EPR evidence of two structurally different diferric sites in Mycobacterium tuberculosis R2-2 ribonucleotide reductase protein

Mixed-valent species were generated in the diiron site of active (with tyrosyl free radical) and met (without radical) forms of protein R2-2 in a class Ib ribonucleotide reductase from Mycobacterium tuberculosis by low temperature reduction (γ-irradiation) at 77 K. The primary mixed-valent EPR signal is a mixture of two components with axial symmetry and g_av<2.0, observable at temperatures up to 77 K, and assigned to antiferromagnetically coupled high spin ferric/ferrous sites. The two components in the primary EPR signal can be explained by the existence of two structurally distinct μ-oxo-bridged diferric centers, possibly related to structural heterogeneity around the iron site, and/or different properties of the two polypeptide chains in the homodimeric protein after the radical reconstitution reaction. Annealing of the irradiated R2-2 samples to 143 K transforms the primary EPR signal into a rhombic spectrum characterized by g_av<1.8 and observable only below 25 K. This spectrum is assigned to a partially relaxed form with a μ-hydroxo-bridge. Further annealing at 228 K produces a new complex rhombic EPR spectrum composed of at least two components. An identical EPR spectrum was observed and found to be stable upon chemical reduction of Mycobacterium tuberculosis RNR R2-2 at 293 K by dithionite.     

Magnetic properties of a cobalt(II) dimer of pseudo tetrahedral geometry [Co2{(CO)9Co3C---COO}5, C14H19N2H]

The crystalline ion pair [Co₂{OOC---CCo₃(CO)₉}₅, C₁₀H₆(N(CH₃)₂)₂H] (1) presents unusual magnetic properties. The X-band EPR spectrum of 1 at room temperature presents two unresolved bands at g=1.98 and 4.55. At a low temperature (20 K), the cluster of clusters 1 presents a complicated spectrum with an intense signal at 1700 G. The magnetic susceptibility of 1 was fit to a two spin S₁=S₂=3/2 Heisenberg model, with J=11.2 cm⁻¹ and a g value of 2.3. There is no field dependence of the magnetization, which suggests intramolecular coupling between the two tetrahedral centers of the cluster. Molecular orbital modeling indicates a sigma path of exchange between two topologically non-equivalent cobalt(II) centers.     

Interconversions between the 3Fe and 4Fe forms of the iron-sulfur clusters in the ferredoxin from Thermodesulfobacterium commune: EPR characterization and potentiometric titration

The amount of 3Fe clusters in Thermodesulfobacterium commune ferredoxin is strongly dependent upon the presence of oxygen during the purification. An average of one 3Fe cluster per monomer can be found when the purification is not strictly anaerobic. These clusters are converted into |4Fe-4S| clusters by adding dithionite at usual pH and without adjunction of Fe²⁺. The EPR potentiometric titration reveals the existence of several types of 3Fe clusters with negative midpoint potentials differing by more than 100 mV. When the |4Fe-4S| clusters are partially reduced the EPR signal is composed of two different rhombic components. The component with g_z = 2.04 could be related to a site implicated in the interconversion processes. In the fully reduced state, the spectrum presents the typical features of two interacting |4Fe-4S| clusters as those observed in two |4Fe-4S| bacterial ferredoxins. From the redox titration curves the midpoint potentials of these clusters are estimated at −395 and −435 mV.     

The oxygen reaction of the cytochrome d-terminated respiratory chain of Escherichia coli at sub-zero temperatures: Kinetic resolution by EPR spectroscopy of two high-spin cytochromes

The oxygen reaction of the fully reduced respiratory chain in membranes from oxygen-limited Escherichia coli was studied at sub-zero temperatures using EPR spectroscopy. Laser photolysis of CO-liganded cytochrome oxidase d precedes oxidation of at least 2 kinetically separable high-spin cytochromes. At −120 to −100°C, a rhombic signal appears, attributable to cytochrome d, followed at above −100°C, by appearance of a second, axial signal near g = 6, here assigned to cytochrome(s) b, and changes in the redox state of iron-sulphur clusters. The data kinetically resolve the 2 high-spin signals attributed to the oxidase complex and suggest schemes for electron flow to oxygen.

