Structure of human spermine oxidase in complex with a highly selective allosteric inhibitor.

Human spermine oxidase (hSMOX) plays a central role in polyamine catabolism. Due to its association with several pathological processes, including inflammation and cancer, hSMOX has garnered interest as a possible therapeutic target. Therefore, determination of the structure of hSMOX is an important step to enable drug discovery and validate hSMOX as a drug target. Using insights from hydrogen/deuterium exchange mass spectrometry (HDX-MS), we engineered a hSMOX construct to obtain the first crystal structure of hSMOX bound to the known polyamine oxidase inhibitor MDL72527 at 2.4 Å resolution. While the overall fold of hSMOX is similar to its homolog, murine N1-acetylpolyamine oxidase (mPAOX), the two structures contain significant differences, notably in their substrate-binding domains and active site pockets. Subsequently, we employed a sensitive biochemical assay to conduct a high-throughput screen that identified a potent and selective hSMOX inhibitor, JNJ-1289. The co-crystal structure of hSMOX with JNJ-1289 was determined at 2.1 Å resolution, revealing that JNJ-1289 binds to an allosteric site, providing JNJ-1289 with a high degree of selectivity towards hSMOX. These results provide crucial insights into understanding the substrate specificity and enzymatic mechanism of hSMOX, and for the design of highly selective inhibitors.

Development and characterization of rabbit monoclonal antibodies that recognize human spermine oxidase and application to immunohistochemistry of human cancer tissues.

The enzyme spermine oxidase (SMOX) is involved in polyamine catabolism and converts spermine to spermidine. The enzymatic reaction generates reactive hydrogen peroxide and aldehydes as by-products that can damage DNA and other biomolecules. Increased expression of SMOX is frequently found in lung, prostate, colon, stomach and liver cancer models, and the enzyme also appears to play a role in neuronal dysfunction and vascular retinopathy. Because of growing evidence that links SMOX activity with DNA damage, inflammation, and carcinogenesis, the enzyme has come into view as a potential drug target. A major challenge in cancer research is the lack of characterization of antibodies used for identification of target proteins. To overcome this limitation, we generated a panel of high-affinity rabbit monoclonal antibodies against various SMOX epitopes and selected antibodies for use in immunoblotting, SMOX quantification assays, immunofluorescence microscopy and immunohistochemistry. Immunohistochemistry analysis with the antibody SMAB10 in normal and transformed tissues confirms that SMOX is upregulated in several different cancers. Together, the panel of antibodies generated herein adds to the toolbox of high-quality reagents to study SMOX biology and to facilitate SMOX drug development.

The interactome of stabilized α-synuclein oligomers and neuronal proteins.

While it is generally accepted that α-synuclein oligomers (αSOs) play an important role in neurodegeneration in Parkinson's disease, the basis for their cytotoxicity remains unclear. We have previously shown that docosahexaenoic acid (DHA) stabilizes αSOs against dissociation without compromising their ability to colocalize with glutamatergic synapses of primary hippocampal neurons, suggesting that they bind to synaptic proteins. Here, we develop a proteomic screen for putative αSO binding partners in rat primary neurons using DHA-stabilized human αSOs as a bait protein. The protocol involved co-immunoprecipitation in combination with a photoactivatable heterobifunctional sulfo-LC-SDA crosslinker which did not compromise neuronal binding and preserved the interaction between the αSOs-binding partners. We identify in total 29 proteins associated with DHA-αSO of which eleven are membrane proteins, including synaptobrevin-2B (VAMP-2B), the sodium-potassium pump (Na+ /K+ ATPase), the V-type ATPase, the voltage-dependent anion channel and calcium-/calmodulin-dependent protein kinase type II subunit gamma; only these five hits were also found in previous studies which used unmodified αSOs as bait. We also identified Rab-3A as a target with likely disease relevance. Three out of four selected hits were subsequently validated with dot-blot binding assays. In addition, likely binding sites on these ligands were identified by computational analysis, highlighting a diversity of possible interactions between αSOs and target proteins. These results constitute an important step in the search for disease-modifying treatments targeting toxic αSOs.

Bi-enzyme sensor for phenolic compounds with fluorescent read-out.

