NADH Binding Site Research Articles

Natural flavonoids as promising lactate dehydrogenase A inhibitors: Comprehensive in vitro and in silico analysis.

The inhibitory potential of 17 flavonoids on lactate dehydrogenase A (LDHA), a key enzyme in the downstream process of aerobic glycolysis in cancer cells, is investigated. Fisetin exhibited excellent inhibitory activity (IC50 = 0.066 µM). Quercetin 3-β-D-glucoside, quercetin 3-galactoside, luteolin, neoeriocitrin, and luteolin 7-O-β-D-glucoside showed good inhibitory activity (IC50 = 1.397-15.730 µM). Biochanin A, baicalein, quercetin, scutellarein-7-glucuronide, diosmetin, baicalein 7-O-β-D-glucuronide, and apigenin 7-apioglucoside demonstrated moderate inhibitory activity (IC50 = 33.007-86.643 µM). Eriodictyol, quercetin 7-O-β-D-glucoside, apigenin 7-O-β-D-glucoside, and epicatechin were inactive. The Lineweaver-Burk plot showed that fisetin competitively inhibits NADH binding (Ki = 0.024 µM). Ki values for other compounds were calculated using the Cheng-Prusoff equation (Ki = 0.2799-2.1661 µM). The study revealed that the inhibitory effect of flavonoids varies with the number and position of OH groups and bound sugars. Molecular docking analyses indicated that flavonoids exhibited strong interactions with the NADH binding site of LDHA through hydrophobic interactions and hydrogen bonds. Molecular dynamic simulations tested the stability of the fisetin-LDHA complex over 100 ns and showed fisetin's high binding affinity to LDHA, maintaining strong hydrogen bonds. The binding energy of fisetin with LDHA was -33.928 kcal/mol, indicating its effectiveness as an LDHA inhibitor. Consequently, flavonoids identified as strong inhibitors could be potential cancer treatment sources through LDHA inhibition.

Functional and structural characterization of a thermostable flavin reductase from Geobacillus mahadii Geo-05

Flavin reductases play a vital role in catalyzing the reduction of flavin through NADH or NADPH oxidation. The gene encoding flavin reductase from the thermophilic bacterium Geobacillus mahadii Geo-05 (GMHpaC) was cloned, overexpressed in Escherichia coli BL21 (DE3) pLysS, and purified to homogeneity. The purified recombinant GMHpaC (Class II) contains chromogenic cofactors, evidenced by maximal absorbance peaks at 370 nm and 460 nm. GMHpaC stands out as the most thermostable and pH-tolerant flavin reductase reported to date, retaining up to 95 % catalytic activity after incubation at 70 °C for 30 min and maintaining over 80 % activity within a pH range of 2–12 for 30 min. Furthermore, GMHpaC's catalytic activity increases by 52 % with FMN as a co-factor compared to FAD and riboflavin. GMHpaC, coupled with 4-hydroxyphenylacetate-3-monooxygenase (GMHpaB) from G. mahadii Geo-05, enhances the hydroxylation of 4-hydroxyphenylacetate (HPA) by 85 %. The modeled structure of GMHpaC reveals relatively conserved flavin and NADH binding sites. Modeling and docking studies shed light on structural features and amino acid substitutions that determine GMHpaC's co-factor specificity. The remarkable thermostability, high catalytic activity, and general stability exhibited by GMHpaC position it as a promising enzyme candidate for various industrial applications.

