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1.
Structure ; 32(5): 594-602.e4, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38460521

ABSTRACT

Apoptosis-inducing factor (AIF), which is confined to mitochondria of normal healthy cells, is the first identified caspase-independent cell death effector. Moreover, AIF is required for the optimal functioning of the respiratory chain machinery. Recent findings have revealed that AIF fulfills its pro-survival function by interacting with CHCHD4, a soluble mitochondrial protein which promotes the entrance and the oxidative folding of different proteins in the inner membrane space. Here, we report the crystal structure of the ternary complex involving the N-terminal 27-mer peptide of CHCHD4, NAD+, and AIF harboring its FAD (flavin adenine dinucleotide) prosthetic group in oxidized form. Combining this information with biophysical and biochemical data on the CHCHD4/AIF complex, we provide a detailed structural description of the interaction between the two proteins, validated by both chemical cross-linking mass spectrometry analysis and site-directed mutagenesis.


Subject(s)
Apoptosis Inducing Factor , Catalytic Domain , Mitochondrial Precursor Protein Import Complex Proteins , Mitochondrial Proteins , Models, Molecular , Protein Binding , Apoptosis Inducing Factor/metabolism , Apoptosis Inducing Factor/chemistry , Apoptosis Inducing Factor/genetics , Humans , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/chemistry , Mitochondrial Proteins/genetics , Allosteric Regulation , Crystallography, X-Ray , NAD/metabolism , NAD/chemistry , Binding Sites , Transcription Factors/metabolism , Transcription Factors/chemistry , Transcription Factors/genetics
2.
Proteins ; 90(1): 96-109, 2022 01.
Article in English | MEDLINE | ID: mdl-34312913

ABSTRACT

The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high-resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV-1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant-free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV-1 protease under native conditions displays rich patterns of transient native and non-native structures, which could be of relevance to its guidance through a complex folding process.


Subject(s)
HIV Protease , Molecular Dynamics Simulation , Protein Denaturation , HIV Protease/chemistry , HIV Protease/metabolism , Nuclear Magnetic Resonance, Biomolecular , Protein Conformation , Protein Folding
3.
Biochem Biophys Res Commun ; 577: 89-94, 2021 11 05.
Article in English | MEDLINE | ID: mdl-34509083

ABSTRACT

The protozoan Plasmodium falciparum is the main aetiological agent of tropical malaria. Characteristic of the phylum is the presence of a plastid-like organelle which hosts several homologs of plant proteins, including a ferredoxin (PfFd) and its NADPH-dependent reductase (PfFNR). The PfFNR/PfFd redox system is essential for the parasite, while mammals share no homologous proteins, making the enzyme an attractive target for novel and much needed antimalarial drugs. Based on previous findings, three chemically reactive residues important for PfFNR activity were identified: namely, the active-site Cys99, responsible for hydride transfer; Cys284, whose oxidation leads to an inactive dimeric form of the protein; and His286, which is involved in NADPH binding. These amino acid residues were probed by several residue-specific reagents and the two cysteines were shown to be promising targets for covalent inhibition. The quantitative and qualitative description of the reactivity of few compounds, including a repurposed drug, set the bases for the development of more potent and specific antimalarial leads.


Subject(s)
Enzyme Inhibitors/pharmacology , Ferredoxin-NADP Reductase/antagonists & inhibitors , Malaria, Falciparum/prevention & control , Plasmodium falciparum/drug effects , Protozoan Proteins/antagonists & inhibitors , Antineoplastic Agents, Alkylating/chemistry , Antineoplastic Agents, Alkylating/metabolism , Antineoplastic Agents, Alkylating/pharmacology , Biocatalysis/drug effects , Carmustine/chemistry , Carmustine/metabolism , Carmustine/pharmacology , Catalytic Domain , Cysteine/chemistry , Cysteine/metabolism , Diamide/chemistry , Diamide/metabolism , Diamide/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Ferredoxin-NADP Reductase/chemistry , Ferredoxin-NADP Reductase/metabolism , Kinetics , Malaria, Falciparum/parasitology , Molecular Structure , NADP/metabolism , Organomercury Compounds/chemistry , Organomercury Compounds/metabolism , Organomercury Compounds/pharmacology , Plasmodium falciparum/enzymology , Plasmodium falciparum/physiology , Protein Binding , Protein Domains , Protozoan Proteins/chemistry , Protozoan Proteins/metabolism , Substrate Specificity
4.
ACS Infect Dis ; 7(7): 1996-2012, 2021 07 09.
Article in English | MEDLINE | ID: mdl-33855850