Cytochrome oxidase Escherichia coli Cytochrome b-d complex Bacterial electron transport Low-temperature technique     

Triketones active against antibiotic-resistant bacteria: synthesis, structure-activity relationships, and mode of action

A series of acylated phloroglucinols and triketones was synthesized and tested for activity against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis (VRE) and multi-drug-resistant Mycobacterium tuberculosis (MDR-TB). A tetra-methylated triketone with a C₁₂ side chain was the most active compound (MIC of around 1.0 μg/ml against MRSA) and was shown to stimulate oxygen consumption by resting cell suspensions, suggesting that the primary target was the cytoplasmic membrane.     

Synthesis and in vitro anti-mycobacterial activity of 5-substituted pyrimidine nucleosides

Mycobacterium tuberculosis and Mycobacterium avium infections cause the two most important mycobacterioses, leading to increased mortality in patients with AIDS. Various 5-substituted 2′-deoxyuridines, uridines, 2′-O-methyluridine, 2′-ribofluoro-2′-deoxyuridines, 3′-substituted-2′,3′-dideoxy uridines, 2′,3′-dideoxyuridines, and 2′,3′-didehydro-2′,3′-dideoxyuridines were synthesized and evaluated for their in vitro inhibitory activity against M. bovis and M. avium. 5-(C-1 Substituted)-2′-deoxyuridine derivatives emerged as potent inhibitors of M. avium (MIC₉₀ = 1–5 μg/mL range). The nature of C-5 substituents in the 2′-deoxyuridine series appeared to be a determinant of anti-mycobacterial activity. This new class of inhibitors could serve as useful compounds for the design and study of new anti-tuberculosis agents.     

Assignment of the g = 4.1 ERP signal to manganese in the S2 state of the photosynthetic oxygen-evolving complex: An X-ray absorption edge spectroscopy study

X-ray absorption spectroscopy at the Mn K-edge has been utilized to study the origin of the g = 4.1 EPR signal associated with the Mn-containing photosynthetic O₂-evolving complex. Formation of the g = 4.1 signal by illumination of Photosystem II preparations at 140 K is associated with a shift of the Mn edge inflection point to higher energy. This shift is similar to that observed upon formation of the S₂ multiline EPR signal by 190 K illumination. The g = 4.1 signal is assigned to the Mn complex in the S₂ state.     

Ferrocenyl-derived face-capping ligands: syntheses and molecular structures of [(FcTt)Cu]4 and [FcTt]2M (M = Fe, Co, Ni; FcTt = ferrocenyltris((methylthio)methyl)borate)

The synthesis and characterization of a ferrocenyl-derived tridentate ligand, ferrocenyltris((methylthio)methyl)borate (FcTtP⁻), and its representative metal complexes, [(FcTt)Cu]₄ and [FcTt]₂M (M = Fe, Co and Ni), are reported. The M = Fe complex exhibits spin-crossover behavior with a μ_eff = 1.19 μ_B at 25°C. The low-spin Co(II) derivative (1.88 μ_B) exhibits a characteristic axial electron paramagnetic resonance (EPR) spectrum, g_av = 2.13, A = 53 G and A_¦ = 43 G. The [FcTt]₂M complexes display reversible two-electron redox processes assigned to ligand-centered events about 200 mV negative of the ferrocene-ferrocenium couple. [(FcTt)Cu]₄ and [FcTt]₂Ni have been characterized by X-ray diffraction. X-ray data for [(FcTt)Cu]₄: monoclinic space group C2/c, with a = 24.3747(3) Å, b = 20.0857(2) Å, c = 17.2747(4) Å, β = 95.843(1)°, V = 8413.5(3) ų, and Z = 4; [FcTt]₂Ni: monoclinic space group C2/c, with a = 12.6220(3) Å, b = 11.6002(3) Å, c = 25.0125(7) Å, β = 94.067(1)°, V = 3653.1(2) ų, and Z = 4.     