Structural robustness of the NADH binding site in NADH:ubiquinone oxidoreductase (complex I)

Energy converting NADH:ubiquinone oxidoreductase, complex I, is the first enzyme of respiratory chains in most eukaryotes and many bacteria. Mutations in genes encoding subunits of human complex I may lead to its dysfunction resulting in a diverse clinical pattern. The effect of mutations on the protein structure is not known. Here, we focus on mutations R88G, E246K, P252R and E377K that are found in subunit NDUFV1 comprising the NADH binding site of complex I. Homologous mutations were introduced into subunit NuoF of Aquifex aeolicus complex I and it was attempted to crystallize variants of the electron input module, NuoEF, with bound substrates in the oxidized and reduced state. The E377K variant did not form crystals most likely due to an improper protein assembly. The architecture of the NADH binding site is hardly affected by the other mutations indicating its unexpected structural robustness. The R88G, E246K and P252R mutations led to small local structural rearrangements that might be related to their pathogenicity. These minor structural changes involve substrate binding, product release and the putative formation of reactive oxygen species. The structural consequences of the mutations as obtained with the bacterial enzyme might thus help to contribute to the understanding of disease causing mutations.

The Na+-translocating NADH:quinone oxidoreductase (Na+-NQR): Physiological role, structure and function of a redox-driven, molecular machine

Many bacterial processes are powered by the sodium motive force (smf) and in case of pathogens, the smf contributes to virulence. Vibrio cholerae, the causative agent of Cholera disease, possesses a Na+-translocating NADH:quinone oxidoreductase (NQR), a six-subunit membrane protein assembly. The 3D structure of NQR revealed the arrangement of the six subunits NqrABCDEF, the position of all redox cofactors (four flavins, two [2Fe-2S] centers) and the binding sites for the substrates NADH (in NqrF) and ubiquinone (in NqrB). Upon oxidation of NADH, electrons are shuttled twice across the membrane, starting with cytoplasmic FADNqrF and electron transfer to the [2Fe2S] clusterNqrF and from there to an intra-membranous [2Fe-2S] clusterNqrDE, periplasmic FMNNqrC, FMNNqrB and from there to riboflavinNqrB. This riboflavin is located at the cytoplasmic entry site of the sodium channel in NqrB, and it donates electrons to ubiquinone-8 positioned at the cytoplasmic side of NqrB. Targeting the substrate binding sites of NQR is a promising strategy to identify new inhibitors against many bacterial pathogens. Detailed structural information on the binding mode of natural inhibitors and small molecules in the active sites of NQR is now available, paving the way for the development of new antibiotics. The NQR shows different conformations as revealed in recent cryo-EM and crystallographic studies combined with spectroscopic analyses. These conformations represent distinct steps in the catalytic cycle. Considering the structural and functional data available, we propose a mechanism of Na+-NQR based on conformational coupling of electron transfer and Na+ translocation reaction steps.

In Silico Screening and Molecular Dynamics Simulation of Potential Anti-Malarial Agents from Zingiberaceae as Potential Plasmodium falciparum Lactate Dehydrogenase (PfLDH) Enzyme Inhibitors.

Malaria continues to be a major public health issue in a number of countries, particularly in tropical regions-the emergence of drug-resistant Plasmodium falciparum encourages new drug discovery research. The key to Plasmodium falciparum survival is energy production up to 100 times greater than other parasites, primarily via the PfLDH. This study targets PfLDH with natural bioactive compounds from the Zingiberaceae family through molecular docking and molecular dynamic studies. Sulcanal, quercetin, shogosulfonic acid C, galanal A and naringenin are the Top 5 compounds with a lower binding energy value than chloroquine, which was used as a control in this study. By binding to NADH and substrate binding site residues, the majority of them are expected to inhibit pyruvate conversion to lactate and NAD+ regeneration. When compared to sulcanal and control drugs, the molecular dynamics (MD) simulation study indicated that quercetin may be the most stable molecule when interacting with PfLDH.

Structural and Functional Characterization of a Mycobacterial Methylenetetrahydrofolate Reductase Utilizing NADH as the Exclusive Cofactor.