ABSTRACT

Plasmodione (PD) is a potent antimalarial redox-active 3-benzyl-menadione acting at low nanomolar range concentrations on different malaria parasite stages. The specific bioactivation of PD was proposed to occur via a cascade of redox reactions starting from one-electron reduction and then benzylic oxidation, leading to the generation of several key metabolites including corresponding benzylic alcohol (PD-bzol, for PD benzhydrol) and 3-benzoylmenadione (PDO, for PD oxide). In this study, we showed that the benzylic oxidation of PD is closely related to the formation of a benzylic semiquinone radical, which can be produced under two conditions: UV photoirradiation or catalysis by Plasmodium falciparum apicoplast ferredoxin-NADP+ reductase (PfFNR) redox cycling in the presence of oxygen and the parent PD. Electrochemical properties of both PD metabolites were investigated in DMSO and in water. The single-electron reduction potential values of PD, PD-bzol, PDO, and a series of 3-benzoylmenadiones were determined according to ascorbate oxidation kinetics. These compounds possess enhanced reactivity toward PfFNR as compared with model quinones. Optimal conditions were set up to obtain the best conversion of the starting PD to the corresponding metabolites. UV irradiation of PD in isopropanol under positive oxygen pressure led to an isolated yield of 31% PDO through the transient semiquinone species formed in a cascade of reactions. In the presence of PfFNR, PDO and PD-bzol could be observed during long lasting redox cycling of PD continuously fueled by NADPH regenerated by an enzymatic system. Finally, we observed and quantified the effect of PD on the production of oxidative stress in the apicoplast of transgenic 3D7[Api-roGFP2-hGrx1]P. falciparum parasites by using the described genetically encoded glutathione redox sensor hGrx1-roGFP2 methodology. The observed fast reactive oxygen species (ROS) pulse released in the apicoplast is proposed to be mediated by PD redox cycling catalyzed by PfFNR.


Subject(s)
Antimalarials , Pharmaceutical Preparations , Catalysis , Ferredoxin-NADP Reductase/metabolism , Ferredoxins/metabolism , NADP/metabolism , Oxidation-Reduction , Plasmodium falciparum/metabolism , Vitamin K 3/analogs & derivatives
5.
Methods Mol Biol ; 2280: 179-187, 2021.
Article in English | MEDLINE | ID: mdl-33751435

ABSTRACT

To perform their action, flavoproteins usually interact with a variety of low molecular weight partners, including electron transporters, yielding transient complexes whose tightness is often controlled by the redox state of the bound flavin cofactor. As a case study, here we describe the quantitative analysis of the redox-dependent interaction of the mammalian apoptosis inducing factor (AIF) with its NAD+ ligand. In particular, we report a protocol for the spectrophotometric titration of AIF in its reduced state under anaerobic conditions with NAD+, in order to determine the dissociation constant of the resulting complex.


Subject(s)
Apoptosis Inducing Factor/metabolism , Escherichia coli/growth & development , NAD/metabolism , Allosteric Regulation , Anaerobiosis , Animals , Apoptosis Inducing Factor/genetics , Escherichia coli/genetics , Mice , Recombinant Proteins/metabolism , Spectrophotometry
6.
Methods Mol Biol ; 2280: 189-198, 2021.
Article in English | MEDLINE | ID: mdl-33751436

ABSTRACT

To perform their action usually flavoproteins interact transiently with a variety of molecular partners, whose binding is reciprocally affected and often controlled by the redox state of the bound flavin cofactor. As a case study, here we describe an approach for the quantitative characterization of the redox-controlled interaction of the mammalian apoptosis inducing factor (AIF) with one of its known protein partners, namely, the mitochondrial coiled-coil-helix-coiled-coil-helix domain-containing protein 4 (CHCHD4). In particular, we report a protocol for the titration of the flavoprotein in both in its oxidized and reduced states with CHCHD4, using an implementation of the MicroScale Thermophoresis (MST) technique.


