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1.
NAR Genom Bioinform ; 5(1): lqad010, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36814457

ABSTRACT

RNA-binding proteins (RBPs) are critical host factors for viral infection, however, large scale experimental investigation of the binding landscape of human RBPs to viral RNAs is costly and further complicated due to sequence variation between viral strains. To fill this gap, we investigated the role of RBPs in the context of SARS-CoV-2 by constructing the first in silico map of human RBP-viral RNA interactions at nucleotide-resolution using two deep learning methods (pysster and DeepRiPe) trained on data from CLIP-seq experiments on more than 100 human RBPs. We evaluated conservation of RBP binding between six other human pathogenic coronaviruses and identified sites of conserved and differential binding in the UTRs of SARS-CoV-1, SARS-CoV-2 and MERS. We scored the impact of mutations from 11 variants of concern on protein-RNA interaction, identifying a set of gain- and loss-of-binding events, as well as predicted the regulatory impact of putative future mutations. Lastly, we linked RBPs to functional, OMICs and COVID-19 patient data from other studies, and identified MBNL1, FTO and FXR2 RBPs as potential clinical biomarkers. Our results contribute towards a deeper understanding of how viruses hijack host cellular pathways and open new avenues for therapeutic intervention.

2.
Front Genet ; 13: 909714, 2022.
Article in English | MEDLINE | ID: mdl-35903362

ABSTRACT

COVID-19 is a heterogeneous disease caused by SARS-CoV-2. Aside from infections of the lungs, the disease can spread throughout the body and damage many other tissues, leading to multiorgan failure in severe cases. The highly variable symptom severity is influenced by genetic predispositions and preexisting diseases which have not been investigated in a large-scale multimodal manner. We present a holistic analysis framework, setting previously reported COVID-19 genes in context with prepandemic data, such as gene expression patterns across multiple tissues, polygenetic predispositions, and patient diseases, which are putative comorbidities of COVID-19. First, we generate a multimodal network using the prior-based network inference method KiMONo. We then embed the network to generate a meaningful lower-dimensional representation of the data. The input data are obtained via the Genotype-Tissue Expression project (GTEx), containing expression data from a range of tissues with genomic and phenotypic information of over 900 patients and 50 tissues. The generated network consists of nodes, that is, genes and polygenic risk scores (PRS) for several diseases/phenotypes, as well as for COVID-19 severity and hospitalization, and links between them if they are statistically associated in a regularized linear model by feature selection. Applying network embedding on the generated multimodal network allows us to perform efficient network analysis by identifying nodes close by in a lower-dimensional space that correspond to entities which are statistically linked. By determining the similarity between COVID-19 genes and other nodes through embedding, we identify disease associations to tissues, like the brain and gut. We also find strong associations between COVID-19 genes and various diseases such as ischemic heart disease, cerebrovascular disease, and hypertension. Moreover, we find evidence linking PTPN6 to a range of comorbidities along with the genetic predisposition of COVID-19, suggesting that this kinase is a central player in severe cases of COVID-19. In conclusion, our holistic network inference coupled with network embedding of multimodal data enables the contextualization of COVID-19-associated genes with respect to tissues, disease states, and genetic risk factors. Such contextualization can be exploited to further elucidate the biological importance of known and novel genes for severity of the disease in patients.

3.
Biomedicines ; 9(7)2021 Jul 07.
Article in English | MEDLINE | ID: mdl-34356852

ABSTRACT

Classical xanthinuria is a rare autosomal recessive metabolic disorder caused by variants in the XDH (type I) or MOCOS (type II) genes. Thirteen Israeli kindred (five Jewish and eight Arab) and two isolated cases from Germany were studied between the years 1997 and 2013. Four and a branch of a fifth of these families were previously described. Here, we reported the demographic, clinical, molecular and biochemical characterizations of the remaining cases. Seven out of 20 affected individuals (35%) presented with xanthinuria-related symptoms of varied severity. Among the 10 distinct variants identified, six were novel: c.449G>T (p.(Cys150Phe)), c.1434G>A (p.(Trp478*)), c.1871C>G (p.(Ser624*)) and c.913del (p.(Leu305fs*1)) in the XDH gene and c.1046C>T (p.(Thr349Ileu)) and c.1771C>T (p.(Pro591Ser)) in the MOCOS gene. Heterologous protein expression studies revealed that the p.Cys150Phe variant within the Fe/S-I cluster-binding site impairs XDH biogenesis, the p.Thr349Ileu variant in the NifS-like domain of MOCOS affects protein stability and cysteine desulfurase activity, while the p.Pro591Ser and a previously described p.Arg776Cys variant in the C-terminal domain affect Molybdenum cofactor binding. Based on the results of haplotype analyses and historical genealogy findings, the potential dispersion of the identified variants is discussed. As far as we are aware, this is the largest cohort of xanthinuria cases described so far, substantially expanding the repertoire of pathogenic variants, characterizing structurally and functionally essential amino acid residues in the XDH and MOCOS proteins and addressing the population genetic aspects of classical xanthinuria.