The distance between cytochromes a and a3 in the azide compound of bovine-heart cytochrome oxidase

The electron-spin relaxation rates of the two species of cytochrome a³⁺₃-azide found in the azide compound of bovine-heart cytochrome oxidase were measured by progressive microwave saturation at T = 10 K. It has been shown previously that Cyt a⁺³₃-azide gives rise to two distinct EPR resonances, depending upon the oxidation state of Cyt a. When Cyt a is ferrous, Cyt a³⁺₃-azide has g = 2.88, 2.19 and 1.64; upon oxidation of Cyt a, the a³⁺₃-azide g-values become g = 2.77, 2.18, and 1.74 (Goodman, G. (1984) J. Biol. Chem. 259, 15094–15099). The relaxation effect of Cyt a on Cyt a₃ could be measured as the difference in microwave field saturation parameter H_1/2 between the g = 2.77 and g = 2.88 species. For each signal the spin-lattice relaxation time T₁ was determined from H_1/2 using the transverse relaxation time T₂. The value of T₂ at 10 K was extrapolated from a plot of line-width vs. temperature at higher temperature. The dipolar contribution to T₁ was related to the Cyt a-Cyt a₃ spin-spin distance utilizing available information on the relative orientation of Cyt a₃-azide and Cyt a (Erecinska, M., Wilson, D.F. and Blasie, J.K. (1979) Biochim. Biophys. Acta 545, 352–364). By taking into account the relaxation parameters for both g_x and g_z components of the Cyt a₃-azide g-tensor, the angle between the g_z components of the Cyt a and Cyt a₃g-tensors was determined to be between 0 and 18°, and the Cyt a-Cyt a₃ spin-spin distance was found to be 19 ± 8 Å.     

Biochemical and biophysical studies on cytochrome c oxidase. XIX. An EPR study of the photodissociation of carboxycytochrome c oxidase in the presence of azide

1. The photodissociation reaction of the cytochrome c oxidase-CO compound in the presence of azide was studied by EPR at 15°K. Addition of CO in the dark to cytochrome c oxidase, partially reduced (2 electrons per 4 metal ions) in the presence of azide brings about a decrease in intensity of the azide-induced low-spin heme signal at g = 2.9, 2.2 and 1.67 and an increase in intensity of both the low-spin heme signal at g = 3 and the copper signal at g = 2. Subsequent illumination with white light at room temperature of this sample causes an enhancement of the azide-induced signal at g = 2.9, and a decrease in intensity of both signals at g = 3 and g = 2. It is shown that these changes in the EPR spectrum are reversible.

2. These results demonstrate that upon photodissociation, CO is replaced by azide wheras upon incubation in the dark CO expels azide from its binding site in cytochrome c oxidase.

3. Concomitantly with the binding of CO and dissociation of the azide molecule, and vice versa, electron redistributions occur as inferred from the changes in the intensity of the copper signal at g = 2.

4. The results are explained in a model of cytochrome c oxidase with either a common binding site (cytochrome a₃)^* for CO and azide or in a model with anti-cooperative interaction between two different sites of binding.

5. Similar types of experiments with cyanide instead of azide show that cyanide is more firmly bound to partially reduced cytochrome c oxidase than CO and azide. The affinity of ligands for partially reduced enzyme decreases in the sequence: cyanide, CO (dark), azide and CO (illuminated).     

Structural diversity in the six-fold redundant set of acyl-CoA carboxyltransferases in Mycobacterium tuberculosis

Mycobacterium tuberculosis contains multiple versions of the accA and accD genes that encode the - and β-subunits of at least three distinct multi-functional acyl-CoA carboxylase complexes. Because of its proposed involvement in pathogenic M. tuberculosis survival, the high-resolution crystal structure of the β-subunit gene accD5 product has been determined and reveals a hexameric 356 kDa complex. Analysis of the active site properties of AccD5 and homology models of the other five M. tuberculosis AccD homologues reveals unexpected differences in their surface composition, providing a molecular rational key for a sorting mechanism governing correct acyl-CoA carboxylase holo complex assembly in M. tuberculosis.     

EPR studies on the respiratory chain of wild-type Saccharomyces cerevisiae and mutants with a deficiency in succinate dehydrogenase

1. Three nuclear mutants of Saccharomyces cerevisiae deficient in succinate dehydrogenase have been isolated. Two of these mutants are allelic.

2. The amount of covalently bound flavin of submitochondrial particles of the two allelic mutants is about 14% and that of the third mutant about 50% of the amount in wild-type particles. The turnover number of succinate dehydrogenase of particles is decreased in all mutants. The turnover number of fumarate reductase is increased in the two allelic mutants, but decreased in the third mutant.