Subject(s)
Apoptosis Inducing Factor/chemistry , Apoptosis Inducing Factor/metabolism , Escherichia coli/growth & development , Mitochondrial Membrane Transport Proteins/metabolism , Allosteric Regulation , Anaerobiosis , Animals , Apoptosis Inducing Factor/genetics , Escherichia coli/genetics , Fluorescence , Mice , Mitochondrial Precursor Protein Import Complex Proteins , Oxidation-Reduction , Protein Binding , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Spectrophotometry
7.
Int J Mol Sci ; 21(9)2020 May 02.
Article in English | MEDLINE | ID: mdl-32370303

ABSTRACT

Ferredoxin:NADP+ oxidoreductase from Plasmodium falciparum (PfFNR) catalyzes the NADPH-dependent reduction of ferredoxin (PfFd), which provides redox equivalents for the biosynthesis of isoprenoids and fatty acids in the apicoplast. Like other flavin-dependent electrontransferases, PfFNR is a potential source of free radicals of quinones and other redox cycling compounds. We report here a kinetic study of the reduction of quinones, nitroaromatic compounds and aromatic N-oxides by PfFNR. We show that all these groups of compounds are reduced in a single-electron pathway, their reactivity increasing with the increase in their single-electron reduction midpoint potential (E17). The reactivity of nitroaromatics is lower than that of quinones and aromatic N-oxides, which is in line with the differences in their electron self-exchange rate constants. Quinone reduction proceeds via a ping-pong mechanism. During the reoxidation of reduced FAD by quinones, the oxidation of FADH. to FAD is the possible rate-limiting step. The calculated electron transfer distances in the reaction of PfFNR with various electron acceptors are similar to those of Anabaena FNR, thus demonstrating their similar "intrinsic" reactivity. Ferredoxin stimulated quinone- and nitro-reductase reactions of PfFNR, evidently providing an additional reduction pathway via reduced PfFd. Based on the available data, PfFNR and possibly PfFd may play a central role in the reductive activation of quinones, nitroaromatics and aromatic N-oxides in P. falciparum, contributing to their antiplasmodial action.


Subject(s)
Ferredoxin-NADP Reductase/metabolism , Plasmodium falciparum/metabolism , Protozoan Proteins/metabolism , Xenobiotics/metabolism , Apicoplasts/enzymology , Biocatalysis , Cyclic N-Oxides/chemistry , Cyclic N-Oxides/metabolism , Electron Transport , Ferredoxins/metabolism , Flavin-Adenine Dinucleotide/metabolism , Kinetics , Molecular Structure , NADP/metabolism , Oxidation-Reduction , Quinones/chemistry , Quinones/metabolism , Substrate Specificity , Xenobiotics/chemistry
8.
Molecules ; 24(24)2019 Dec 10.
Article in English | MEDLINE | ID: mdl-31835450

ABSTRACT

With the aim to clarify the mechanism(s) of action of nitroaromatic compounds against the malaria parasite Plasmodium falciparum, we examined the single-electron reduction by P. falciparum ferredoxin:NADP+ oxidoreductase (PfFNR) of a series of nitrofurans and nitrobenzenes (n = 23), and their ability to inhibit P. falciparum glutathione reductase (PfGR). The reactivity of nitroaromatics in PfFNR-catalyzed reactions increased with their single-electron reduction midpoint potential (E17). Nitroaromatic compounds acted as non- or uncompetitive inhibitors towards PfGR with respect to NADPH and glutathione substrates. Using multiparameter regression analysis, we found that the in vitro activity of these compounds against P. falciparum strain FcB1 increased with their E17 values, octanol/water distribution coefficients at pH 7.0 (log D), and their activity as PfGR inhibitors. Our data demonstrate that both factors, the ease of reductive activation and the inhibition of PfGR, are important in the antiplasmodial in vitro activity of nitroaromatics. To the best of our knowledge, this is the first quantitative demonstration of this kind of relationship. No correlation between antiplasmodial activity and ability to inhibit human erythrocyte GR was detected in tested nitroaromatics. Our data suggest that the efficacy of prooxidant antiparasitic agents may be achieved through their combined action, namely inhibition of antioxidant NADPH:disulfide reductases, and the rapid reduction by single-electron transferring dehydrogenases-electrontransferases.


Subject(s)
Antimalarials/chemistry , Antimalarials/pharmacology , Glutathione Reductase/antagonists & inhibitors , Oxidation-Reduction/drug effects , Plasmodium falciparum/drug effects , Plasmodium falciparum/enzymology , Antioxidants/chemistry , Antioxidants/pharmacology , Dose-Response Relationship, Drug , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Erythrocytes/drug effects , Erythrocytes/metabolism , Erythrocytes/parasitology , Ferredoxin-NADP Reductase/metabolism , Humans , Inhibitory Concentration 50 , Molecular Structure , NADP/metabolism
9.
Environ Microbiol ; 19(11): 4551-4563, 2017 11.
Article in English | MEDLINE | ID: mdl-28892259