5,10-Methylenetetraydrofolate reductase (MTHFR) is a key enzyme in folate metabolism. MSMEG_6649, a non-canonical MTHFR from Mycobacterium smegmatis, was previously reported as a monomeric protein lacking the flavin coenzyme. However, the structural basis for its unique flavin-independent catalytic mechanism remains poorly understood. Here, we determined the crystal structures of apo MTHFR MSMEG_6649 and its complex with NADH from M. smegmatis. Structural analysis revealed that the groove formed by the loops 4 and 5 of non-canonical MSMEG_6649 interacting with FAD was significantly larger than that of canonical MTHFR. Meanwhile, the NADH binding site in MSMEG_6649 is highly similar to the FAD binding site in canonical MTHFR, suggesting that NADH plays the same role (immediate hydride donor for methylenetetraydrofolate) as FAD in the catalytic reaction. Using biochemical analysis, molecular modeling, and site-directed mutagenesis, the critical residues participating in the binding of NADH and the substrate 5,10-methylenetetrahydrofolate as well as the product 5-methyltetrahydrofolate were identified and validated. Taken together, this work not only provides a good starting point for understanding the potential catalytic mechanism for MSMEG_6649, but also identifies an exploitable target for the development of anti-mycobacterial drugs.

Proton-translocating NADH:ubiquinone oxidoreductase of Paracoccus denitrificans plasma membranes catalyzes FMN-independent reverse electron transfer to hexaammineruthenium (III)

NADH-OH, the specific inhibitor of NADH-binding site of the mammalian complex I, is shown to completely block FMN-dependent reactions of P. denitrificans enzyme in plasma membrane vesicles: NADH oxidation (in a competitive manner with Ki of 1 nM) as well as reduction of pyridine nucleotides, ferricyanide and oxygen in the reverse electron transfer. In contrast to these activities, the reverse electron transfer to hexaammineruthenium (III) catalyzed by plasma membrane vesicles is insensitive to NADH-OH. To explain these results, we hypothesize the existence of a non-FMN redox group of P. denitrificans complex I that is capable of reducing hexaammineruthenium (III), which is corroborated by the complex kinetics of NADH: hexaammineruthenium (III)-reductase activity, catalyzed by this enzyme. A new assay procedure for measuring succinate-driven reverse electron transfer catalyzed by P. denitrificans complex I to hexaammineruthenium (III) is proposed.

Uncovering the inhibitory potentials of Phyllanthus nivosus leaf and its bioactive compounds against Plasmodium lactate dehydrogenase for malaria therapy

Malaria control efforts have been hampered due to the emergence of resistant malaria parasite strains and the coinciding events of Covid-19. The quest for more effective and safe treatment alternatives is driving a slew of new studies that must be accelerated if malaria can be overcome. Due to its reported antimalarial activity, we studied the effects of extract and fractions of Phyllanthus nivosus leaf on Plasmodium lactate dehydrogenase (pLDH) activity using an in vitro assay. This was followed by an anti-plasmodial study using Plasmodium berghei-infected mice and an in silico identification of the plant’s phytochemicals with possible pLDH-inhibitory activity. The activity of pLDH was significantly reduced in the presence of ethanol extract and various solvent fractions of Phyllanthus nivosus leaf, with the ethyl acetate fraction having the best inhibitory activity, which was comparable to that of the standard drug (chloroquine). The ethyl acetate fraction at 100 and 200 mg/Kg also suppressed the parasitaemia of Plasmodium berghei-infected mice by 76 and 80% respectively. Among the 53 compounds docked against pLDH, (-)-alpha-Cadinol, (+)-alpha-phellandrene, and spathulenol, all terpenes from the ethyl acetate fraction of P. nivosus leaf extract, demonstrated docking scores comparable to that of chloroquine. The three chemicals, like chloroquine, displayed important molecular interactions with the amino acid residues of the enzyme’s NADH-binding site. According to the in silico ADMET study, the three terpenes have suitable drug-like abilities, pharmacokinetic features, and safety profiles. Hence, they could be considered for further development as antimalarial drugs. Communicated by Ramaswamy H. Sarma

Elucidation of the anti-plasmodial activity of novel imidazole and oxazole compounds through computational and in vivo experimental approaches