3. EPR spectra, measured at 82 °K, show that the amplitude of the g = 1.93 signal in particles of the two allelic mutants is less than 10% of that in wild-type particles. It is concluded that iron-sulphur centres other than those of succinate dehydrogenase make only a negligible contribution to the line at g = 1.93 in wild-type particles.

4. EPR measurements below 20 °K show that the amplitude of the signal at g = 2.01 detected in oxidized particles is decreased in particles of the two allelic mutants.

5. A signal with lines at g = 2.027 and g = 1.933 is detected at low temperatures in all particle preparations, even in those from a cytoplasmic petite mutant. It is suggested that this signal is derived from a contaminant and not from the inner membrane.     

Synthesis and antitubercular activity of substituted phenylmethyl- and pyridylmethyl amines

A total of 42 benzyl- and pyridylmethyl amines were synthesized either by reductive amination of aromatic/heteroaromatic aldehydes with amines or by conjugate addition of amines to the cinnamates followed by reduction of the ester group with lithium aluminium hydride to the respective propanolamines. All the synthesized compounds were evaluated against both avirulent and virulent strains of Mycobacterium tuberculosis. Many of the compounds exhibited MIC as low as 1.56 μg/mL. Few of potent compounds were also evaluated against clinical isolates of MDR TB and found to be active at one or other concentrations with MIC as low as 3.12 μg/mL.     

The electron spin relaxation of the electron acceptors of Photosystem I reaction centre studied by microwave power saturation

Photosystem I particles from spinach were reduced by illumination at 77 K. Under these conditions the one-electron transfer from P-700 resulted in a reduction of only one acceptor molecule of the reaction centre. The EPR signals at g = 2.05, 1.94 and 1.86 were attributed to reduced centre A and the smaller signals at g = 2.07, 1.92 and 1.89 to reduced centre B. Reduction of both centres by dithionite in the dark lead to signals at g = 2.05, 1.99, 1.96, 1.94, 1.92 and 1.89. Thus, the features at g = 2.07 and 1.86 disappeared and new signals at g = 1.99 and 1.96 were observed. From the spectral changes it followed that the iron-sulphur centres A and B interact magnetically. Temperature dependent EPR spectra demonstrated a faster electron spin relaxation of centre A than of centre B.

These conclusions were corroborated using microwave power saturation of the respective EPR signals. The saturation data of the fully reduced centres A and B could not be fitted using the saturation equation for a one-electron spin system. The magnetic interaction between the [4Fe-4S] centres of the electron acceptors A and B resulted in saturation properties which are similar to those of the 2[4Fe-4S] ferredoxin from Clostridium pasteurianum.

For centre X a high proportion of homogeneous broadening of the EPR lines was inferred from the inhomogeneity parameter (b = 1.83). It was, therefore, concluded that centre X is most probably an anion radical of chlorophyll. From the low temperature necessary for observing the EPR signal of centre X followed that the drastic relaxation enhancement has to be attributed to a magnetic interaction of the anion radical with iron.     

EPR studies by Fe isotopic substitution on the nature of an unknown electron acceptor in Azotobacter vinelandii phosphorylating particles

1. EPR ⁵⁷Fe isotopic substitution studies provide unequivocal evidence that the g = 2.011 signal found in oxidized Azotobacter vinelandii phosphorylating particles is due to an iron-containing structure. The broadening constant determined as a result of this electron—nuclear hyperfine interaction was 15.7 G.

2. A similar signal found in a number of iron—sulfur containing proteins was found by quantitative EPR estimations to exist in a variable but substantial concentration when compared to the intensity of the reduced g = 1.9 type EPR resonance.

3. Reaction of the phosphorylating particles with excess potassium ferricyanide resulted in an alteration of the initial g = 2.011 iron signal resulting in the detection by microwave power studies of at least two different iron species which exhibited major g-values at 1.992 and 2.027.     

A novel, stable bioradical

Several cellular systems have shown a novel EPR spectrum at 77 K, comprising a slightly anisotropic doublet centred on the free-spin g-value, with a hyperfine splitting of ca. 120 G. It is suggested that this species is an occluded protein radical centred on a tryptophan unit.     