ABSTRACT

Production of cellulose, a stress response-mediated process in enterobacteria, is modulated in Escherichia coli by the activity of the two pyrimidine nucleotide biosynthetic pathways, namely, the de novo biosynthetic pathway and the salvage pathway, which relies on the environmental availability of pyrimidine nitrogenous bases. We had previously reported that prevalence of the salvage over the de novo pathway triggers cellulose production via synthesis of the second messenger c-di-GMP by the DgcQ (YedQ) diguanylate cyclase. In this work, we show that DgcQ enzymatic activity is enhanced by UTP, whilst being inhibited by N-carbamoyl-aspartate, an intermediate of the de novo pathway. Thus, direct allosteric control by these ligands allows full DgcQ activity exclusively in cells actively synthesizing pyrimidine nucleotides via the salvage pathway. Inhibition of DgcQ activity by N-carbamoyl-aspartate appears to be favoured by protein-protein interaction between DgcQ and PyrB, a subunit of aspartate transcarbamylase, which synthesizes N-carbamoyl-aspartate. Our results suggest that availability of pyrimidine bases might be sensed, somehow paradoxically, as an environmental stress by E. coli. We hypothesize that this link might have evolved since stress events, leading to extensive DNA/RNA degradation or lysis of neighbouring cells, can result in increased pyrimidine concentrations and activation of the salvage pathway.


Subject(s)
Aspartic Acid/analogs & derivatives , Cellulose/biosynthesis , Cyclic GMP/analogs & derivatives , Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Phosphorus-Oxygen Lyases/metabolism , Uridine Triphosphate/metabolism , Aspartate Carbamoyltransferase , Aspartic Acid/metabolism , Biosynthetic Pathways , Cellulose/metabolism , Cyclic GMP/biosynthesis , DNA/metabolism , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Phosphorus-Oxygen Lyases/genetics , RNA/metabolism
10.
FEBS J ; 284(19): 3302-3319, 2017 10.
Article in English | MEDLINE | ID: mdl-28783258

ABSTRACT

Ferredoxin: NADP+ reductase (FNR) is an FAD-containing enzyme best known for catalysing the transfer of electrons from ferredoxin (Fd) to NADP+ to make NADPH during photosynthesis. It is also the prototype for a broad enzyme superfamily, including the NADPH oxidases (NOXs) that all catalyse similar FAD-enabled electron transfers between NAD(P)H and one-electron carriers. Here, we define further mechanistic details of the NAD(P)H ⇌ FAD hydride-transfer step of the reaction based on spectroscopic studies and high-resolution (~ 1.5 Å) crystallographic views of the nicotinamide-flavin interaction in crystals of corn root FNR Tyr316Ser and Tyr316Ala variants soaked with either nicotinamide, NADP+ , or NADPH. The spectra obtained from FNR crystal complexes match those seen in solution and the complexes reveal active site packing interactions and patterns of covalent distortion of the FAD that imply significant active site compression that would favour catalysis. Furthermore, anisotropic B-factors show that the mobility of the C4 atom of the nicotinamide in the FNR:NADP+ complex has a directionality matching that expected for boat-like excursions of the nicotinamide ring thought to enhance hydride transfer. Arguments are made for the relevance of this binding mode to catalysis, and specific consideration is given to how the results extrapolate to provide insight to structure-function relations for the membrane-bound NOX enzymes for which little structural information has been available. DATABASES: Structural data are available in the PDB database under the accession numbers 3LO8 (wild-type), 5VW4 [Y316S:nicotinamide (P32 21)], 5VW9 [Y316S:nicotinamide (P31 21)], 5VW3 [Y316S:NADP+ (P32 21)], 5VW8 [Y316S:NADP+ (P31 21)], 5VW2 [Y316S:NADPH (P32 21)], 5VW5 [Y316A:nicotinamide (P32 21)], 5VW6 [Y316A:NADP+ (P32 21)], 5VW7 [Y316A:NADPH (P32 21)], 5VWA [Y316F (P32 21)], and 5VWB [Y316F:NADP+ (P31 21)]. Enzyme Commission number: ferredoxin:NADP+ reductase - E C1.18.1.2.


