Conformational changes in pediocin AcH upon vesicle binding and approximation of the membrane-bound structure in detergent micelles.

Pediocin AcH is a 44-residue antimicrobial peptide with bactericidal potency against Gram-positive bacteria such as Listeria. It belongs to a family of bacteriocins that, when membrane-associated, is predicted to contain beta-sheet and alpha-helical regions. All bacteriocins in this family have a conserved N-terminal disulfide bond. An additional C-terminal disulfide bond in pediocin AcH is thought to confer enhanced potency and broader specificity range against sensitive bacteria. The C-terminal disulfide bond may also affect the conformation of the C-terminus. The secondary structures of pediocin AcH in aqueous solution and vesicles from susceptible cells, as well as the ability of trifluoroethanol (TFE) and detergent systems to induce secondary structures like those induced in vesicles, were studied by circular dichroism (CD) spectroscopy. Like related peptides, pediocin AcH was highly unordered in aqueous solution, 56%. However, it also contained 20% beta-strand and 15% beta-turn structures. Upon complete binding to vesicles, 32% alpha-helical structure formed, the unordered structure decreased to 32%, and the beta-strand and beta-turn structures remained largely unchanged. Thus, a betaalpha domain structure formed in vesicles. The helical structure likely forces the C-terminal tail to loop back on the helix so that the C24-C44 disulfide bond can form. Detergent micelles were superior to TFE in their ability to induce secondary structural fractions in pediocin AcH comparable to those observed in vesicles. This demonstrates the importance of a hydrocarbon-water interface to pediocin AcH structure induction and suggests that it is preferable to use detergent micelles as solvents in NMR studies of pediocin AcH structure.

Multiplicity control in the polygeminal diazeniumdiolation of active hydrogen bearing carbons: chemistry of a new type of trianionic molecular propeller.

Over a century ago, Traube reported the reaction of four nitric oxides with acetone and sodium ethoxide to yield sodium methanebis(diazene-N-oxide-N'-hydroxylate) and sodium acetate. However, when this reaction is carried out in the presence of nitric oxide at slightly elevated pressures (35-40 psi), a product corresponding to the addition of six nitric oxides, sodium methanetris(diazene-N-oxide-N'-hydroxylate), forms as the main product in addition to a trace of the previously observed sodium methanebis(diazene-N-oxide-N'-hydroxylate) and sodium acetate. The corresponding potassium salts form when potassium hydroxide is employed as the base, while lithium hydroxide results in the formation of lithium methanebis(diazene-N-oxide-N'-hydroxylate) exclusively. Nitric oxide reacts with 3,3-dimethylbutan-2-one in the presence of sodium and potassium hydroxide in methanol to yield sodium and potassium 3,3-dimethylbutan-2-one-1,1,1-tris(diazene-N-oxide-N'-hydroxylate), respectively. In contrast, the reaction in the presence of lithium hydroxide forms lithium methanebis(diazene-N-oxide-N'-hydroxylate) and lithium pivalate. The differential reactivity of nitric oxide with acetone and 3,3-dimethylbutan-2-one in the presence of the three bases is attributed to competing hydrolytic reactions of the acetyl and trimethylacetyl group-containing intermediates. A mechanism is proposed for the nitric oxide addition to active methyl groups in these reactions, where the product distribution between the di- and trisubstituted methanes is under kinetic control of the competing reactions. The products are characterized by NMR and IR spectroscopy, differential scanning calorimetry, and elemental analysis. Two differentially hydrated forms of potassium methanetris(diazene-N-oxide-N'-hydroxylate) are characterized by single-crystal X-ray diffraction. From the metathesis reaction of the silver salt of methanetris(diazene-N-oxide-N'-hydroxylate) with ammonium iodide, the corresponding ammonium salt is isolated in 59% yield, but only trace amounts of methylated products form in the reaction of the silver salt with methyl iodide. Density functional calculations (B3LYP/6-311++G) are used to evaluate the bonding, ground-state structures, and energy landscape for the different conformers of methanetris(diazene-N-oxide-N'-hydroxylate)(3-) trianion, a new type of a molecular propeller, and its corresponding triprotonated acid.

