatus (Bath) with high activity and in high yields, we devised a method to process cell growth in a fermentor adapted with a hollow-fiber bioreactor that allows easy control and quantitative adjustment of the copper ion concentration in NMS medium over the time course of cell culture. This technical improvement in the method for culturing bacterial cells allowed us to study the effects of copper ion concentration in the growth medium on the copper content in the membranes, as well as the specific activity of the enzyme. The optimal copper concentration in the growth medium was found to be 30 to 35 μM. Under these conditions, the pMMO is highly expressed, accounting for 80% of the total cytoplasmic membrane proteins and having a specific activity as high as 88.9 nmol of propylene oxide/min/mg of protein with NADH as the reductant. The copper stoichiometry is ∼13 atoms per pMMO molecule. Analysis of other metal contents provided no evidence of zinc, and only traces of iron were present in the pMMO-enriched membranes. Further purification by membrane solubilization in dodecyl β-d-maltoside followed by fractionation of the protein-detergent complexes according to molecular size by gel filtration chromatography resulted in a good yield of the pMMO-detergent complex and a high level of homogeneity. The pMMO-detergent complex isolated in this way had a molecular mass of 220 kDa and consisted of an αβγ protein monomer encapsulated in a micelle consisting of ca. 240 detergent molecules. The enzyme is a copper protein containing 13.6 mol of copper/mol of pMMO and essentially no iron (ratio of copper to iron, 80:1). Both the detergent-solubilized membranes and the purified pMMO-detergent complex exhibited reasonable, if not excellent, specific activity. Finally, our ability to control the level of expression of the pMMO allowed us to clarify the sensitivity of the enzyme to NADH and duroquinol, the two common reductants used to assay the enzyme.

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Pérez-Pinzón, Miguel A., Patricia L. Mumford, VeróAnica Carranza i Thomas J. Sick. "Calcium Influx from the Extracellular Space Promotes NADH Hyperoxidation and Electrical Dysfunction after Anoxia in Hippocampal Slices". Journal of Cerebral Blood Flow & Metabolism 18, nr 2 (luty 1998): 215–21. http://dx.doi.org/10.1097/00004647-199802000-00013.

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A characteristic event during reperfusion after cerebral ischemia in vivo, and reoxygenation after anoxia in vitro, is hyperoxidation of the electron carriers of the mitochondrial respiratory chain. Current studies have tested the hypothesis that there is a relation among calcium molecules derived from extracellular sources, mitochondrial hyperoxidation, and electrical recovery after anoxia in hippocampal slices. Rat hippocampal slices were superfused with artificial cerebrospinal fluids (ACSF) containing calcium chloride (CaCl2) in concentrations of: 0.5, 1, 2, and 4 mmol/L. Slices were made anoxic and then allowed to recover for 60 minutes. Reduction–oxidation shifts of NADH were measured by rapid-scanning spectrofluorometry. Synaptic activity was indicated by population spike amplitudes in the CA1 pyramidal cell subfield of the hippocampus in response to stimulation of the Schaffer collaterals. Low calcium ACSF concentrations ameliorated NADH hyperoxidation and improved synaptic transmission recovery after anoxia. High calcium ACSF concentrations had opposite effects. These data suggest a link between mitochondrial hyperoxidation and electrical recovery after postanoxia reoxygenation and support the hypothesis that cytosolic calcium overload promotes mitochondrial hyperoxidation and limits electrical recovery.

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Nakatani, Yoshio, Wanting Jiao, David Aragão, Yosuke Shimaki, Jessica Petri, Emily J. Parker i Gregory M. Cook. "Crystal structure of type II NADH:quinone oxidoreductase from Caldalkalibacillus thermarum with an improved resolution of 2.15 Å". Acta Crystallographica Section F Structural Biology Communications 73, nr 10 (23.09.2017): 541–49. http://dx.doi.org/10.1107/s2053230x17013073.