4.
Sci Rep ; 10(1): 19103, 2020 Oct 30.
Article in English | MEDLINE | ID: mdl-33127946

ABSTRACT

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

5.
Sci Rep ; 10(1): 11539, 2020 07 20.
Article in English | MEDLINE | ID: mdl-32686707

ABSTRACT

We have created a new architected material, which is both highly deformable and ultra-resistant to dynamic point loads. The bio-inspired metallic cellular structure (with an internal grid of large ceramic segments) is non-cuttable by an angle grinder and a power drill, and it has only 15% steel density. Our architecture derives its extreme hardness from the local resonance between the embedded ceramics in a flexible cellular matrix and the attacking tool, which produces high-frequency vibrations at the interface. The incomplete consolidation of the ceramic grains during the manufacturing also promoted fragmentation of the ceramic spheres into micron-size particulate matter, which provided an abrasive interface with increasing resistance at higher loading rates. The contrast between the ceramic segments and cellular material was also effective against a waterjet cutter because the convex geometry of the ceramic spheres widened the waterjet and reduced its velocity by two orders of magnitude. Shifting the design paradigm from static resistance to dynamic interactions between the material phases and the applied load could inspire novel, metamorphic materials with pre-programmed mechanisms across different length scales.

6.
Proc Natl Acad Sci U S A ; 115(47): 11958-11963, 2018 11 20.
Article in English | MEDLINE | ID: mdl-30397129

ABSTRACT

Biotransformation enzymes ensure a viable homeostasis by regulating reversible cycles of oxidative and reductive reactions. The metabolism of nitrogen-containing compounds is of high pharmaceutical and toxicological relevance because N-oxygenated metabolites derived from reactions mediated by cytochrome P450 enzymes or flavin-dependent monooxygenases are in some cases highly toxic or mutagenic. The molybdenum-dependent mitochondrial amidoxime-reducing component (mARC) was found to be an extremely efficient counterpart, which is able to reduce the full range of N-oxygenated compounds and thereby mediates detoxification reactions. However, the 3D structure of this enzyme was unknown. Here we present the high-resolution crystal structure of human mARC. We give detailed insight into the coordination of its molybdenum cofactor (Moco), the catalytic mechanism, and its ability to reduce a wide range of N-oxygenated compounds. The identification of two key residues will allow future discrimination between mARC paralogs and ensure correct annotation. Since our structural findings contradict in silico predictions that are currently made by online databases, we propose domain definitions for members of the superfamily of Moco sulfurase C-terminal (MOSC) domain-containing proteins. Furthermore, we present evidence for an evolutionary role of mARC for the emergence of the xanthine oxidase protein superfamily. We anticipate the hereby presented crystal structure to be a starting point for future descriptions of MOSC proteins, which are currently poorly structurally characterized.


Subject(s)
Mitochondrial Proteins/chemistry , Mitochondrial Proteins/ultrastructure , Oxidoreductases/chemistry , Oxidoreductases/ultrastructure , Catalysis , Coenzymes , Crystallography, X-Ray/methods , Eukaryotic Cells/metabolism , Humans , Metalloproteins , Mitochondria/metabolism , Mitochondrial Proteins/metabolism , Molybdenum/metabolism , Molybdenum Cofactors , Oxidation-Reduction , Oxidoreductases/metabolism , Protein Structure, Tertiary , Pteridines
7.
Chem Res Toxicol ; 31(6): 447-453, 2018 06 18.
Article in English | MEDLINE | ID: mdl-29856598