Chemistry of the diazeniumdiolates. I. Structural and spectral characteristics of the [N(O)NO]- functional group.

Ions of structure X[N(O)NO]-, examples of which have seen increasing use as probes for studying the biology of nitric oxide (NO) over the past decade, have a varied chemical history spanning nearly two centuries. Nevertheless, they have not been widely appreciated for their physicochemical similarities. Here we begin a series of systematic inquiries into the fundamental chemistry of such compounds aimed at identifying both the characteristics that justify considering them as a group and the factors that contribute to observed differences in their physicochemical properties. In the present paper, X-ray structures in which X is SO3- (1), O- (2), Ph (3), and Et2N (5), as well as that of the gem-disubstituted carbon derivative CH2[N(O)NO]2-(2) (4), are compared. All their O-N-N-O systems are essentially planar, with cis oxygens and an N-N linkage exhibiting considerable double-bond character. The ultraviolet spectrum of the isolated chromophore consists of a relatively intense ( approximately 6-10 mM(-1) x cm(-1) per [N(O)NO]- group) absorption at 248-250 nm (for 2 and 5) that is red shifted by through-space Stark interactions (e.g., by approximately 10 nm in 1 and 4) as well as by conjugative interaction with X (lambda(max) = 284 nm for 3). Infrared and Raman spectra for the widely used pharmacological probe 5 were determined, with analysis of vibrational modes being aided by comparison with the spectra of the [15N(O)15NO]- isotopomer and density functional theory calculations at the B3LYP/6-311++G** level. To address confusion that has arisen in the literature resulting from rather widespread use of differing trivial designations for this class of compounds, a unifying nomenclature system is recommended in which compounds containing the [N(O)NO]- moiety are named as diazeniumdiolates. It is hoped that these and other efforts to understand and predict the physicochemical similarities and differences among different members of the diazeniumdiolate class will aid in reaping their full potential in the area of rational drug design.

New insights into the metal center of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase.

Metal binding properties for a series of metal-substituted forms of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, DAHPS(Tyr), have been followed by UV-vis and EPR spectroscopy. The results show that there are two metal species present at pH = 7.0 and these are coordinated in a distorted metal binding site with a mixed nitrogen and oxygen donor atom coordination set. There is no spectroscopic evidence for strong M-S interactions in this system at any pH. Metal saturation occurs at a substoichiometric ratio of 0.8-0.85 metal/monomer, and the binding trends mirror previously published enzyme activity profiles. There is a conformational change for CuDAHPS under basic conditions, and equivalent protein handling for apoDAHPS leads to apparent loss of metal binding ability. Addition of the substrate PEP does not alter the UV-vis spectra, but there are small changes in the EPR spectra of CuDAHPS(Tyr). Further addition of the substrate analogue A5P has no effect on either spectra. Taken together, these results serve to link previous studies on enzyme activity with the recently determined X-ray crystal structure for DAHPS(Phe) and represent the first detailed spectroscopic characterization of the metal binding properties of DAHPS(Tyr).

Radical dinitroalkane dianions from the nitration of nitroalkanes by peroxynitrite.

In alkaline solutions at pH >10, peroxynitrite (ONOO(-)) rapidly and efficiently nitrates aci-nitroalkane anions, RCH=NO(2)(-) (R = H, CH(3), or CH(3)CH(2)), to give the radical dinitrodianions, RC(NO(2))(2)(2-). These anions have been characterized by EPR and have multiplets based on 1:2:3:2:1 pentets consistent with a hyperfine coupling with two equivalent (14)N nuclei of the nitro groups, and the following hyperfine coupling constants, in gauss: R = H, a(N) = 9.96 and a(H) = 1.85; R = CH(3), a(N) = 9.90 and a(H) = 3.22; and R = CH(3)CH(2), a(N) = 9.57 and a(H) = 4.01. Nitration is attributed to the trapping of nitrogen dioxide, formed by ONO-OCO(2)(-) homolysis for the carbon dioxide adduct of peroxynitrite, by the aci-nitroalkane anion. In air, the radical dinitrodianions are oxidized to the monoanions, and the kinetics of its formation is readily followed by UV/vis spectroscopy of the rise in absorption at 380 nm. This report represents the first successful spin trapping of nitrogen dioxide formed from peroxynitrite, and the method may be a useful one for preparing geminal dinitroalkanes.