In this paper, the use of tyrosinase (Ty) from Streptomyces antibioticus, labeled with a fluorescent tag, in combination with soluble quinoprotein (PQQ-containing) glucose dehydrogenase (s-GDH) to measure trace amounts of phenols is explored. Proof of concept is provided by a series of experiments, which show a clear quantitative dependence of the response on the phenol concentration. One of the advantages of the detection system is that apart from a standard fluorimeter no further instrumentation is required.

Involvement of Tyr108 in the enzyme mechanism of the small laccase from Streptomyces coelicolor.

The enzyme mechanism of the multicopper oxidase (MCO) SLAC from Streptomyces coelicolor was investigated by structural (XRD), spectroscopic (optical, EPR), and kinetics (stopped-flow) experiments on variants in which residue Tyr108 had been replaced by Phe or Ala through site-directed mutagenesis. Contrary to the more common three-domain MCOs, a tyrosine in the two-domain SLAC is found to participate in the enzyme mechanism by providing an electron during oxygen reduction, giving rise to the temporary appearance of a tyrosyl radical. The relatively low k(cat)/K(M) of SLAC and the involvement of Y108 in the enzyme mechanism may reflect an adaptation to a milieu in which there is an imbalance between the available reducing and oxidizing co-substrates. The purported evolutionary relationship between the two-domain MCOs and human ceruloplasmin appears to extend not only to the 3D structure and the mode of binding of the Cu's in the trinuclear center, as noted before, but also to the enzyme mechanism.

Sensitive detection of histamine using fluorescently labeled oxido-reductases.

A detection scheme is described by which the histamine contents of biological samples can be established. The scheme is based on the use of methylamine dehydrogenase (MADH) which converts primary amines into the corresponding aldehydes and ammonia. The generated reducing equivalents are subsequently transferred to the physiological partner of MADH, amicyanin, which thereby is converted from the oxidized blue-colored form into the reduced colorless form. The change in absorption is detected by monitoring the fluorescence of a covalently attached Cy5 dye label whose fluorescence is (partly) quenched by Förster resonance energy transfer (FRET) to the Cu-site of the amicyanin. The quenching efficiency and, thereby, the label fluorescence, depends on the oxidation state of the amicyanin. When adding histamine to the assay mixture the proportionality between the substrate concentration and the observed rate of the fluorescence increase has enabled this assay as a sensor method with high sensitivity. The MADH and amicyanin composition can be tuned so that the sensor can be adapted over a broad range of histamine concentrations (13 nM-225 µM). The lowest concentration detected so far is 13 nM of histamine. The sensor retained its linearity up to 225 µM with a coefficient of variation of 11% for 10 measurements of 100nM histamine in a 100 µL sample volume. The use of a label fluorescing around 660 nm helps circumventing the interference from background fluorescence in biological samples. The sensor has been tested to detect histamine in biological fluids such as fish extracts and blood serum.

Channeling of electrons within SLAC, the small laccase from Streptomyces coelicolor.

The reduction kinetics of the fluorescently labeled small laccase (SLAC) from Streptomyces coelicolor was studied by stopped flow kinetic measurements. The tryptophan fluorescence and the emission from a covalently attached label were used to selectively follow the progress of the reduction of the trinuclear copper center (TNC) and the type-1 (T1) Cu site in the enzyme as a function of time. A numerical analysis of the kinetic traces provided new insight into the midpoint potential difference between the T1 and the TNC site as the TNC becomes stepwise charged with electrons. The change in fluorescence of the TNC as the reduction of the TNC proceeds provided evidence that the type-3 dinuclear part of the TNC becomes charged prior to the reduction of the type-2 (T2) center of the TNC. The rate of reduction of the enzyme by dithionite (DT) appeared proportional to the square root of the DT concentration with a rate constant of k(red) = 0.28 +/- 0.02 microM(-1/2) s(-1).

Electrical contacting of an assembly of pseudoazurin and nitrite reductase using DNA-directed immobilization.