ABSTRACT

Although known for years, the toxic effects of trimethylamine N-oxide (TMAO), a physiological metabolite, were just recently discovered and are currently under investigation. It is known that elevated TMAO plasma levels correlate with an elevated risk for cardiovascular disease (CVD). Even though there is a general consensus about the existence of a causal relationship between TMAO and CVD, the underlying mechanisms are not fully understood. TMAO is an oxidation product of the hepatic flavin-containing monooxygenases (FMO), mainly of isoform 3, and it is conceivable that humans also have an enzyme reversing this toxification by reducing TMAO to its precursor trimethylamine (TMA). All prokaryotic enzymes that use TMAO as a substrate have molybdenum-containing cofactors in common. Such molybdenum-containing enzymes also exist in mammals, with the so-called mitochondrial amidoxime reducing component (mARC) representing the most recently discovered mammalian molybdenum enzyme. The enzyme has been found to exist in two isoforms, mARC1 and mARC2, both being capable of reducing a variety of N-oxygenated compounds, including nonphysiological N-oxides. To investigate whether the two isoforms of this enzyme are able to reduce and detoxify TMAO, we developed a suitable analytical method and tested TMAO reduction with a recombinant enzyme system. We found that one of the two recombinant human mARC proteins, namely, hmARC1, reduces TMAO to TMA. The N-reductive activity is relatively low and identified via the kinetic parameters with Km = (30.4 ± 9.8) mM and Vmax = (100.5 ± 12.2) nmol/(mg protein·min). Nevertheless, the ubiquitous tissue expression of hmARC1 allows a continuous reduction of TMAO whereas the counter-reaction, the production of TMAO through FMO3, can take place only in the liver where FMO3 is expressed. TMAO reduction in porcine liver subfractions showed the characteristic enrichment of N-reductive activity in the outer mitochondrial membrane. TMAO reduction was also found in human cell cultures. These findings indicate the role of hmARC1 in the metabolomic pathway of TMAO, which might contribute to the prevention of CVD. This also hints at a physiological function of the molybdenum enzyme, which remains mainly unknown to date.


Subject(s)
Methylamines/metabolism , Mitochondrial Proteins/metabolism , Oxidoreductases/metabolism , Animals , Cell Line, Tumor , Humans , Inactivation, Metabolic , Liver/metabolism , Methylamines/chemistry , Mitochondria/metabolism , Oxidation-Reduction , Swine
8.
Acta Crystallogr F Struct Biol Commun ; 74(Pt 6): 337-344, 2018 06 01.
Article in English | MEDLINE | ID: mdl-29870017

ABSTRACT

The human mitochondrial amidoxime reducing component (hmARC) is a molybdenum cofactor-dependent enzyme that is involved in the reduction of a diverse range of N-hydroxylated compounds of either physiological or xenobiotic origin. In this study, the use of a fusion-protein approach with T4 lysozyme (T4L) to determine the structure of this hitherto noncrystallizable enzyme by X-ray crystallography is described. A set of four different hmARC-T4L fusion proteins were designed. Two of them contained either an N-terminal or a C-terminal T4L moiety fused to hmARC, while the other two contained T4L as an internal fusion partner tethered to the hmARC enzyme between two predicted secondary-structure elements. One of these internal fusion constructs could be expressed and crystallized successfully. The hmARC-T4L crystals diffracted to 1.7 Šresolution using synchrotron radiation and belonged to space group P212121 with one molecule in the asymmetric unit. Initial attempts to solve the structure by molecular replacement using T4L did not result in electron-density distributions that were sufficient for model building and interpretation of the hmARC moiety. However, this study emphasizes the utility of the T4L fusion-protein approach, which can be used for the crystallization and structure determination of membrane-bound proteins as well as soluble proteins.