Subject(s)
Ferredoxin-NADP Reductase/chemistry , Flavin-Adenine Dinucleotide/chemistry , NADPH Oxidases/chemistry , NADP/chemistry , NAD/chemistry , Plant Proteins/chemistry , Amino Acid Sequence , Binding Sites , Biocatalysis , Catalytic Domain , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Ferredoxin-NADP Reductase/genetics , Ferredoxin-NADP Reductase/metabolism , Flavin-Adenine Dinucleotide/metabolism , Gene Expression , Humans , Kinetics , Models, Molecular , NAD/metabolism , NADP/metabolism , NADPH Oxidases/genetics , NADPH Oxidases/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Plant Roots/chemistry , Plant Roots/enzymology , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Secondary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Substrate Specificity , Zea mays/chemistry , Zea mays/enzymology
11.
Biochem Biophys Res Commun ; 490(3): 1011-1017, 2017 08 26.
Article in English | MEDLINE | ID: mdl-28666871

ABSTRACT

The apoptosis-inducing factor (AIF) is a FAD-containing protein playing critical roles in caspase-independent apoptosis and mitochondrial respiratory chain biogenesis and maintenance. While its lethal role is well known, the details of its mitochondrial function remain elusive. So far, nineteen allelic variants of AIF have been associated to human diseases, mainly affecting the nervous system. A strict correlation is emerging between the degree of impairment of its ability to stabilize the charge-transfer (CT) complex between FAD and NAD+ and the severity of the resulting pathology. Recently, we demonstrated that the G307E replacement in murine AIF (equivalent to the pathogenic G308E in the human protein) dramatically decreases the rate of CT complex formation through the destabilization of the flavoprotein interaction with NAD(H). To provide further insights into the structural bases of its altered functional properties, here we report the first crystal structure of an AIF pathogenic mutant variant in complex with NAD+ (murine AIF-G307ECT) in comparison with its oxidized form. With respect to wild type AIF, the mutation leads to an altered positioning of NAD+ adenylate moiety, which slows down CT complex formation. Moreover, the altered balance between the binding of the adenine/nicotinamide portions of the coenzyme determines a large drop in AIF-G307E ability to discriminate between NADH and NADPH.


Subject(s)
Apoptosis Inducing Factor/genetics , Apoptosis Inducing Factor/metabolism , NADP/metabolism , NAD/metabolism , Point Mutation , Animals , Apoptosis Inducing Factor/chemistry , Crystallography, X-Ray , Mice , Models, Molecular , Protein Conformation , Substrate Specificity
12.
J Chromatogr A ; 1496: 25-36, 2017 May 05.
Article in English | MEDLINE | ID: mdl-28351538

ABSTRACT

The production of sugars from lignocellulosic biomass is the key to a sustainable, renewable chemical industry. Glucose, xylose and other monosaccharides can be easily produced by hydrolyzing cellulose and hemicellulose, the primary polysaccharides in biomass. However, the hydrolysis of biomass generates byproducts that, together with the mineral acid normally added in the hydrolysis step, have to be removed before the downstream conversion processes. In this work, the recovery of monosaccharides from lignocellulosic hydrolysates by means of Ion Exclusion Chromatography (IEC) has been studied. The analyzed process relies on new pretreatment and hydrolysis steps, involving the neutralization of the hydrolysate with sodium hydroxide. The adsorption behavior of the main components involved in the separation has been experimentally investigated. Pulse tests at the high loading encountered in preparative conditions have been performed for a selected group of model components found in the hydrolysates. For all the electrolytes, the retention volume fraction was always between the interparticle porosity and the total column porosity, confirming that ion exclusion was the dominant retention mechanism. On the other hand, sugars eluted before the total column porosity, indicating partial steric exclusion from the resin pores. This observation was then confirmed by size-exclusion experiments with polyethylene glycol standards, from which the distribution coefficient of the studied sugars has been determined. The comparison between the elution profiles of the same sugars in pure form and as a mixture present in the hydrolysate showed differences in both peak shape and retention times. Therefore, an investigation of the influence of the main electrolytes contained in the hydrolysates on sugars adsorption has been performed through the pulse on a plateau method. The electrolytes were found to enhance the sugars retention by promoting their adsorption onto the resin. However, this effect was not sufficient to explain the observed differences, which were effectively explained in terms of viscous fingering, due to the high viscosity differences between the eluent and the sample. A previously developed model for IEC has been updated to take into account all the observed phenomena and applied to simulate the experimental results. The proposed model was in good agreement with the batch-column elution profiles both for the pure components and for the actual hydrolysate, allowing a quantitative description of the separation.