Cyclohexadienone diazeniumdiolates from nitric oxide addition to phenolates.

Sterically hindered phenols react with nitric oxide under basic condititons to give either cyclohexadienone diazeniumdiolates or oximates. Phenols with 2,6-di-tert-butyl and 4-methyl (butylated hydroxy toluene, BHT), 4-ethyl, or 4-methoxy methylene substituents yield the corresponding 2,6-di-tert-butyl-2, 5-cyclohexadienone-4-alkyl-4-diazeniumdiolate salts (4-methyl 1a, 4-ethyl 3a, 4-methoxymethylene 5a). Phenols with 2,6-di-tert-butyl and 4-methylene (2,6-di-tert-butylphenol) substituents yield 4-methoxymethylenediazeniumdiolate (5a) together with 2, 6-di-tert-butyl benzoquinone oximate (6a), while phenols with 2, 6-di-tert-butyl and 4-methylenedimethylamino or hydrogen substituents yield exclusively 2,6-di-tert-butyl benzoquinone oximate (6a). Alkylation of the silver salts of 1a, or treating the O(2)-protonated diazeniumdiolate with diazomethane, both yield mixtures of O(1)- and O(2)-methylated isomers. All the compounds exhibit exothermic thermal decomposition except the quinuclidinium (1e, 3e, 5e) and triethylenediammonium (1f) salts which decompose endothermically. Three of the compounds namely "O(2)-protonated" (Z)-1-[4-(2, 6-di-tert-butyl-4-methyl-cyclohexadienonyl)]diazen-1-ium+ ++-1, 2-diolinic acid (1b), O(2)-methyl (Z)-1-[4-(2, 6-di-tert-butyl-4-methyl-cyclohexadienonyl)]diazen-1-ium+ ++-1,2-diolate (1c), and "O(2)-protonated" (Z)-1-[4-(2, 6-di-tert-butyl-4-methoxymethylenecyclohexadienonyl)]diazen- 1-ium-1, 2-diolinic acid (5b) were characterized by single-crystal X-ray diffraction studies. The diazeniumdiolate framework in all the structures is coplanar with considerable pi-bonding delocalized over the O-N-N-O framework.

The structure of malaria pigment beta-haematin.

Despite the worldwide public health impact of malaria, neither the mechanism by which the Plasmodium parasite detoxifies and sequesters haem, nor the action of current antimalarial drugs is well understood. The haem groups released from the digestion of the haemoglobin of infected red blood cells are aggregated into an insoluble material called haemozoin or malaria pigment. Synthetic beta-haematin (FeIII-protoporphyrin-IX)2 is chemically, spectroscopically and crystallographically identical to haemozoin and is believed to consist of strands of FeIII-porphyrin units, linked into a polymer by propionate oxygen-iron bonds. Here we report the crystal structure of beta-haematin determined using simulated annealing techniques to analyse powder diffraction data obtained with synchrotron radiation. The molecules are linked into dimers through reciprocal iron-carboxylate bonds to one of the propionic side chains of each porphyrin, and the dimers form chains linked by hydrogen bonds in the crystal. This result has implications for understanding the action of current antimalarial drugs and possibly for the design of new therapeutic agents.

Salicylaldiminato derivatives of cyclotriveratrylene: flexible strategy for new rim-metalated CTV complexes.