Subject(s)
Coenzymes/chemistry , Metalloproteins/chemistry , Mitochondrial Proteins/chemistry , Muramidase/chemistry , Oxidoreductases/chemistry , Peptide Fragments/chemistry , Pteridines/chemistry , Amino Acid Sequence , Coenzymes/genetics , Crystallization/methods , Humans , Metalloproteins/genetics , Mitochondrial Proteins/genetics , Molybdenum Cofactors , Muramidase/genetics , Oxidoreductases/genetics , Peptide Fragments/genetics , X-Ray Diffraction/methods
9.
Materials (Basel) ; 11(2)2018 Feb 02.
Article in English | MEDLINE | ID: mdl-29393910

ABSTRACT

The low-temperature fabrication of flexible ZnO photo-anodes for dye-sensitized solar cells (DSSCs) by templated electrochemical deposition of films was performed in an enlarged and technical simplified deposition setup to demonstrate the feasibility of the scale-up of the deposition process. After extraction of eosin Y (EY) from the initially deposited ZnO/EY hybrid films, mesoporous ZnO films with an area of about 40 cm² were reproducibly obtained on fluorine doped tin oxide (FTO)-glass as well as flexible indium tin oxide (ITO)-polyethylenterephthalate (PET) substrates. With a film thickness of up to 9 µm and a high specific surface area of up to about 77 m²·cm-3 the ZnO films on the flexible substrates show suitable properties for DSSCs. Operative flexible DSSC modules proved the suitability of the ZnO films for use as DSSC photo-anodes. Under a low light intensity of about 0.007 sun these modules achieved decent performance parameters with conversion efficiencies of up to 2.58%. With rising light intensity the performance parameters deteriorated, leading to conversion efficiencies below 1% at light intensities above 0.5 sun. The poor performance of the modules under high light intensities can be attributed to their high series resistances.

10.
Plant Cell Physiol ; 58(8): 1421-1430, 2017 Aug 01.
Article in English | MEDLINE | ID: mdl-28633475

ABSTRACT

The most prominent alkaloid of Chelidonium majus is dihydrocoptisine, revealing the characteristic benzophenanthridine skeleton. To date, any informationon on the enzymes responsible for its biosynthesis and the related genes in C. majus is lacking. Based on sequence similarities to the corresponding methylenedioxy bridge-forming Cyt P450 enzymes involved in isoquinoline alkaloid biosynthesis in Eschscholzia californica, genes for a cheilanthifoline synthase and a stylopine synthase from C. majus were isolated, sequenced and heterologously expressed in yeast. The activity of the heterologously expressed Cyt P450 enzymes was determined in situ as well as on the basis of microsomal fractions. It was shown that cheilanthifoline synthase (c8931) converts scoulerine into cheilanthifoline, the latter subsequently being converted to stylopine by the action of a stylopine synthase (c1128). Based on the well-known instability of stylopine, it can be assumed that in vivo-under the acidic conditions in the vacuole-this alkaloid is converted to dihydrocoptisine, which accumulates in C. majus leaves. Both methylenedioxy bridge-forming Cyt P450 enzymes from C. majus are characterized by their high substrate specificity. Apart from their genuine substrates, i.e. scoulerine and cheilanthifoline, cheilanthifoline synthase and stylopine synthase do not accept other substrates tested; the only alternative substrate identified was scoulerine, which is converted by stylopine synthase to yield minor amounts of nandinine. Quantitative real-time PCR revealed that the expression of cheilanthifoline synthase and stylopine synthase genes is very similar in both roots and leaves from C. majus, although the alkaloid accumulation patterns in these organs are quite different.


Subject(s)
Alkaloids/metabolism , Chelidonium/genetics , Cytochrome P-450 Enzyme System/metabolism , Isoquinolines/metabolism , Plant Proteins/genetics , Berberine Alkaloids/metabolism , Chelidonium/metabolism , Cloning, Molecular , Cytochrome P-450 Enzyme System/genetics , Gene Expression Regulation, Plant , Genes, Plant , Plant Proteins/metabolism , Substrate Specificity
11.
New Phytol ; 213(3): 1222-1241, 2017 Feb.
Article in English | MEDLINE | ID: mdl-27735062

ABSTRACT

Molybdenum (Mo) and iron (Fe) are essential micronutrients required for crucial enzyme activities in plant metabolism. Here we investigated the existence of a mutual control of Mo and Fe homeostasis in cucumber (Cucumis sativus). Plants were grown under single or combined Mo and Fe starvation. Physiological parameters were measured, the ionomes of tissues and the ionomes and proteomes of root mitochondria were profiled, and the activities of molybdo-enzymes and the synthesis of molybdenum cofactor (Moco) were evaluated. Fe and Mo were found to affect each other's total uptake and distribution within tissues and at the mitochondrial level, with Fe nutritional status dominating over Mo homeostasis and affecting Mo availability for molybdo-enzymes in the form of Moco. Fe starvation triggered Moco biosynthesis and affected the molybdo-enzymes, with its main impact on nitrate reductase and xanthine dehydrogenase, both being involved in nitrogen assimilation and mobilization, and on the mitochondrial amidoxime reducing component. These results, together with the identification of > 100 proteins differentially expressed in root mitochondria, highlight the central role of mitochondria in the coordination of Fe and Mo homeostasis and allow us to propose the first model of the molecular interactions connecting Mo and Fe homeostasis.