A method for the electrical contacting of redox enzymes that obtain oxidizing or reducing equivalents from small electron-transfer proteins is demonstrated. The electrochemical contacting of redox enzymes through their immobilization onto electrode supports offers great potential for technological applications and for fundamental studies, but finding appropriate methods to immobilize the enzymes in an orientation allowing rapid electron transfer with the electrode has proven difficult. The copper enzyme nitrite reductase (NiR) and its natural electron-exchange partner pseudoazurin (Paz) are conjugated to a specific DNA tag and immobilized to a gold electrode into a stoichiometrically defined assembly. The DNA tethered to the electrode surface acts as flexible place-holder for the protein components, allowing both proteins to move within the construct. It is shown that Paz efficiently shuttles electrons between the electrode and the NiR enzyme, allowing the electrochemically driven NiR catalysis to be monitored. The activity of the NiR enzyme remains unperturbed by the immobilization. The rate-limiting step of the system is tentatively ascribed to the dissociation of the Paz/NiR complex. The electrochemical response of the system reports not only on the NiR catalysis and on interfacial electron transfer but also on the interaction between NiR and Paz.

Site-site interactions enhances intramolecular electron transfer in Streptomyces coelicolor laccase.

Control of electron transfer rates, caused by intrinsic protein structural properties, is an intriguing feature of internal biological electron transfer (ET) reactions. The small laccase (SLAC) isolated from Streptomyces coelicolor has recently been shown to have structural and reactivity features distinct from those of other laccases. While other copper oxidases contain three cupredoxin domains, the SLAC 3D structure has recently been determined and shown to consist of only two, and a different reaction intermediate has been reported for it. It was therefore of particular interest to investigate the intramolecular ET between the type 1 and the trinuclear copper center in SLAC which is a crucial step in the catalytic cycle of the multicopper oxidases, leading to dioxygen reduction to water. This ET step was found to markedly depend on the reduction state of the enzyme, possibly reflecting site-site interactions so far not observed in other multicopper oxidases.

Shape and release control of a peptide decorated vesicle through pH sensitive orthogonal supramolecular interactions.

A pH sensitive carrier is obtained by coating a cyclodextrin vesicle with an adamantane-terminated octapeptide through the formation of an inclusion complex. Upon lowering the pH from 7.4 to 5.0, the formation of peptide beta-sheets on the vesicle surface induces a transition of the bilayer from a sphere to a fiber. This transition is fully reversible and repeatable. The vesicles release their cargo upon fiber formation.

Identification of a radical intermediate in the enzymatic reduction of oxygen by a small laccase.

The enzyme mechanism of the Cu-containing small laccase (SLAC) from Streptomyces coelicolor has been investigated by optical and electron paramagnetic resonance spectroscopy. A new intermediate was identified after the reaction of molecular oxygen with the reduced trinuclear site of the type-1-depleted (T1D) form of the enzyme. It has the fingerprint of a biradical with a triplet ground state. One of the spins resides on a Cu in the trinuclear site, tentatively identified as the type-2 site, while the other spin derives from a protein-based radical. The latter is tentatively identified as a tyrosyl radical on the basis of the similarity of the optical characteristics with those observed for a Cu tyrosyl radical pair. The spin-spin distance was found to be 5.0 +/- 0.2 A.

A protein-based oxygen biosensor for high-throughput monitoring of cell growth and cell viability.

Fluorescently labeled hemocyanin has been previously proposed as an oxygen sensor. In this study, we explored the efficacy of this biosensor for monitoring the biological oxygen consumption of bacteria and its use in testing bacterial cell growth and viability of Escherichia coli, Pseudomonas aeruginosa, Paracoccus denitrificans, and Staphylococcus simulans. Using a microwell plate, the time courses for the complete deoxygenation of samples with different initial concentrations of cells were obtained and the doubling times were extracted. The applicability of our fluorescence-based cell growth assay as an antibacterial drug screening method was also explored. The results provide a proof-of-principle for a simple, quantitative, and sensitive method for high-throughput monitoring of prokaryotic cell growth and antibiotic susceptibility screening.

Tryptophan-to-dye fluorescence energy transfer applied to oxygen sensing by using type-3 copper proteins.