The development of resistance to conventional antimalarial therapies, along with the unfavorable impact of the COVID-19 pandemic on the global malaria fight, necessitates a greater focus on the search for more effective antimalarial drugs. Targeting a specific enzyme of the malaria parasite to alter its metabolic pathways is a reliable technique for finding antimalarial drug candidates. In this study, we used an in silico technique to test four novel imidazoles and an oxazole derivative for inhibitory potential against Plasmodium lactate dehydrogenase (pLDH), a unique glycolytic enzyme necessary for parasite survival and energy production. The promising imidazole compounds and the oxazole derivative were then tested for anti-plasmodial efficacy in Plasmodium berghei-infected mice. With a binding energy of −6.593 kcal/mol, IM-3 had the best docking score against pLDH, which is close to that of NADH (−6.758 kcal/mol) and greater than that of chloroquine (−3.917 kcal/mol). The test compounds occupied the enzyme’s NADH binding site, with IM-3 forming four hydrogen bonds with Thr-101, Pro-246, His-195 and Asn-140. Infected mice treatment with IM-3, IM-4 and OX-1 exhibited significantly reduced parasitemia over a four-day treatment period when compared to the infected untreated animals. At 5, 10 and 20 mg/kg, IM-3 demonstrated the highest anti-plasmodial activity, suppressing parasitemia by 86.13, 97.71 and 94.11%, respectively. PCV levels were restored by IM-3 and IM-4, and the three selected compounds reduced the lipid peroxidation induced by P. berghei infection in mice. Thus, these compounds may be considered for further development as antimalarial medicines. Communicated by Ramaswamy H. Sarma

Structural Features of Cytochrome b5-Cytochrome b5 Reductase Complex Formation and Implications for the Intramolecular Dynamics of Cytochrome b5 Reductase.

Membrane cytochrome b5 reductase is a pleiotropic oxidoreductase that uses primarily soluble reduced nicotinamide adenine dinucleotide (NADH) as an electron donor to reduce multiple biological acceptors localized in cellular membranes. Some of the biological acceptors of the reductase and coupled redox proteins might eventually transfer electrons to oxygen to form reactive oxygen species. Additionally, an inefficient electron transfer to redox acceptors can lead to electron uncoupling and superoxide anion formation by the reductase. Many efforts have been made to characterize the involved catalytic domains in the electron transfer from the reduced flavoprotein to its electron acceptors, such as cytochrome b5, through a detailed description of the flavin and NADH-binding sites. This information might help to understand better the processes and modifications involved in reactive oxygen formation by the cytochrome b5 reductase. Nevertheless, more than half a century since this enzyme was first purified, the one-electron transfer process toward potential electron acceptors of the reductase is still only partially understood. New advances in computational analysis of protein structures allow predicting the intramolecular protein dynamics, identifying potential functional sites, or evaluating the effects of microenvironment changes in protein structure and dynamics. We applied this approach to characterize further the roles of amino acid domains within cytochrome b5 reductase structure, part of the catalytic domain, and several sensors and structural domains involved in the interactions with cytochrome b5 and other electron acceptors. The computational analysis results allowed us to rationalize some of the available spectroscopic data regarding ligand-induced conformational changes leading to an increase in the flavin adenine dinucleotide (FAD) solvent-exposed surface, which has been previously correlated with the formation of complexes with electron acceptors.