Subject(s)
Cucumis sativus/metabolism , Homeostasis/drug effects , Iron/pharmacology , Molybdenum/pharmacology , Cluster Analysis , Coenzymes/metabolism , Cucumis sativus/drug effects , Formate Dehydrogenases/metabolism , Metabolome/drug effects , Metalloproteins/metabolism , Mitochondria/drug effects , Mitochondria/metabolism , Mitochondrial Proteins/metabolism , Models, Biological , Molybdenum Cofactors , Oxidoreductases/metabolism , Plant Leaves/drug effects , Plant Leaves/metabolism , Plant Roots/drug effects , Plant Roots/metabolism , Proteome/metabolism , Pteridines/metabolism
12.
Drug Metab Dispos ; 44(10): 1617-21, 2016 10.
Article in English | MEDLINE | ID: mdl-27469001

ABSTRACT

The importance of the mitochondrial amidoxime reducing component (mARC)-containing enzyme system in N-reductive metabolism has been studied extensively. It catalyzes the reduction of various N-hydroxylated compounds and therefore acts as the counterpart of cytochrome P450- and flavin-containing monooxygenase-catalyzed oxidations at nitrogen centers. This enzyme system was found to be responsible for the activation of amidoxime and N-hydroxyguanidine prodrugs in drug metabolism. The synergy of three components (mARC, cytochrome b5, and the appropriate reductase) is crucial to exert the N-reductive catalytic effect. Previous studies have demonstrated the involvement of the specific isoforms of the molybdoenzyme mARC and the electron transport protein cytochrome b5 in N-reductive metabolism. To date, the corresponding reductase involved in N-reductive metabolism has yet to be defined because previous investigations have presented ambiguous results. Using small interfering RNA-mediated knockdown in human cells and assessing the stoichiometry of the enzyme system reconstituted in vitro, we provide evidence that NADH-cytochrome-b5 reductase 3 is the principal reductase involved in the mARC enzyme system and is an essential component of N-reductive metabolism in human cells. In addition, only minimal levels of cytochrome-b5 reductase 3 protein are sufficient for catalysis, which impeded previous attempts to identify the reductase.


Subject(s)
Cytochrome-B(5) Reductase/metabolism , Mitochondria/enzymology , NAD/metabolism , Oximes/metabolism , HEK293 Cells , Humans
13.
Plant Cell ; 28(5): 1108-26, 2016 05.
Article in English | MEDLINE | ID: mdl-27152019

ABSTRACT

While plants produce reactive oxygen species (ROS) for stress signaling and pathogen defense, they need to remove excessive ROS induced during stress responses in order to minimize oxidative damage. How can plants fine-tune this balance and meet such conflicting needs? Here, we show that XANTHINE DEHYDROGENASE1 (XDH1) in Arabidopsis thaliana appears to play spatially opposite roles to serve this purpose. Through a large-scale genetic screen, we identified three missense mutations in XDH1 that impair XDH1's enzymatic functions and consequently affect the powdery mildew resistance mediated by RESISTANCE TO POWDERY MILDEW8 (RPW8) in epidermal cells and formation of xanthine-enriched autofluorescent objects in mesophyll cells. Further analyses revealed that in leaf epidermal cells, XDH1 likely functions as an oxidase, along with the NADPH oxidases RbohD and RbohF, to generate superoxide, which is dismutated into H2O2 The resulting enrichment of H2O2 in the fungal haustorial complex within infected epidermal cells helps to constrain the haustorium, thereby contributing to RPW8-dependent and RPW8-independent powdery mildew resistance. By contrast, in leaf mesophyll cells, XDH1 carries out xanthine dehydrogenase activity to produce uric acid in local and systemic tissues to scavenge H2O2 from stressed chloroplasts, thereby protecting plants from stress-induced oxidative damage. Thus, XDH1 plays spatially specified dual and opposing roles in modulation of ROS metabolism during defense responses in Arabidopsis.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/enzymology , Arabidopsis/metabolism , Xanthine Dehydrogenase/metabolism , Arabidopsis/genetics , Arabidopsis/microbiology , Arabidopsis Proteins/genetics , Ascomycota/pathogenicity , Disease Resistance/genetics , Disease Resistance/physiology , Host-Pathogen Interactions/genetics , Host-Pathogen Interactions/physiology , Plant Diseases/microbiology , Reactive Oxygen Species/metabolism , Xanthine Dehydrogenase/genetics
14.
J Am Chem Soc ; 137(16): 5276-9, 2015 Apr 29.
Article in English | MEDLINE | ID: mdl-25897643