A fluorescence-based system to sense oxygen in solution is described. The method exploits the sensitivity of the endogenous fluorescence of type-3 copper proteins towards the presence of oxygen by translating the near-UV emission of the protein to label fluorescence in the visible range through a FRET mechanism. The main protein in this study, a recombinant tyrosinase from the soil bacterium Streptomyces antibioticus, has been covalently labeled with a variety of fluorescent dye molecules with emission maxima spanning the whole visible wavelength range. In all cases, the emission of the label varied considerably between O2-bound and O2-free protein with a contrast exceeding that of the Trp emission for some labels. It is shown that different constructs may be simultaneously observed using a single excitation wavelength. Next to the described application in oxygen sensing, the method may be applicable to any protein showing variations in tryptophan fluorescence, for example as a function of ligand binding or catalysis.

Paramagnetic properties of the halide-bound derivatives of oxidised tyrosinase investigated by 1H NMR spectroscopy.

The (1)H NMR relaxation characteristics of the histidines in the oxidised type-3 copper site of tyrosinase (Ty(met)) from the bacterium Streptomyces antibioticus in the halide-bound forms (Ty(met)X with X = F(-), Cl(-), Br(-)) have been determined and analysed. The (1)H NMR spectra of the Ty(met)X species display remarkably sharp, well-resolved, paramagnetically shifted (1)H signals, which originate from the protons of the six His residues coordinated to the two Cu(II) ions in the type-3 centre. From the temperature-dependence of the (1)H paramagnetic shifts the following values for the exchange-coupling parameter -2J were determined: 260 (Ty(met)F), 200 (Ty(met)Cl) and 162 cm(-1) (Ty(met)Br). The (1)H T(1) relaxation is dipolar in origin and correlates with the Cu--H distances. Electronic relaxation times tau(S) derived from the (1)H T(1) data amount to about 10(-11) s and follow the order Ty(met)F>Ty(met)Cl>Ty(met)Br. They are two orders of magnitude shorter than the tau(S) values reported for mononuclear copper systems, in accordance with the sharpness of the (1)H signals. The results corroborate the Cu(2) bridging mode of the halide ions. On the basis of the measured hyperfine interaction constants for the ligand histidine nuclei, it is concluded that 70-80 % of the spin density in the excited triplet state resides on the two copper ions and the bridging atoms.

Interaction between the type-3 copper protein tyrosinase and the substrate analogue p-nitrophenol studied by NMR.

The interaction of the monooxygenating type-3 copper enzyme Tyrosinase (Ty) from Streptomyces antibioticus with its inhibitor p-nitrophenol (pnp) was studied by paramagnetic NMR methods. The pnp binds to oxidized Ty (Ty(met)) and its halide (F(-), Cl(-)) bound derivatives with a dissociation constant in the mM range. The Cu(2) bridging halide ion is not displaced upon the binding of pnp showing that the pnp does not occupy the Cu(2) bridging position. The binding of pnp to Ty(met) or Ty(met)Cl leads to localized changes in the type-3 (Cu-His(3))(2) coordination geometry reflecting a change in the coordination of a single His residue that, still, remains coordinated to Cu. The binding of pnp to Ty(met)Cl causes a decrease in the Cu(2) magnetic exchange parameter -2J from 200 cm(-)(1) in the absence to 150 +/- 10 cm(-)(1) in the presence of pnp. From the (1)H and (2)D NMR relaxation parameters of pnp bound to Ty(met), a structural model of pnp coordination to the Ty type-3 center could be derived. The model explains the absence of hydroxylase activity in the closely related type-3 copper protein catechol oxidase. The relevance of the experimental findings toward the Ty catalytic mechanism is discussed.

What are the structural features of the active site that define binuclear copper proteins function?

The structural basis that define the physiological functions of binuclear copper enzymes is discussed in the frame of the data generated by a broad spectroscopic approach, spanning from paramagnetic NMR and pulsed EPR to x-ray absorption spectroscopies. The structural features discussed for the different oxidation and ligation states accessible to a binuclear copper sites are the coordination geometry for the first and second shell, the metal-metal distance and the role of the bridging exogenous ligand(s). A structural model will be presented to rationalize both the differentiation in function within the protein families and the reaction mechanism of those proteins that are enzymatically active.

Stopped-flow fluorescence studies of inhibitor binding to tyrosinase from Streptomyces antibioticus.