Unique Aspects of Lipid Metabolism in the Human Gut Microbiome

Fatty acids are abundant nutrients in the gut, and this work identified the biochemical pathway for fatty acid utilization in the prominent anaerobic, Gram‐negative inhabitants of the gut microbiome, the phylum Bacteroidetes. Alistipes finegoldii is a representative Bacteroidetes resident of the human gut. This organism has not been well studied until recently developed culture conditions enabled growth of the organism in the laboratory setting. This study identifies two unique aspects of lipid metabolism in A. finegoldii.The glycerolipid phosphatidylethanolamine (PE) synthesis is initiated by the PlsX/PlsY/PlsC pathway, whereas the sphingolipid sulfonolipid (SL) pathway is predicted to be related to sphingolipid biosynthesis. Neither phosphatidylglycerol nor cardiolipin were present. A. finegoldii incorporates medium‐chain fatty acids (£ 14 carbons) into PE or the SL after their elongation, whereas long‐chain fatty acids (³ 16 carbons) are not elongated. Acyl‐ACP >16 carbons were only incorporated into the 2‐position due to the selectivity of PlsC, the only biosynthetic enzyme that efficiently utilizes long‐chain unsaturated acyl‐ACP. This ability to assimilate a broad‐spectrum of fatty acid chain lengths is due to the expression of two acyl‐acyl carrier protein (ACP) synthetases. Biochemical characterization of these enzymes showed that acyl‐ACP synthetase 1 had a substrate preference for medium‐chain fatty acids and synthetase 2 had a substrate preference for long‐chain fatty acids. This unique combination of synthetases allows A. finegoldii to efficiently utilize both medium‐and long‐chain fatty acid nutrients available in the gut environment to assemble its membrane lipids.Bioinformatics analysis of A. finegoldii suggests the genes involved in the central fatty acid elongation cycle are present. Enoyl‐acyl carrier protein reductase (FabI) catalyzes a FASII rate‐controlling step. We studied A. finegoldii FabI (AfFabI) because phylogenetic analysis places enzymes from phylum Bacteroidetes in a distinct, uncharacterized 4th FabI clade. AfFabI displays typical FabI cooperative kinetics and uses NADH as a substrate, and has the prototypical α‐helix β‐sheet dimerization and antiparallel four‐helical bundle tetramerization domains that link adjoining protomers that characterize FabI enzymes.The distinct features of AfFabI are a coiled coil domain that links the carboxy termini of adjacent protomers of the homotetramer. The AfFabI•NADH crystal structure shows each coiled coil undergoes a conformational change to form part of the NADH binding site of the adjacent protomer. Residues throughout the coiled coil contact the base of the adjacent protomer’s “flipping loop” to stabilize the open substrate‐free and closed NADH‐bound conformations. Deletion of the coiled coil causes a 20‐fold NADH Km defect, showing the coiled coils are required for high affinity NADH binding. 4th clade enzymes are distinguished by a unique coiled coil domain involved in cooperative NADH binding and a unique active site that explains why FabI compounds in the clinic don’t affect the gut microbiome.Support or Funding InformationNIH grant GM34496, American Lebanese Syrian Associated CharitiesPhylogenetic analysis places enzymes from phylum Bacteroidetes in a distinct, uncharacterized 4th FabI cladeFigure 1

A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I

Respiratory complex I plays a central role in cellular energy metabolism coupling NADH oxidation to proton translocation. In humans its dysfunction is associated with degenerative diseases. Here we report the structure of the electron input part of Aquifex aeolicus complex I at up to 1.8 Å resolution with bound substrates in the reduced and oxidized states. The redox states differ by the flip of a peptide bond close to the NADH binding site. The orientation of this peptide bond is determined by the reduction state of the nearby [Fe-S] cluster N1a. Fixation of the peptide bond by site-directed mutagenesis led to an inactivation of electron transfer and a decreased reactive oxygen species (ROS) production. We suggest the redox-gated peptide flip to represent a previously unrecognized molecular switch synchronizing NADH oxidation in response to the redox state of the complex as part of an intramolecular feed-back mechanism to prevent ROS production.

Glutamate dehydrogenase: Structure of a hyperinsulinism mutant, corrections to the atomic model, and insights into a regulatory site.