Subject(s)
Chromatography, Gel , Lignin/chemistry , Monosaccharides/chemistry , Monosaccharides/isolation & purification , Adsorption , Electrolytes/chemistry , Electrolytes/isolation & purification , Hydrolysis , Ions , Polyethylene Glycols , Porosity
13.
Biochemistry ; 56(8): 1029-1032, 2017 02 28.
Article in English | MEDLINE | ID: mdl-28168877

ABSTRACT

The human immunodeficiency virus-1 (HIV-1) protease is a complex protein that in its active form adopts a homodimer dominated by ß-sheet structures. We have discovered a cold-denatured state of the monomeric subunit of HIV-1 protease that is populated above 0 °C and therefore directly accessible to various spectroscopic approaches. Using nuclear magnetic resonance secondary chemical shifts, temperature coefficients, and protein dynamics, we suggest that the cold-denatured state populates a compact wet globule containing transient non-native-like α-helical elements. From the linearity of the temperature coefficients and the hydrodynamic radii, we propose that the overall architecture of the cold-denatured state is maintained over the temperature range studied.


Subject(s)
Cold Temperature , HIV Protease/chemistry , Protein Denaturation , Protein Conformation, alpha-Helical , Protein Multimerization
14.
Biochem Biophys Res Commun ; 481(1-2): 51-58, 2016 Dec 02.
Article in English | MEDLINE | ID: mdl-27836547

ABSTRACT

Although the precise functions of ether phospholipids are still poorly understood, significant alterations in their physiological levels are associated either to inherited disorders or to aggressive metastatic cancer. The essential precursor, alkyl-dihydroxyacetone phosphate (DHAP), for all ether phospholipids species is synthetized in two consecutive reactions performed by two enzymes sitting on the inner side of the peroxisomal membrane. Here, we report the characterization of the recombinant human DHAP acyl-transferase, which performs the first step in alkyl-DHAP synthesis. By exploring several expression systems and designing a number of constructs, we were able to purify the enzyme in its active form and we found that it is tightly bound to the membrane through the N-terminal residues.


Subject(s)
Acyltransferases/chemistry , Acyltransferases/metabolism , Membrane Proteins/metabolism , Peroxisomes/metabolism , Pichia/enzymology , Acyltransferases/genetics , Binding Sites , HEK293 Cells , Humans , Membrane Proteins/chemistry , Pichia/genetics , Protein Binding , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism
15.
Biochem Biophys Res Commun ; 479(1): 48-53, 2016 10 07.
Article in English | MEDLINE | ID: mdl-27613098

ABSTRACT

Microtubule (MT) dynamic behaviour is an attractive drug target for chemotherapy, whose regulation by MT-stabilizing and destabilizing agents has been fruitfully applied in treating several types of cancers. MT-stabilizing agents are also emerging as potential remedies for neurodegenerative conditions, such as Alzheimer's and Parkinson's disease, although single-target drugs are not expected to fully cure these complex pathologies. Drug combination often displays enhanced efficacy with respect to mono-therapies. In particular, MT-targeting bivalent compounds (MTBCs) represent a promising class of molecules; however, surprisingly, the majority of MTBCs reported so far exhibit equal if not less efficacy than their building monomers. In order to shed light on MTBCs poor performance, we characterised through a set of complementary approaches thiocolchine (TH) and two bivalent TH-homodimers as prototype molecules. First, the binding affinities of these three molecules were assessed, then we obtained the crystallographic structure of a tubulin-TH complex. The binding affinities were interpreted in light of structural data and of molecular dynamics simulations. Finally, their effects on MT cytoskeleton and cell survival were validated on HeLa cells. The ensemble of these data provides chemical and structural considerations on how a successful rational design of MTBCs should be conceived.


Subject(s)
Antineoplastic Agents/metabolism , Drug Design , Microtubules/metabolism , Tubulin Modulators/metabolism , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Binding, Competitive , Cell Proliferation/drug effects , Crystallography, X-Ray , Depsipeptides/chemistry , Depsipeptides/metabolism , Depsipeptides/pharmacology , Dimerization , HeLa Cells , Humans , Microscopy, Fluorescence , Microtubules/chemistry , Models, Molecular , Molecular Structure , Protein Binding , Protein Domains , Tubulin/chemistry , Tubulin/metabolism , Tubulin Modulators/chemistry , Tubulin Modulators/pharmacology
16.
Sci Rep ; 6: 33289, 2016 09 15.
Article in English | MEDLINE | ID: mdl-27628239