ABSTRACT

A combination of electron paramagnetic resonance (EPR) spectroscopy and computational approaches has provided insight into the nature of the reaction coordinate for the one-electron reduction of nitrite by the mitochondrial amidoxime reducing component (mARC) enzyme. The results show that a paramagnetic Mo(V) species is generated when reduced enzyme is exposed to nitrite, and an analysis of the resulting EPR hyperfine parameters confirms that mARC is remarkably similar to the low-pH form of sulfite oxidase. Two mechanisms for nitrite reduction have been considered. The first shows a modest reaction barrier of 14 kcal/mol for the formation of ·NO from unprotonated nitrite substrate. In marked contrast, protonation of the substrate oxygen proximal to Mo in the Mo(IV)-O-N-O substrate-bound species results in barrierless conversion to products. A fragment orbital analysis reveals a high degree of Mo-O(H)-N-O covalency that provides a π-orbital pathway for one-electron transfer to the substrate and defines orbital constraints on the Mo-substrate geometry for productive catalysis in mARC and other pyranopterin molybdenum enzymes that catalyze this one-electron transformation.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/enzymology , Hydroxyl Radical/metabolism , Mitochondria/enzymology , Nitrites/metabolism , Oxidoreductases/metabolism , Arabidopsis/metabolism , Electron Spin Resonance Spectroscopy/methods , Electron Transport , Mitochondria/metabolism , Models, Molecular , Molybdenum/chemistry , Molybdenum/metabolism , Oxidation-Reduction , Sulfite Oxidase/metabolism
15.
Nat Commun ; 6: 6148, 2015 Feb 04.
Article in English | MEDLINE | ID: mdl-25649206

ABSTRACT

Formate dehydrogenases (FDHs) are of interest as they are natural catalysts that sequester atmospheric CO2, generating reduced carbon compounds with possible uses as fuel. FDHs activity in Escherichia coli strictly requires the sulphurtransferase EcFdhD, which likely transfers sulphur from IscS to the molybdenum cofactor (Mo-bisPGD) of FDHs. Here we show that EcFdhD binds Mo-bisPGD in vivo and has submicromolar affinity for GDP-used as a surrogate of the molybdenum cofactor's nucleotide moieties. The crystal structure of EcFdhD in complex with GDP shows two symmetrical binding sites located on the same face of the dimer. These binding sites are connected via a tunnel-like cavity to the opposite face of the dimer where two dynamic loops, each harbouring two functionally important cysteine residues, are present. On the basis of structure-guided mutagenesis, we propose a model for the sulphuration mechanism of Mo-bisPGD where the sulphur atom shuttles across the chaperone dimer.


Subject(s)
Coenzymes/chemistry , Escherichia coli/metabolism , Formate Dehydrogenases/chemistry , Guanosine Diphosphate/chemistry , Hydrogenase/chemistry , Molecular Chaperones/chemistry , Molybdenum/chemistry , Multienzyme Complexes/chemistry , Binding Sites , Biocatalysis , Carbon Cycle , Carbon Dioxide/metabolism , Carbon-Sulfur Lyases/metabolism , Cloning, Molecular , Coenzymes/metabolism , Crystallography, X-Ray , Escherichia coli/chemistry , Escherichia coli/genetics , Formate Dehydrogenases/genetics , Formate Dehydrogenases/metabolism , Formates/chemistry , Formates/metabolism , Gene Expression , Guanosine Diphosphate/metabolism , Hydrogenase/genetics , Hydrogenase/metabolism , Models, Molecular , Molecular Chaperones/genetics , Molecular Chaperones/metabolism , Molybdenum/metabolism , Multienzyme Complexes/genetics , Multienzyme Complexes/metabolism , Oxidation-Reduction , Plasmids/chemistry , Plasmids/metabolism , Protein Binding , Protein Multimerization , Protein Structure, Secondary , Protein Structure, Tertiary , Sulfur/chemistry , Sulfur/metabolism
16.
ChemMedChem ; 10(2): 360-7, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25512261