Mammalian glutamate dehydrogenase (GDH) has complex allosteric regulation and the loss of GTP inhibition causes the hyperinsulinism/hyperammonemia syndrome (HHS) where insulin is hypersecreted upon consumption of protein. The archetypical HHS lesion is H454Y and lies in the GTP binding pocket. To better understand the mechanism of HHS, we determined the crystal structure of H454Y. When the bovine GDH crystal structures were minimized to prepare for further computational analysis, unusually large deviations were found at the allosteric NADH binding site due to chemical sequence errors. Notably, 387 lies in an allosteric where several activators and inhibitors bind and should be lysine rather than asparagine. All structures were re-refined and the consequence of this sequence error on NADH binding was calculated using free energy perturbation. The binding free energy penalty going from the correct to incorrect sequence found is +5 kcal/mol per site and therefore has a significant impact on drug development. BROADER AUDIENCE ABSTRACT: Glutamate dehydrogenase is a key enzyme involved in amino acid catabolism. As such, it is heavily regulated in animals by a wide array of metabolites. The importance of this regulation is most apparent in a genetic disorder called hyperinsulinism/hyperammonemia (HHS) where patients hypersecrete insulin upon the consumption of protein. We determined the atomic structure of one of these HHS mutants to better understand the disease and also analyzed an allosteric regulatory site.

FMN site-independent energy-linked reverse electron transfer in mitochondrial respiratory complex I.

A simple assay procedure for measuring ATP-dependent reverse electron transfer from ubiquinol to hexaammineruthenium (III) (HAR) catalyzed by mitochondrial respiratory complex I is introduced. The specific activity of the enzyme in this reaction and its sensitivity to the standard inhibitors and uncoupling are the same as with other well-known electron acceptors, NAD+ and ferricyanide. In contrast to the reactions with these acceptors, the energy-dependent HAR reduction is not inhibited by NADH-OH, the specific inhibitor of NADH-binding site. These results suggest that a catalytically competent electron connection exists between HAR and a redox component of complex I that is different from flavin mononucleotide bound at the substrate-binding site.

Mapping the protein phosphorylation sites in human mitochondrial complex I (NADH: Ubiquinone oxidoreductase): A bioinformatics study with implications for brain aging and neurodegeneration

In eukaryotes, mitochondrial complex I (NADH: ubiquinone oxidoreductase; CI) is central to oxidative phosphorylation (OXPHOS). Mammalian CI is a 45 subunit complex that forms supercomplexes with other OXPHOS complexes. Since CI defects are associated with aging and neurodegeneration, it is pertinent to understand its structure-function relationship. Although genetic mutations could lower CI activity causing mitochondrial dysfunction in several pathologies, post-translational modifications (PTMs) have emerged as a key mechanism contributing to altered CI activity. Among non-oxidative PTMs, protein phosphorylation is the most intricate regulatory mechanism controlling CI structure and function during normal physiology, aging and neurodegeneration. To comprehend this, we carried out a comprehensive bioinformatics analysis of protein phosphorylation of human CI subunits using software-based prediction of phosphorylation (phospho) sites and associated kinases. Phosphorylation was higher among core subunits and active domains of the complex. Among the subunits, NDUFS1 displayed significantly higher number as well as percent phospho sites compared to others. Analysis of the subunits containing iron-sulfur (Fe-S) cluster, NADH and FMN binding sites and quinone binding sites indicated the presence of phospho sites in close proximity to the binding sites of these cofactors with potential functional implications. Phosphoproteomics experiment in rat and human muscle mitochondria identified specific phospho sites in CI subunits, thereby validating the bioinformatic analysis. Molecular modeling of CI subunits indicated structural implications following phosphorylation. We surmise that protein phosphorylation, a transient and regulatory event could influence the structure-function relationship of CI thereby impinging on bioenergetics and ultimately contributing to aging and neurodegeneration.

Affiliation of Dihydrolipoyl Dehydrogenase Allozymes in Mycorrhizae of European Forest Trees and Characterization of the Enzyme of the Matt Bolete (<i>Xerocomus pruinatus</i>) and the Bay Bolete (<i>X. badius</i>)