ABSTRACT

α-Synuclein is a presynaptic protein associated to Parkinson's disease, which is unstructured when free in the cytoplasm and adopts α helical conformation when bound to vesicles. After decades of intense studies, α-Synuclein physiology is still difficult to clear up due to its interaction with multiple partners and its involvement in a pletora of neuronal functions. Here, we looked at the remarkably neglected interplay between α-Synuclein and microtubules, which potentially impacts on synaptic functionality. In order to identify the mechanisms underlying these actions, we investigated the interaction between purified α-Synuclein and tubulin. We demonstrated that α-Synuclein binds to microtubules and tubulin α2ß2 tetramer; the latter interaction inducing the formation of helical segment(s) in the α-Synuclein polypeptide. This structural change seems to enable α-Synuclein to promote microtubule nucleation and to enhance microtubule growth rate and catastrophe frequency, both in vitro and in cell. We also showed that Parkinson's disease-linked α-Synuclein variants do not undergo tubulin-induced folding and cause tubulin aggregation rather than polymerization. Our data enable us to propose α-Synuclein as a novel, foldable, microtubule-dynamase, which influences microtubule organisation through its binding to tubulin and its regulating effects on microtubule nucleation and dynamics.


Subject(s)
Parkinson Disease/genetics , Protein Aggregation, Pathological/genetics , Tubulin/metabolism , alpha-Synuclein/metabolism , Humans , Microtubules/chemistry , Microtubules/metabolism , Parkinson Disease/metabolism , Parkinson Disease/pathology , Protein Binding , Protein Folding , Protein Multimerization/genetics , Tubulin/chemistry , Tubulin/genetics , alpha-Synuclein/chemistry , alpha-Synuclein/genetics
17.
Biochemistry ; 54(47): 6996-7009, 2015 Dec 01.
Article in English | MEDLINE | ID: mdl-26535916

ABSTRACT

Apoptosis-inducing factor (AIF) is a mitochondrial flavoprotein with pro-life and pro-death activities, which plays critical roles in mitochondrial energy metabolism and caspase-independent apoptosis. Defects in AIF structure or expression can cause mitochondrial abnormalities leading to mitochondrial defects and neurodegeneration. The mechanism of AIF-induced apoptosis was extensively investigated, whereas the mitochondrial function of AIF is poorly understood. A unique feature of AIF is the ability to form a tight, air-stable charge-transfer (CT) complex upon reaction with NADH and to undergo a conformational switch leading to dimerization, proposed to be important for its vital and lethal functions. Although some aspects of interaction of AIF with NAD(+)/H have been analyzed, its precise mechanism is not fully understood. We investigated how the oxidized and photoreduced wild-type and G307A and -E variants of murine AIF associate with NAD(+)/H and nicotinamide mononucleotide (NMN(+)/H) to determine the role of the adenylate moiety in the binding process. Our results indicate that (i) the adenylate moiety of NAD(+)/H is crucial for the association with AIF and for the subsequent structural reorganization of the complex, but not for protein dimerization, (ii) FAD reduction rather than binding of NAD(+)/H to AIF initiates conformational rearrangement, and (iii) alteration of the adenylate-binding site by the G307E (equivalent to a pathological G308E mutation in human AIF) or G307A replacements decrease the affinity and association rate of NAD(+)/H, which, in turn, perturbs CT complex formation and protein dimerization but has no influence on the conformational switch in the regulatory peptide.


Subject(s)
Apoptosis Inducing Factor/metabolism , Apoptosis , Mitochondrial Proteins/metabolism , NAD/metabolism , Animals , Apoptosis Inducing Factor/chemistry , Apoptosis Inducing Factor/genetics , Binding Sites , Humans , Kinetics , Mice , Mitochondrial Proteins/chemistry , Mitochondrial Proteins/genetics , Models, Molecular , Mutation , NAD/chemistry , Oxidation-Reduction , Protein Binding , Protein Multimerization , Protein Stability , Temperature
18.
ACS Chem Biol ; 10(11): 2589-97, 2015 Nov 20.
Article in English | MEDLINE | ID: mdl-26322624

ABSTRACT

Dysregulated ether lipid metabolism is an important hallmark of cancer cells. Previous studies have reported that lowering ether lipid levels by genetic ablation of the ether lipid-generating enzyme alkyl-glycerone phosphate synthase (AGPS) lowers key structural and oncogenic ether lipid levels and alters fatty acid, glycerophospholipid, and eicosanoid metabolism to impair cancer pathogenicity, indicating that AGPS may be a potential therapeutic target for cancer. In this study, we have performed a small-molecule screen to identify candidate AGPS inhibitors. We have identified several lead AGPS inhibitors and have structurally characterized their interactions with the enzyme and show that these inhibitors bind to distinct portions of the active site. We further show that the lead AGPS inhibitor 1a selectively lowers ether lipid levels in several types of human cancer cells and impairs their cellular survival and migration. We provide here the first report of in situ-active pharmacological tools for inhibiting AGPS, which may provide chemical scaffolds for future AGPS inhibitor development for cancer therapy.