The amino-derivatized cyclotriveratrylene analogue, triaminotrimethoxytribenzocyclononene [CTV(NH2)3(OMe)3], 1, is readily converted into triply substituted imine compounds [CTV(sal)3(OMe)3], 2, in high yield by treatment of the acid salt of 1 with a variety of substituted salicylaldehydes. Cleavage of the protecting methoxy group generates the tristridentate chelate CTV(sal)3(OH)3, 3, which is readily converted into new rim-metalated species CTV(sal)3(ONiL)3, 4a (a, L = pyrrolidine; b, L = 1-n-butyl-imidazole). Taken together, these results illustrate the remarkable synthetic flexibility that is possible for the CTV-based metal complexes by alteration of the metal, the salicylaldehyde component of the CTV ligand, or the ancillary ligands coordinated to the metal.

Synthesis and characterization of nickel(II) bis(alkylthio)salen complexes.

NiX2(2-RSC6H4CH=NCH2CH2N=CHC6H4SR-2) (NiX2L; L = 5) (1a, X = Br, R = C6H13; 1b, X = Cl, R = C12H25) and NiX2(2-C6H13SC6H4CH2NHCH2CH2NHCH2C6H4SC6H13-2) (NiX2L; L = 6) (2a, X = Br; 2b, X = Cl; 2c, X = OClO3) were prepared from ligands 5 and 6, respectively. The 1:2 metal-ligand complex Ni(OClO3)2(2-RSC6H4CH2NHCH2CH2NHCH2C6H4SR-2)2 3, was obtained from an EtOH solution of 2c. The characterization of paramagnetic 1-3 included single-crystal X-ray diffraction studies of 1a and 3. Complex 2c converted into 3 in the presence of excess ligand 6 in CHCl3.

Reversible and irreversible hemichrome generation by the oxygenation of nitrosylmyoglobin.

The repeated oxygenation/reduction/nitrosylation of nitrosylmyoglobin produces low-spin ferric heme hemichromes which have been characterized by electron spin resonance spectroscopy. The predominant myoglobin hemichrome is a chemically reversible dihistidyl complex identified by the g values 1.53, 2.21, and 2.97. Also present is a low-spin ferric hydroxide derivative which is represented by the g values 1.83, 2.18, and 2.59. The formation of these species goes undetected by UV-vis spectroscopy, but the oxygenation of myoglobin to metmyoglobin is correlated with complete conversion of nitric oxide to nitrate which is released following a clear induction period. These results are interpreted in terms of the intermediates generated during the MbNO oxygenation reaction.

Pathophysiological chemistry of nitric oxide and its oxygenation by-products.

Nitric oxide is not only an important intracellular regulator and cytostatic effector but it is also the starting point for a cascade of physiologically important oxygenation reactions, whose by-products and intermediates have a largely unexplored biochemistry. These new biological discoveries are reshaping our appreciation of the remarkably complex chemistry that underlies it.

Sperm motility enhancement by nitric oxide produced by the oocytes of fathead minnows, Pimephelas promelas.

The effects of nitric oxide (NO) on sperm motility were examined in the fathead minnow, Pimephelas promelas, using computer-assisted sperm analysis (CASA). The observed effects underscore the dual nature of NO as both a low-concentration regulatory agent and, at higher doses, a cytotoxic agent. At 1 x 10(-6) M concentration, NO donor sodium nitroprusside (SNP) enhanced sperm motility percentages and increased CASA velocity parameters curvilinear velocity, straight-line velocity, and average path velocity, whereas 1 x 10(-2) M concentration inhibited percent motility and decreased velocities. Fathead minnow ova-produced NO was subsequently trapped as a paramagnetic ferrous iron complex and detected by electron spin resonance spectroscopy. The distinctive triplet spectrum, with a(N) = 12.5G and g(iso) = 2.04, was recorded during a critical 5-minute period following laying. Nitric oxide synthase (NOS) was histochemically localized at the micropyle of mature unfertilized fathead eggs, and an inhibitor of NOS blocked histochemical staining. CASA analysis of sperm motility in the presence of ovaproduced NO over an 8-minute time course reveals an optimum motility enhancement at 4 minutes that is similar to the effect of 1 x 10(-6) M SNP. This transient NO production by freshly laid ova and the localization of NOS near the site of sperm entry, together with the motility-enhancing effect of 1 x 10(-6) M SNP on sperm, indicates an active role for low-concentration NO in fertilization.