Mycorrhizal roots of the deciduous trees European beech (Fagus sylvatica (L.)) and Sessile oak (Quercus petraea (MattuschkaLiebl.)) and the conifers Norway spruce (Picea abies (L.) H. Karst.) and European larch (Larix decidua (Mill.)) associated with the ectomycorrhizal fungi matt bolete (Xerocomus pruinatus (Fries 1835)) or bay bolete (X. badius (Fries 1818)) were analysed with respect to the occurrence of dihydrolipoyl dehydrogenase (EC 1.8.1.4) allozymes. In root tissues of the two deciduous trees, two gene loci could be visualized after cellulose acetate electrophoresis while three loci were expressed in root tissues of the two coniferous species. The two fungal species and further ectomycorrhizal fungi expressed exclusively one dihydrolipoyl dehydrogenase gene. In Xerocomus pruinatus and X. badius, the dihydrolipoyl dehydrogenase gene consists of 1460 bp and 1370 bp, respectively, including five introns each consisting of 52 bp. Their DNA sequences correspond to 70 to 90% to other fungal dihydrolipoyl dehydrogenase genes. One monomer of the dimeric dihydrolipoyl dehydrogenase enzyme consists of 486 (X. pruinatus) or 454 (X. badius) amino acids which sum up to a molecular mass of 55 kDa (X. pruinatus), respectively 52 kDa (X. badius). The number of positively charged amino acid residues makes 79 (X. pruinatus) and 68 (X. badius) and the number of negatively charged amino acid residues was calculated to make 46 (X. pruinatus) and 48 (X. badius); isoelectric points make 9.99 (X. pruinatus) and 9.68 (X. badius). Calculated three dimensional structures reveal a short NADH binding site being part of a larger FAD-binding site and a binding/dimerization domain.

Structural insights into the dimer-tetramer transition of FabI from Bacillus anthracis

Enoyl-ACP reductase (ENR, also known as FabI) has received considerable interest as an anti-bacterial target due to its essentiality in fatty acid synthesis. All the FabI structures reported to date, regardless of the organism, are composed of homo-tetramers, except for two structures: Bacillus cereus and Staphylococcus aureus FabI (bcFabI and saFabI, respectively), which have been reported as dimers. However, the reason for the existence of the dimeric form in these organisms and the biological meaning of dimeric and tetrameric forms of FabI are ambiguous. Herein, we report the high-resolution crystal structure of a dimeric form of Bacillus anthracis FabI (baFabI) and the crystal structures of tetrameric forms of baFabI in the apo state and in complex with NAD+ and with NAD+-triclosan, at 1.7 Å, 1.85 Å, 1.96 Å, and 1.95 Å, respectively. Interestingly, we found that baFabI with a His6-tag at its C-terminus exists as a dimer, whereas untagged-baFabI exists as a tetramer. The His6-tag may block the dimer-tetramer transition, since baFabI has relatively short-length amino acids (255LG256) after the 310-helix η7 compared to those of FabI of other organisms. The dimeric form of baFabI is catalytically inactive, because the α-helix α5 occupies the NADH-binding site. During the process of dimer-tetramer transition, this α5 helix rotates about 55° toward the tetramer interface and the active site is established. Therefore, tetramerization of baFabI is required for cofactor binding and catalytic activity.

Impact of cyclometalated ruthenium(II) complexes on lactate dehydrogenase activity and cytotoxicity in gastric and colon cancer cells

Lactate dehydrogenase (LDH) is a redox enzyme often overexpressed in cancer cells allowing their survival in stressful metabolic tumor environment. Ruthenium(II) complexes have been shown to impact on the activity of purified horseradish peroxidase and glucose oxidase but the physiological relevance remains unclear. In this study we investigated how ruthenium complexes impact on the activity of LDH in vitro and in cancer cells and performed a comparative study using polypyridine ruthenium(II) complex [Ru(bpy)3]2+ (1) and its structurally related cyclometalated 2-phenylpyridinato counterpart [Ru(phpy)(bpy)2]+ (2) (bpy=2,2′-bipyridine, phpyH=2-phenylpyridine). We show that the cytotoxicity in gastric and colon cancer cells induced by 2 is significantly higher compared to 1. The kinetic inhibition mechanisms on purified LDH and the corresponding inhibition constants Ki or i0.5 values were calculated. Though complexes 1 and 2 are structurally very similar (one Ru−C bond in 2 replaces one Ru−N bond in 1), their inhibition modes are different. Cyclometalated complex 2 behaves exclusively as a non-competitive inhibitor of LDH from rabbit muscle (LDHrm), strongly suggesting that 2 does not interact with LDH in the vicinities of either lactate/pyruvate or NAD+/NADH binding sites. Sites of interaction of 1 and 2 with LDHrm were revealed theoretically through computational molecular docking. Inhibition of LDH activity by 2 was confirmed in cancer cells. Altogether, these results revealed an inhibition of LDH activity by ruthenium complex through a direct interaction structurally tuned by a Ru−C bond.