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Type II NADH:quinone oxidoreductase (NDH-2) is a respiratory enzyme found in the electron-transport chain of many species, with the exception of mammals. It is a 40–70 kDa single-subunit monotopic membrane protein that catalyses the oxidation of NADH and the reduction of quinone molecules via the cofactor FAD. NDH-2 is a promising new target for drug development given its essential role in many bacterial species and intracellular parasites. Only two bacterial NDH-2 structures have been reported and these structures are at moderate resolution (2.3–2.5 Å). In this communication, a new crystallization platform is reported that produced high-quality NDH-2 crystals that diffracted to high resolution (2.15 Å). The high-resolution NDH-2 structure was used for in silico quinone substrate-docking studies to investigate the binding poses of menadione and ubiquinone molecules. These studies revealed that a very limited number of molecular interactions occur at the quinone-binding site of NDH-2. Given that the conformation of the active site is well defined, this high-resolution structure is potentially suitable for in silico inhibitor-compound screening and ligand-docking applications.

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Ma, Liang, Shuting Lv, Jianxin Tang, Jianxin Liu, Wen Li, Jing Deng, Yan Deng, Jingjing Du, Xueying Liu i Xiaoxi Zeng. "Study on bioactive molecules involved in extracellular biosynthesis of silver nanoparticles by Penicillium aculeatum Su1". Materials Express 9, nr 5 (1.08.2019): 475–83. http://dx.doi.org/10.1166/mex.2019.1508.

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In this paper, the biosynthesis of high-stable and biocompatible silver nanoparticles (AgNPs) was implemented by employing cell-free filtrate of Penicillium aculeatum Su1. The compositions analysis of reducing biomolecules in reaction system before and after AgNPs synthesis suggested that proteins were mainly involved in the biosynthesis process of AgNPs. Polyacrylamide gel electrophoresis (SDS-PAGE) analysis displayed that two main protein bands with molecular weights ranging from 66.2 to 116 KDa and 35 to 45 KDa were capped on the surface of AgNPs. The further identification of these protein bands by liquid chromatography-mass spectrometry (LC-MS/MS) analysis indicated that actin as a major protein component was responsible for stabilization of prepared AgNPs. The activity of nitrate reductase secreted by P. aculeatum Su1 was 73.73 ± 3.89 μg/(g · h). Furthermore, the dialysis assay showed that small molecular components had significant impacts on yield and particle size of biosynthesized AgNPs. Reduced nicotinamide adenine dinucleotide or reduced nicotinamide adenine dinucleotide phosphate (NADH or NADPH)-dependent nitrate reductases and other types of reductases or non-enzymatic bioactive molecules (≥ 3.5 KDa) might simultaneously participate in the biosynthesis process of AgNPs mediated by P. aculeatum Su1.

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Bottoni, Patrizia, Giulia Gionta i Roberto Scatena. "Remarks on Mitochondrial Myopathies". International Journal of Molecular Sciences 24, nr 1 (21.12.2022): 124. http://dx.doi.org/10.3390/ijms24010124.

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Mitochondrial myopathies represent a heterogeneous group of diseases caused mainly by genetic mutations to proteins that are related to mitochondrial oxidative metabolism. Meanwhile, a similar etiopathogenetic mechanism (i.e., a deranged oxidative phosphorylation and a dramatic reduction of ATP synthesis) reveals that the evolution of these myopathies show significant differences. However, some physiological and pathophysiological aspects of mitochondria often reveal other potential molecular mechanisms that could have a significant pathogenetic role in the clinical evolution of these disorders, such as: i. a deranged ROS production both in term of signaling and in terms of damaging molecules; ii. the severe modifications of nicotinamide adenine dinucleotide (NAD)+/NADH, pyruvate/lactate, and α-ketoglutarate (α-KG)/2- hydroxyglutarate (2-HG) ratios. A better definition of the molecular mechanisms at the basis of their pathogenesis could improve not only the clinical approach in terms of diagnosis, prognosis, and therapy of these myopathies but also deepen the knowledge of mitochondrial medicine in general.

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Karagüler, N. G., R. B. Sessions, B. Binay, E. B. Ordu i A. R. Clarke. "Protein engineering applications of industrially exploitable enzymes: Geobacillus stearothermophilus LDH and Candida methylica FDH". Biochemical Society Transactions 35, nr 6 (23.11.2007): 1610–15. http://dx.doi.org/10.1042/bst0351610.