ABSTRACT

The mitochondrial amidoxime reducing component (mARC) activates amidoxime prodrugs by reduction to the corresponding amidine drugs. This study analyzes relationships between the chemical structure of the prodrug and its metabolic activation and compares its enzyme-mediated vs. electrochemical reduction. The enzyme kinetic parameters KM and Vmax for the N-reduction of ten para-substituted derivatives of the model compound benzamidoxime were determined by incubation with recombinant proteins and subcellular fractions from pig liver followed by quantification of the metabolites by HPLC. A clear influence of the substituents at position 4 on the chemical properties of the amidoxime function was confirmed by correlation analyses of (1) H NMR chemical shifts and the redox potentials of the 4-substituted benzamidoximes with Hammett's σ. However, no clear relationship between the kinetic parameters for the enzymatic reduction and Hammett's σ or the lipophilicity could be found. It is thus concluded that these properties as well as the redox potential of the amidoxime can be largely ignored during the development of new amidoxime prodrugs, at least regarding prodrug activation.


Subject(s)
Benzamidines/chemistry , Oxidoreductases/metabolism , Prodrugs/chemistry , Amidines/chemistry , Amidines/metabolism , Animals , Benzamidines/metabolism , Biocatalysis , Humans , Kinetics , Liver/metabolism , Mitochondria/enzymology , Molybdenum/chemistry , Molybdenum/metabolism , Oxidation-Reduction , Oxidoreductases/genetics , Prodrugs/metabolism , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Swine
17.
Inorg Chem ; 53(18): 9460-2, 2014 Sep 15.
Article in English | MEDLINE | ID: mdl-25166909

ABSTRACT

Mo K-edge X-ray absorption spectroscopy has been used to probe as-isolated structures of the MOSC family proteins pmARC-1 and HMCS-CT. The Mo K-edge near-edge spectrum of HMCS-CT is shifted ~2.5 eV to lower energy compared to the pmARC-1 spectrum, which indicates that as-isolated HMCS-CT is in a more reduced state than pmARC-1. Extended X-ray absorption fine structure analysis indicates significant structural differences between pmARC-1 and HMCS-CT, with the former being a dioxo site and the latter possessing only a single terminal oxo ligand. The number of terminal oxo donors is consistent with pmARC-1 being in the Mo(VI) oxidation state and HMCS-CT in the Mo(IV) state. These structures are in accord with oxygen-atom-transfer reactivity for pmARC-1 and persulfide bond cleavage chemistry for HMCS-CT.


Subject(s)
Molybdenum/chemistry , Oxidoreductases/chemistry , Humans , Oxidation-Reduction , Protein Conformation , X-Ray Absorption Spectroscopy
18.
Chem Res Toxicol ; 27(10): 1687-95, 2014 Oct 20.
Article in English | MEDLINE | ID: mdl-25170804

ABSTRACT

Under high dose treatment with sulfamethoxazole (SMX)/trimethoprim (TMP), hypersensitivity reactions occur with a high incidence. The mechanism of this adverse drug reaction is not fully understood. Several steps in the toxification pathway of SMX were investigated. The aim of our study was to investigate the reduction of sulfamethoxazole hydroxylamine (SMX-HA) in this toxification pathway, which can possibly be catalyzed by the mARC-containing N-reductive enzyme system. Western blot analyses of subcellular fractions of porcine tissue were performed with antibodies against mARC-1, mARC-2, cytochrome b5 type B, and NADH cytochrome b5 reductase. Incubations of porcine and human subcellular tissue fractions and of the heterologously expressed human components of the N-reductive enzyme system were carried out with SMX-HA. mARC-1 and mARC-2 knockdown was performed in HEK-293 cells. Kinetic parameters of the heterologously expressed human protein variants V96L, A165T, M187 K, C246S, D247H, and M268I of mARC-1 and G244S and C245W of mARC-2 and N-reductive activity of 2SF, D14G, K16E, and T22A of cytochrome b5 type B were analyzed. Western blot analyses were consistent with the hypothesis that the mARC-containing N-reductive enzyme system might be involved in the reduction of SMX-HA. In agreement with these results, highest reduction rates were found in mitochondrial subcellular fractions of porcine tissue and in the outer membrane vesicle (OMV) of human liver tissue. Knockdown studies in HEK-293 cells demonstrated that mARC-1 and mARC-2 were capable of reducing SMX-HA in cell metabolism. Investigations with the heterologously expressed human mARC-2 protein showed a higher catalytic efficiency toward SMX-HA than mARC-1, but none of the investigated human protein variants showed statistically significant differences of its N-reductive activity and was therefore likely to participate in the pathogenesis of hypersensitivity reaction under treatment with SMX.