Tyrosinase (Ty) is a type 3 copper protein involved in the rate-limiting step of melanin synthesis. It is shown that the endogenous Trp fluorescence of tyrosinase from Streptomyces antibioticus is remarkably sensitive to the redox state. The fluorescence emission intensity of the [(Cu(I) Cu(I)] reduced species is more than twice that of the oxygen-bound [Cu(II)-O(2)(2-)-Cu(II)] form. The emission intensity of the oxidized [Cu(II)-OH(-)-Cu(II)] protein (Ty(met)) appears to be dependent on an acid-base equilibrium with a pK(a) value of 4.5 +/- 0.1. The binding of fluoride was studied under pseudo first-order conditions using stopped-flow fluorescence spectroscopy. The kinetic parameters k(on), K(d), and the fraction of fluorescence emission quenched upon fluoride binding show a similar pH dependence as above with an average pK(a) value of 4.62 +/- 0.05. Both observations are related to the dissociation of Cu(2)-bridging hydroxide at low pH. It is further shown that Ty is rapidly inactivated at low pH and that halide protects the enzyme from this inactivation. All results support the hypothesis that halide displaces hydroxide as the Cu(2)-bridging ligand in Ty(met). The relevance of the experimental findings for the catalytic cycle is discussed. The data are consistent with the data obtained from other techniques, validating the use of fluorescence quenching as a sensitive and effective tool in studying ligand binding and substrate conversion.

Tyrosinase-catalyzed oxidation of fluorophenols.

The activity of the type 3 copper enzyme tyrosinase toward 2-, 3-, and 4-fluorophenol was studied by kinetic methods and (1)H and (19)F NMR spectroscopy. Whereas 3- and 4-fluorophenol react with tyrosinase to give products that undergo a rapid polymerization process, 2-fluorophenol is not reactive and actually acts as a competitive inhibitor in the enzymatic oxidation of 3,4-dihydroxyphenylalanine (L-dopa). The tyrosinase-mediated polymerization of 3- and 4-fluorophenols has been studied in detail. It proceeds through a phenolic coupling pathway in which the common reactive fluoroquinone, produced stereospecifically by tyrosinase, eliminates an inorganic fluorine ion. The enzymatic reaction studied as a function of substrate concentration shows a prominent lag that is completely depleted in the presence of L-dopa. The kinetic parameters of the reactions can be correlated to the electronic and steric effects of the fluorine substituent position. Whereas the fluorine electron withdrawing effect appears to control the binding of the substrates (K(m) for 3- and 4-fluorophenols and K(I) for 2-fluorophenol), the k(cat) parameters do not follow the expected trend, indicating that in the transition state some additional steric effect rules the reactivity.

Structural basis and mechanism of the inhibition of the type-3 copper protein tyrosinase from Streptomyces antibioticus by halide ions.

The inhibition of the type-3 copper enzyme tyrosinase by halide ions was studied by kinetic and paramagnetic (1)H NMR methods. All halides are inhibitors in the conversion of l-3,4-dihydroxyphenylalanine (l-DOPA) with apparent inhibition constants that follow the order I(-) < F(-) << Cl(-) < Br(-) at pH 6.80. The results show that the inhibition arises from the interaction of halide with both the oxidized (affinity F(-) > Cl(-) > Br(-) >> I(-)) and reduced (affinity I(-) > Br(-) > Cl(-) >> F(-)) enzyme. The paramagnetic (1)H NMR of the oxidized enzyme complexed with the halides is consistent with a direct interaction of halide with the type-3 site and shows that the (Cu-His(3))(2) coordination occurs in all halide-bound species. It is surmised that halides bridge both of the copper ions in the active site. Fluoride and chloride are shown to bind only to the low pH form of oxidized tyrosinase, explaining the strong pH dependence of the inhibition by these ions. We further show that p-toluic acid and the bidentate transition state analogue, Kojic acid, displace chloride from the oxidized active site, whereas the monodentate substrate analogue, p-nitrophenol, forms a ternary complex with the enzyme and the chloride ion. On the basis of the experimental results, a model is formulated for the inhibitor action and for the reaction of diphenols with the oxidized enzyme.