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Enzymes have become important tools in several industries due to their ability to produce chirally pure and complex molecules with interesting biological properties. The NAD+-dependent LDH (lactate dehydrogenase) [bsLDH [Geobacillus stearothermophilus (formerly Bacillus stearothermophilus) LDH] from G. stearothermophilus and the NAD+-dependent FDH (formate dehydrogenase) [cmFDH (Candida methylica FDH)] enzyme from C. methylica are particularly crucial enzymes in the pharmaceutical industry and are related to each other in terms of NADH use and regeneration. LDH catalyses the interconversion of pyruvate (oxo acid) and lactate (α-hydroxy acid) using the NADH/NAD+ pair as a redox cofactor. Employing LDH to reduce other oxo acids can generate chirally pure α-hydroxy acids of use in the production of pharmaceuticals. One important use of FDH is to regenerate the relatively expensive NADH cofactor that is used by NAD+-dependent oxidoreductases such as LDH. Both LDH and FDH from organisms of interest were previously cloned and overproduced. Therefore they are available at a low cost. However, both of these enzymes show disadvantages in the large-scale production of chirally pure compounds. We have applied two routes of protein engineering studies to improve the properties of these two enzymes, namely DNA shuffling and site-directed mutagenesis. Altering the substrate specificity of bsLDH by DNA shuffling and changing the coenzyme specificity of cmFDH by site-directed mutagenesis are the most successful examples of our studies. The present paper will also include the details of these examples together with some other applications of protein engineering regarding these enzymes.

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Laroussi, Arwa, Małgorzata Kot, Jan Ingo Flege, Noureddine Raouafi i Vladimir Mirsky. "Self-Assembled Monolayers from Symmetrical Di-Thiols: Preparation, Characterization and Application for the Assembly of Electrochemically Active Films". Engineering Proceedings 6, nr 1 (17.05.2021): 17. http://dx.doi.org/10.3390/i3s2021dresden-10112.

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1,3-dimercaptopropan-2-ol, a symmetrical di-thiol, has been synthesized and applied as a new type of anchor molecule to prepare a self-assembled monolayer (SAM) on a gold surface. The formed monolayers were studied by cyclic voltammetry, impedance spectroscopy, X-ray photoelectron spectroscopy, kinetic capacitance, and contact angle measurements. The SAM structure depends on the adsorption conditions. A short incubation time of the electrode at high concentration of this di-thiol leads to the predominating binding through one thiol group of the adsorbate to the gold surface, while a long incubation at low concentration leads to the predominating binding by both thiol groups. A comparative study of the desorption and replacement of SAMs indicates a strong stability increase when the SAM molecules bond gold surfaces by two bonds mainly. This monolayer was used to immobilize electrochemically active p-benzoquinone moiety. The surface concentration of p-benzoquinone obtained from cyclic voltammetry is 2.5 ± 0.2 × 10−10 mol cm−2, which corresponds to the functionalization of 65 ± 5% of SAM molecules. The obtained highly stable SAM with redox-active terminal group can be applied for different tasks of chemical sensing and biosensing. As an example, an application of this system for electrocatalytical oxidation of dihydronicotinamide adenosine dinucleotide (NADH) was tested.

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Blatter, E. E., M. L. Tasayco, G. Prestwich i R. Pietruszko. "Chemical modification of aldehyde dehydrogenase by a vinyl ketone analogue of an insect pheromone". Biochemical Journal 272, nr 2 (1.12.1990): 351–58. http://dx.doi.org/10.1042/bj2720351.

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A major component of the sex pheromone from the tobacco budworm moth Heliothis virescens is a C16 straight-chain aldehyde with a single unsaturation at the eleventh position. The sex pheromones are inactivated when metabolized to their corresponding acids by insect aldehyde dehydrogenase. During this investigation it was demonstrated that the C16 aldehyde is a good substrate for human aldehyde dehydrogenase (EC 1.2.1.3) isoenzymes E1 and E2 with Km and Kcat. values at pH 7.0 of 2 microM and 0.4 mumol of NADH/min per mg and of 0.6 microM and 0.24 mumol of NADH/min per mg respectively. A vinyl ketone analogue of the pheromone inhibited insect pheromone metabolism; it also inactivated human aldehyde dehydrogenase. Total inactivation of both isoenzymes was achieved at stoichiometric (equal or less than the subunit number) concentrations of vinyl ketone, incorporating 2.1-2.6 molecules/molecule of enzyme. Substrate protection was observed in the presence of the parent aldehyde and 5′-AMP. Peptide maps of tryptic digests of the E2 isoenzyme modified with 3H-labelled vinyl ketone showed that incorporation occurred into a single peptide peak. The labelled peptide of E2 isoenzyme was further purified on h.p.l.c. and sequenced. The label was incorporated into cysteine-302 in the primary structure of E2 isoenzyme, thus indicating that cysteine-302 is located in the aldehyde substrate area of the active site of aldehyde dehydrogenase. Affinity labelling of aldehyde dehydrogenase with vinyl ketones may prove to be of general utility in biochemical studies of these enzymes.