Three-iron-sulfur centers of pea mitochondria

EPR signals of three distinct types of three-iron-sulfur center were observed in pea mitochondria: the signal of Center S-3 (low-field peak at g = 2.016), the signal of Center ISP-1 (low-field peak at g = 2.024) and the signal of the axial Center ISP-2 with two maxima, at g = 2.027 and 2.016. Succinate increases the signal amplitude of Center ISP-1 and diminishes that of Center ISP-2; malate has an opposite effect. Membrane damage enhances the effect of malate and decreases that of succinate.     

Metal complexes of carboxamidrazone analogs as antitubercular agents. 1. Synthesis,X-ray crystal-structures,spectroscopic properties and antimycobacterial activity against Mycobacterium tuberculosis H(37)Rv

N¹-Benzylidene-pyridine carboxamidrazones and their metal conjugates have emerged as a new class of potential antimycobacterial agents. Nine such carboxamidrazone analogs (L₁–L₉) along with their Cu(II) (MC₁–MC₉) and Fe(III) (MC₁₀–MC₁₈) complexes were synthesized. Single crystal X-ray structures of copper complexes MC₁ and MC₅ were determined which suggest slightly distorted square planer geometries for copper complexes and octahedral geometries for ferric compounds. All compounds were evaluated for their in vitro antimycobacterial activity against Mycobacterium tuberculosis H₃₇Rv. The results show 32–64-fold enhancement in antitubercular activity upon copper complexation.     

Mitochondrial respiratory chain of Tetrahymena pyriformis The properties of submitochondrial particles and the soluble b and c type pigments

Submitochondrial particles isolated from Tetrahymena pyriformis contain essentially the same redox carriers as those present in parental mitochondria: at pH 7.2 and 22 °C there are two b-type pigments with half-reduction potentials of −0.04 and −0.17 V, a c-type cytochrome with a half reduction potential of 0.215 V, and a two-component cytochrome a₂ with E_m7.2 of 0.245 and 0.345 V.

EPR spectra of the aerobic submitochondrial particles in the absence of substrate show the presence of low spin ferric hemes with g values at 3.4 and 3.0, a high spin ferric heme with g = 6, and a g = 2.0 signal characteristic of oxidized copper. In the reduced submitochondrial particles signals of various iron-sulfur centers are observed.

Cytochrome c₅₅₃ is lost from mitochondria during preparation of the submitochondrial particles. The partially purified cytochrome c₅₅₃ is a negatively charged protein at neutral pH with an E_m7.2 of 0.25 V which binds to the cytochrome c-depleted Tetrahymena mitochondria in the amount of 0.5 nmol/mg protein with a K_D of 0.8 · 10⁻⁶ M. Reduced cytochrome c₅₅₃ serves as an efficient substrate in the reaction with its own oxidase. The EPR spectrum of the partially purified cytochrome c₅₅₃ shows the presence of a low spin ferric heme with the dominant resonance signal at g = 3.28.

A pigment with an absorption maximum at 560 nm can be solubilized from the Tetrahymena cells with butanol. This pigments has a molecular weight of approx. 18 000, and E_m7.2 of −0.17 V and exhibits a high spin ferric heme signal at g = 6.     

Studies on (beta,1-->5) and (beta,1-->6) linked octyl Gal(f) disaccharides as substrates for mycobacterial galactosyltransferase activity.

The emergence of multi-drug resistant (MDR) strains of Mycobacterium tuberculosis (MTB) and the continuing pandemic of tuberculosis emphasizes the urgent need for the development of new anti-tubercular agents with novel drug targets. The recent structural elucidation of the mycobacterial cell wall highlights a large variety of structurally unique components that may be a basis for new drug development. This publication describes the synthesis, characterization, and screening of several octyl Galf(β,1→5)Galf and octyl Galf(β,1→6)Galf derivatives. A cell-free assay system has been utilized for galactosyltransferase activity using UDP[¹⁴C]Galf as the glycosyl donor, and in vitro inhibitory activity has been determined in a colorimetric broth microdilution assay system against MTB H37Ra and three clinical isolates of Mycobacterium avium complex (MAC). Certain derivatives showed moderate activities against MTB and MAC. The biological evaluation of these disaccharides suggests that more hydrophobic analogues with a blocked reducing end showed better activity as compared to totally deprotected disaccharides that more closely resemble the natural substrates in cell wall biosynthesis.