Apoptosis-inducing Factor (AIF) and Its Family Member Protein, AMID, Are Rotenone-sensitive NADH:Ubiquinone Oxidoreductases (NDH-2)

Apoptosis-inducing factor (AIF) and AMID (AIF-homologous mitochondrion-associated inducer of death) are flavoproteins. Although AIF was originally discovered as a caspase-independent cell death effector, bioenergetic roles of AIF, particularly relating to complex I functions, have since emerged. However, the role of AIF in mitochondrial respiration and redox metabolism has remained unknown. Here, we investigated the redox properties of human AIF and AMID by comparing them with yeast Ndi1, a type 2 NADH:ubiquinone oxidoreductase (NDH-2) regarded as alternative complex I. Isolated AIF and AMID containing naturally incorporated FAD displayed no NADH oxidase activities. However, after reconstituting isolated AIF or AMID into bacterial or mitochondrial membranes, N-terminally tagged AIF and AMID displayed substantial NADH:O₂ activities and supported NADH-linked proton pumping activities in the host membranes almost as efficiently as Ndi1. NADH:ubiquinone-1 activities in the reconstituted membranes were highly sensitive to 2-n-heptyl-4-hydroxyquinoline-N-oxide (IC₅₀ = ∼1 μm), a quinone-binding inhibitor. Overexpressing N-terminally tagged AIF and AMID enhanced the growth of a double knock-out Escherichia coli strain lacking complex I and NDH-2. In contrast, C-terminally tagged AIF and NADH-binding site mutants of N-terminally tagged AIF and AMID failed to show both NADH:O₂ activity and the growth-enhancing effect. The disease mutant AIFΔR201 showed decreased NADH:O₂ activity and growth-enhancing effect. Furthermore, we surprisingly found that the redox activities of N-terminally tagged AIF and AMID were sensitive to rotenone, a well known complex I inhibitor. We propose that AIF and AMID are previously unidentified mammalian NDH-2 enzymes, whose bioenergetic function could be supplemental NADH oxidation in cells.

Complete topology of the RNF complex from Vibrio cholerae.

RNF is a redox-driven ion (Na(+) and in one case possibly H(+)) transporter present in many prokaryotes. It has been proposed that RNF performs a variety of reactions in different organisms, delivering low-potential reducing equivalents for specific cellular processes. RNF shares strong homology with the Na(+)-pumping respiratory enzyme Na(+)-NQR, although there are significant differences in subunit and redox cofactor composition. Here we report a topological analysis of the six subunits of RNF from Vibrio cholerae. Although individual subunits from other organisms have previously been studied, this is the first complete, experimentally derived, analysis of RNF from any one source. This has allowed us to identify and confirm key properties of RNF. The putative NADH binding site in RnfC is located on the cytoplasmic side of the membrane. FeS centers in RnfB and RnfC are also located on the cytoplasmic side. However, covalently attached FMNs in RnfD and RnfG are both located in the periplasm. RNF also contains a number of acidic residues that correspond to functionally important groups in Na(+)-NQR. The acidic residues involved in Na(+) uptake and many of those implicated in Na(+) translocation are topologically conserved. The topology of RNF closely matches the topology represented in the newly published structure of Na(+)-NQR, consistent with the close relation between the two enzymes. The topology of RNF is discussed in the context of the current structural model of Na(+)-NQR, and the proposed functionality of the RNF complex itself.