Subject(s)
Mitochondria/metabolism , Sulfamethoxazole/analogs & derivatives , Amino Acid Substitution , Animals , Biocatalysis , Chromatography, High Pressure Liquid , Cytochrome-B(5) Reductase/metabolism , Cytochromes b5/genetics , Cytochromes b5/metabolism , HEK293 Cells , Humans , Kinetics , Liver/metabolism , Mitochondrial Proteins/antagonists & inhibitors , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Oxidation-Reduction , Oxidoreductases/antagonists & inhibitors , Oxidoreductases/genetics , Oxidoreductases/metabolism , RNA Interference , RNA, Small Interfering/metabolism , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Sulfamethoxazole/chemistry , Sulfamethoxazole/metabolism , Swine
19.
ChemMedChem ; 9(10): 2381-7, 2014 Oct.
Article in English | MEDLINE | ID: mdl-25045021

ABSTRACT

The mitochondrial amidoxime reducing component (mARC) is a molybdenum-containing enzyme and capable of reducing N-hydroxylated structures such as amidoxime prodrugs. In this study, we tested the involvement of mARC in the reduction of N-oxides (amitriptyline-N-oxide, nicotinamide-N-oxide), oximes ((E)-/(Z)-2,4,6-trimethylacetophenonoxime) and a N-hydroxyamidinohydrazone (guanoxabenz). All groups are reduced by mARC proteins, and the enzymes are therefore involved in the interconversion of N-oxygenated metabolites originating from cytochrome P450s and flavin-containing monooxygenases. In addition, these structures open up further options for serving as prodrugs. Thus, with respect to these reactions, testing of candidates with N-oxygenated structures should not solely be carried out in microsomal enzyme sources but as well in mitochondria. However, differences in the reduction of oximes and N-oxides between the two isoforms, namely mARC1 and mARC2, were detectable; N-oxides are exclusively reduced by mARC1. We therefore assume differences between the so far unknown 3D structures of the two proteins.


Subject(s)
Hydrazones/chemistry , Mitochondria/drug effects , Oxides/pharmacology , Oximes/pharmacology , Mitochondria/metabolism
20.
Front Plant Sci ; 5: 28, 2014.
Article in English | MEDLINE | ID: mdl-24570679

ABSTRACT

In the form of molybdate the transition metal molybdenum is essential for plants as it is required by a number of enzymes that catalyze key reactions in nitrogen assimilation, purine degradation, phytohormone synthesis, and sulfite detoxification. However, molybdate itself is biologically inactive and needs to be complexed by a specific organic pterin in order to serve as a permanently bound prosthetic group, the molybdenum cofactor, for the socalled molybdo-enyzmes. While the synthesis of molybdenum cofactor has been intensively studied, only little is known about the uptake of molybdate by the roots, its transport to the shoot and its allocation and storage within the cell. Yet, recent evidence indicates that intracellular molybdate levels are tightly controlled by molybdate transporters, in particular during plant development. Moreover, a tight connection between molybdenum and iron metabolisms is presumed because (i) uptake mechanisms for molybdate and iron affect each other, (ii) most molybdo-enzymes do also require iron-containing redox groups such as iron-sulfur clusters or heme, (iii) molybdenum metabolism has recruited mechanisms typical for iron-sulfur cluster synthesis, and (iv) both molybdenum cofactor synthesis and extramitochondrial iron-sulfur proteins involve the function of a specific mitochondrial ABC-type transporter.

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