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Moreau, Patrice L. "Diversion of the Metabolic Flux from Pyruvate Dehydrogenase to Pyruvate Oxidase Decreases Oxidative Stress during Glucose Metabolism in Nongrowing Escherichia coli Cells Incubated under Aerobic, Phosphate Starvation Conditions". Journal of Bacteriology 186, nr 21 (1.11.2004): 7364–68. http://dx.doi.org/10.1128/jb.186.21.7364-7368.2004.

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ABSTRACT Ongoing aerobic metabolism in nongrowing cells may generate oxidative stress. It is shown here that the levels of thiobarbituric acid-reactive substances (TBARSs), which measure fragmentation products of oxidized molecules, increased strongly at the onset of starvation for phosphate (Pi). This increase in TBARS levels required the activity of the histone-like nucleoid-structuring (H-NS) protein. TBARS levels weakly increased further in ΔahpCF mutants deficient in alkyl hydroperoxide reductase (AHP) activity during prolonged metabolism of glucose to acetate. Inactivation of pyruvate oxidase (PoxB) activity decreased the production of acetate by half and significantly increased the production of TBARS. Overall, these data suggest that during incubation under aerobic, Pi starvation conditions, metabolic flux is diverted from the pyruvate dehydrogenase (PDH) complex (NAD dependent) to PoxB (NAD independent). This shift may decrease the production of NADH and in turn the adventitious production of H2O2 by NADH dehydrogenase in the respiratory chain. The residual low levels of H2O2 produced during prolonged incubation can be scavenged efficiently by AHP. However, high levels of H2O2 may be reached transiently at the onset of stationary phase, primarily because H-NS may delay the metabolic shift from PDH to PoxB.

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Ohnishi, S. Tsuyoshi, Kyoko Shinzawa-Itoh, Shinya Yoshikawa i Tomoko Ohnishi. "EPR detection of protein-associated ubiquinone molecules in purified bovine heart NADH–ubiquinone oxidoreductase (complex I)". Biochimica et Biophysica Acta (BBA) - Bioenergetics 1797 (lipiec 2010): 21–22. http://dx.doi.org/10.1016/j.bbabio.2010.04.082.

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Folkerts, O., i M. R. Hanson. "The male sterility-associated pcf gene and the normal atp9-1 gene in Petunia are located on different mitochondrial DNA molecules." Genetics 129, nr 3 (1.11.1991): 885–95. http://dx.doi.org/10.1093/genetics/129.3.885.

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Abstract A mitochondrial DNA (mtDNA) region termed the S-pcf locus has previously been correlated with cytoplasmic male sterility (CMS) in Petunia. In order to understand the relationship of the S-pcf locus to homologous sequences found elsewhere in mtDNAs of both CMS and fertile lines, the structure of the mitochondrial genome of CMS Petunia line 3688 was determined by cosmid walking. The S-pcf locus, which includes the only copies of genes for NADH dehydrogenase subunit 3 (nad3) and small ribosomal subunit protein 12 (rps12) was found to be located on a circular map of 396 kb, while a second almost identical circular map of 407 kb carries the only copies of the genes for 18S and 5S rRNA (rrn18 and rrn5), the only copy of a conserved unidentified gene (orf25), and the only known functional copy of atp9. Three different copies of a recombination repeat were found in six genomic environments, predicting sub-genomic circles of 277, 266 and 130 kb. The ratio of atp9 to S-pcf mtDNA sequences was approximately 1.5 to 1, indicating that sub-genomic molecules carrying these genes differ in abundance. Comparison of the mtDNA organization of the CMS line with that of the master circle of fertile Petunia line 3704 reveals numerous changes in order and orientation of ten different sectors.

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