Spin-trapping of free radicals formed during the oxidation of glutathione by tetramethylammonium peroxynitrite.

Glutathionyl radical (GS.) formed during the oxidation of glutathione by tetramethylammonium peroxynitrite ([NMe4][ONOO]) was spin-trapped with 5,5'-dimethyl-1-pyrroline N-oxide (DMPO) and 5-diethoxyphosphoryl-5-methyl-1-pyrroline N-oxide (DEPMPO). This radical reacted with ammonium formate to form the carbon dioxide anion radical (CO2-.). The superoxide anion formed during oxidation of GSH by peroxynitrite salt was trapped with DMPO and detected as the DMPO-hydroxyl adduct. Addition of SOD mimic completely abolished the spectrum of the hydroxyl adduct but not the spectrum of the DMPO-glutathionyl radical adduct. Addition of seleno-DL-cystine or its reduced form caused a dramatic inhibition in the formation of spin adducts, suggesting that seleno-DL-cysteine is a more effective scavenger of peroxynitrite. The oxygen uptake observed during oxidation of GSH by peroxynitrite salt was inhibited by spin traps. In the presence of catalase, approximately 50% of the oxygen consumed was restored, indicating stoichiometric conversion of O2 to H2O2 during oxidation of GSH by peroxynitrite salt. Results indicate that nitrite and glutathione disulfide are formed as the major products during oxidation of GSH by peroxynitrite.

Heme compounds in dinosaur trabecular bone.

Six independent lines of evidence point to the existence of heme-containing compounds and/or hemoglobin breakdown products in extracts of trabecular tissues of the large theropod dinosaur Tyrannosaurus rex. These include signatures from nuclear magnetic resonance and electron spin resonance that indicate the presence of a paramagnetic compound consistent with heme. In addition, UV/visible spectroscopy and high performance liquid chromatography data are consistent with the Soret absorbance characteristic of this molecule. Resonance Raman profiles are also consistent with a modified heme structure. Finally, when dinosaurian tissues were extracted for protein fragments and were used to immunize rats, the resulting antisera reacted positively with purified avian and mammalian hemoglobins. The most parsimonious explanation of this evidence is the presence of blood-derived hemoglobin compounds preserved in the dinosaurian tissues.

Metabolic fate of peroxynitrite in aqueous solution. Reaction with nitric oxide and pH-dependent decomposition to nitrite and oxygen in a 2:1 stoichiometry.

Peroxynitrite, the reaction product of nitric oxide (NO) and superoxide (O-2) is assumed to decompose upon protonation in a first order process via intramolecular rearrangement to NO3-. The present study was carried out to elucidate the origin of NO2- found in decomposed peroxynitrite solutions. As revealed by stopped-flow spectroscopy, the decay of peroxynitrite followed first-order kinetics and exhibited a pKa of 6.8 +/- 0.1. The reaction of peroxynitrite with NO was considered as one possible source of NO2-, but the calculated second order rate constant of 9.1 x 10(4) M-1 s-1 is probably too small to explain NO2- formation under physiological conditions. Moreover, pure peroxynitrite decomposed to NO2- without apparent release of NO. Determination of NO2- and NO3- in solutions of decomposed peroxynitrite showed that the relative amount of NO2- increased with increasing pH, with NO2- accounting for about 30% of decomposition products at pH 7.5 and NO3- being the sole metabolite at pH 3.0. Formation of NO2- was accompanied by release of stoichiometric amounts of O2 (0.495 mol/mol of NO2-). The two reactions yielding NO2- and NO3- showed distinct temperature dependences from which a difference in Eact of 26.2 +/- 0.9 kJ mol-1 was calculated. The present results demonstrate that peroxynitrite decomposes with significant rates to NO2- plus O2 at physiological pH. Through formation of biologically active intermediates, this novel pathway of peroxynitrite decomposition may contribute to the physiology and/or cytotoxicity of NO and superoxide.

Characterization of the products of the heme detoxification pathway in malarial late trophozoites by X-ray diffraction.