Subject(s)
Alkyl and Aryl Transferases/antagonists & inhibitors , Drug Discovery , Small Molecule Libraries/chemistry , Small Molecule Libraries/pharmacology , Animals , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Crystallography, X-Ray , Drug Stability , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Humans , Models, Molecular , Molecular Structure , Swine , Temperature
19.
Protein Expr Purif ; 114: 48-57, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26118699

ABSTRACT

The receptor for the advanced glycation end products (RAGE) is a type I transmembrane glycoprotein belonging to the immunoglobulin superfamily and binds a variety of unrelated ligands sharing a negative charge. Most ligands bind to the extracellular V or VC1 domains of the receptor. In this work, V and VC1 of human RAGE were produced in the methylotrophic yeast Pichia pastoris and directed to the secretory pathway. Fusions to a removable C-terminal His-tag evidenced proteolytic processing of the tag by extracellular proteases and also intracellular degradation of the N-terminal portion of V-His. Expression of untagged forms was attempted. While the V domain was retained intracellularly, VC1 was secreted into the medium and was functionally active in binding AGEs. The glycosylation state of VC1 was analyzed by mass spectrometry and peptide-N-glycosidase F digestion. Like RAGE isolated from mammalian sources, the degree of occupancy of the N-glycosylation sites was full at Asn25 and partial at Asn81 which was also subjected to non-enzymatic deamidation. A simple procedure for the purification to homogeneity of VC1 from the medium was developed. The folded state of the purified protein was assessed by thermal shift assays. Recombinant VC1 from P. pastoris showed a remarkably high thermal stability as compared to the protein expressed in bacteria. Our in vivo approach indicates that the V and C1 domains constitute a single folding unit. The stability and solubility of the yeast-secreted VC1 may be beneficial for future in vitro studies aimed to identify new ligands or inhibitors of RAGE.


Subject(s)
Pichia/genetics , Receptor for Advanced Glycation End Products/chemistry , Receptor for Advanced Glycation End Products/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Glycosylation , Protein Stability , Protein Structure, Tertiary/genetics , Receptor for Advanced Glycation End Products/genetics , Receptor for Advanced Glycation End Products/isolation & purification , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification
20.
Curr Pharm Des ; 19(14): 2540-51, 2013.
Article in English | MEDLINE | ID: mdl-23116393

ABSTRACT

Renalase is a flavoprotein recently discovered in humans, preferentially expressed in the proximal tubules of the kidney and secreted in blood and urine. It is highly conserved in vertebrates, with homologs identified in eukaryotic and prokaryotic organisms. Several genetic, epidemiological, clinical and experimental studies show that renalase plays a role in the modulation of the functions of the cardiovascular system, being particularly active in decreasing the catecholaminergic tone, in lowering blood pressure and in exerting a protective action against myocardial ischemic damage. Deficient renalase synthesis might be the cause of the high occurrence of hypertension and adverse cardiac events in kidney disease patients. Very recently, recombinant human renalase has been structurally and functionally characterized in vitro. Results show that it belongs to the p-hydroxybenzoate hydroxylase structural family of flavoenzymes, contains non-covalently bound FAD with redox features suggestive of a dehydrogenase activity, and is not a catecholamine-degrading enzyme,either through oxidase or NAD(P)H-dependent monooxygenase reactions. The biochemical data now available will hopefully provide the basis for a systematic and rational quest toward the identification of the reaction catalyzed by renalase and of the molecular mechanism of its physiological action, which in turn are expected to favor the development of novel therapeutic tools for the treatment of kidney and cardiovascular diseases.


Subject(s)
Catecholamines/metabolism , Flavoproteins/physiology , Monoamine Oxidase/physiology , Signal Transduction/physiology , Animals , Binding Sites , Cardiovascular Diseases/enzymology , Cardiovascular Diseases/epidemiology , Cardiovascular Diseases/genetics , Drug Discovery , Flavoproteins/chemistry , Flavoproteins/genetics , Humans , Kidney Diseases/enzymology , Kidney Diseases/epidemiology , Kidney Diseases/genetics , Monoamine Oxidase/chemistry , Monoamine Oxidase/genetics , Polymorphism, Single Nucleotide , Protein Conformation , Risk Factors
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