In a process inhibited by the quinoline antimalarial drugs, Plasmodia detoxify heme released during the degradation of hemoglobin by aggregating it into malarial pigment, an insoluble crystalline heme coordination polymer. Synchrotron x-ray powder diffraction patterns for intact desiccated malarial trophozoites and synthetic beta-hematin have been measured; both materials correspond to a single crystalline triclinic lattice with unit cell parameters a = 12.2176(4), b = 14.7184(5), c = 8.0456(3) A; alpha = 90.200(2), beta = 96.806(3), gamma = 97.818(3) degrees and Z = 2. These results unambiguously demonstrate that hemozoin crystallites are identical to synthetic beta-hematin.

O-atom scrambling in the aqueous isomerization of pernitrous acid.

Raman spectroscopy has been used to determine the isotopic distribution of oxygen during the isomerization of pernitrous acid to nitrate in 18OH2. Decomposition of unlabeled pernitrous acid in carbon-dioxide-free phosphate-buffered solutions of 18OH2 at pH 6.8 results in the incorporation of 13 +/- 1% 18O into the nitrate product with no detectable double-isotopic incorporation and 83% of the product having complete retention of its oxygen atoms. The mechanistic implications of this are contrasted for three frequently considered pathways for peroxide bond cleavage and it is concluded that the results are most consistent with the formation of reactive intermediate which can either rearrange or undergo hydrolytic O-atom exchange with water.

Modulation of superoxide-dependent oxidation and hydroxylation reactions by nitric oxide.

The rapid and spontaneous interaction between superoxide (O2-.) and nitric oxide (NO) to yield the potent oxidants peroxynitrite (ONOO-) and peroxynitrous acid (ONOOH), has been suggested to represent an important pathway by which tissue may be injured during inflammation. Although several groups of investigators have demonstrated substantial oxidizing and cytotoxic activities of chemically synthesized ONOO-, there has been little information available quantifying the interaction between O2-. and NO in the absence or the presence of redox-active iron. Using the hypoxanthine (HX)/xanthine oxidase system to generate various fluxes of O2-. and H2O2 and the spontaneous decomposition of the spermine/NO adduct to produce various fluxes of NO, we found that in the absence of redox-active iron, the simultaneous production of equimolar fluxes of O2-. and NO increased the oxidation of dihydrorhodamine (DHR) from normally undetectable levels to approximately 15 microM, suggesting the formation of a potent oxidant. Superoxide dismutase, but not catalase, inhibited this oxidative reaction, suggesting that O2-. and not hydrogen peroxide (H2O2) interacts with NO to generate a potent oxidizing agent. Excess production of either radical virtually eliminated the oxidation of DHR. In the presence of 5 microM Fe+3-EDTA to insure optimum O2-.-driven Fenton chemistry, NO enhanced modestly HX/xanthine oxidase-induced oxidation of DHR. As expected, both superoxide dismutase and catalase inhibited this Fe-catalyzed oxidation reaction. Excess NO production with respect to O2-. flux produced only modest inhibition (33%) of DHR oxidation. In a separate series of studies, we found that equimolar fluxes of O2-. and NO in the absence of iron only modestly enhanced hydroxylation of benzoic acid from undetectable levels to 0.6 microM 2-hydroxybenzoate. In the presence of 5 microM Fe+3-EDTA, HX/xanthine oxidase-mediated hydroxylation of benzoic acid increased dramatically from undetectable levels to 4.5 microM of the hydroxylated product. Superoxide dismutase and catalase were both effective at inhibiting this classic O2-.-driven Fenton reaction. Interestingly, NO inhibited this iron-catalyzed hydroxylation reaction in a concentration-dependent manner such that fluxes of NO approximating those of O2-. and H2O2 virtually abolished the hydroxylation of benzoic acid. We conclude that in the absence of iron, equimolar fluxes of NO and O2-. interact to yield potent oxidants such as ONOO-/ONOOH, which oxidize organic compounds. Excess production of either radical remarkably inhibits these oxidative reactions. In the presence of low molecular weight redox-active iron complexes, NO may enhance or inhibit O2-.-dependent oxidation and hydroxylation reactions depending upon their relative fluxes.