The biological and structural characterization of Mycobacterium tuberculosis UvrA provides novel insights into its mechanism of action

Mycobacterium tuberculosis is an extremely well adapted intracellular human pathogen that is exposed to multiple DNA damaging chemical assaults originating from the host defence mechanisms. As a consequence, this bacterium is thought to possess highly efficient DNA repair machineries, the nucleotide excision repair (NER) system amongst these. Although NER is of central importance to DNA repair in M. tuberculosis, our understanding of the processes in this species is limited. The conserved UvrABC endonuclease represents the multi-enzymatic core in bacterial NER, where the UvrA ATPase provides the DNA lesion-sensing function. The herein reported genetic analysis demonstrates that M. tuberculosis UvrA is important for the repair of nitrosative and oxidative DNA damage. Moreover, our biochemical and structural characterization of recombinant M. tuberculosis UvrA contributes new insights into its mechanism of action. In particular, the structural investigation reveals an unprecedented conformation of the UvrB-binding domain that we propose to be of functional relevance. Taken together, our data suggest UvrA as a potential target for the development of novel anti-tubercular agents and provide a biochemical framework for the identification of small-molecule inhibitors interfering with the NER activity in M. tuberculosis.

Ferrocene-Conjugated L-Tryptophan Copper(II) Complexes of Phenanthroline Bases Showing DNA Photocleavage Activity and Cytotoxicity

Ferrocene-conjugated L-tryptophan (L-Trp) reduced Schiff base (Fc-TrpH) copper(II) complexes [Cu(Fc-Trp)(L)](ClO(4)) of phenanthroline bases (L), viz. 2,2'-bipyridine (bpy in 1), 1,10-phenanthroline (phen in 2), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq in 3), and dipyrido[3,2-a:2',3'-c]phenazine (dppz in 4), were prepared and characterized and their photocytotoxicity studied. Cationic reduced Schiff base (Ph-TrpH) complexes [Cu(Ph-Trp)(L)(H(2)O)] (ClO(4)) (L = phen in 5; dppz in 6) having the ferrocenyl moiety replaced by a phenyl group and the Zn(II) analogue (7) of complex 4 were prepared and used as control species. The crystal structures of 1 and 5 with respective square-planar CuN(3)O and square-pyramidal CuN(3)O(2) coordination geometry show significantly different core structures. Complexes 1-4 exhibit a Cu(II)-Cu(I) redox couple near -0.1 V and the Fc(+)-Fc couple at similar to 0.5 V vs SCE in DMF-0.1 M [Bu(4)(n)N] (ClO(4)) (Fc = ferrocenyl moiety). The complexes display a copper(II)-based d-d band near 600 nm and a Fc-centered band at similar to 450 nm in DMF-Tris-HCl buffer. The complexes are efficient binders to calf thymus DNA. They are synthetic chemical nucleases in the presence of thiol or H(2)O(2), forming hydroxyl radicals. The photoactive complexes are cleavers of pUC19 DNA in visible light, forming hydroxyl radicals. Complexes 2-6 show photocytotoxicity in HeLa cancer cells, giving IC(50) values of 4.7, 10.2, 1.3, 4.8, and 4.3 mu M, respectively, in visible light with the appearance of apoptotic bodies. The complexes also show photocytotoxicity in MCF-7 cancer cells. Nuclear chromatin cleavage has been observed with acridine orange/ethidium bromide (AO/EB) dual staining with complex 4 in visible light. The complexes induce caspase-independent apoptosis in the HeLa cells.

Solubility and activity of oxygen in liquid indium and copper indium alloys

The solubility of oxygen in liquid indium in the temperature range 650–820 °C and in liquid copper-indium alloys at 1100 °C in equilibrium with indium sesquioxide has been measured by a phase equilibration technique. The solubility of oxygen in pure indium is given by the relation log(at.% O) = −4726/T + 3.73 (±0.08) Using the recently measured values for the standard free energy of formation of In2O3 and assuming that oxygen obeys Sievert's law up to saturation, the standard free energy of solution of molecular oxygen in liquid indium is calculated as View the MathML sourceΔG°= −51 440 + 8.07 T (±500) cal where the standard state for dissolved oxygen is an infinitely dilute solution in which activity is equal to atomic per cent. The effect of indium additions on the activity coefficient of oxygen dissolved in liquid copper was measured by a solid oxide galvanic cell. The interaction parameter ϵ0In is given by View the MathML source The experimentally determined variation of the activity coefficient of oxygen in dilute solution in Cu-In alloys is in fair agreement with that predicted by a quasichemical model in which each oxygen atom is assumed to be interstitially coordinated to four metal atoms and the nearest neighbour metal atoms are assumed to lose approximately half their metallic cohesive energies.

Solubility and activity of oxygen in liquid germanium and germanium copper alloys

The solubility of oxygen in liquid germanium in the temperature range 1233 to 1397 K, and in liquid germanium-copper alloys at 1373 K, in equilibrium with GeO2 has been measured by the phase equilibration technique. The solubility of oxygen in pure germanium is given by the relation R470 log(at. pct 0)=-6470/T+4.24 (±0.07). The standard free energy of solution of oxygen in liquid germanium is calculated from the saturation solubility, and recently measured values for the free energy of formation of GeO2, assuming that oxygen obeys Sievert’s law up to the saturation limit. For the reaction, 1/2 O2(g)→ OGe ΔG° =-39,000 + 3.21T (±500) cal = -163,200 + 13.43T (±2100) J. where the standard state for dissolved oxygen is that which makes the value of activity equal to the concentration (in at. pct), in the limit, as concentration approaches zero. The effect of copper on the activity of oxygen dissolved in liquid germanium is found to be in good agreement with that predicted by a quasichemical model in which each oxygen was assumed to be bonded to four metal atoms and the nearest neighbor metal atoms to an oxygen atom are assumed to lose approximately half of their metallic bonds.

Solubility and activity of oxygen in liquid antimony

The solubility limit of oxygen in liquid antimony has been measured by a novel isopiestic technique in the temperature range 995--1175 deg K. The results can be expressed by the equation log c = --5500/T + 3.754 ( plus/minus 0.04) with c in at.% O and T in deg K. The oxygen potential over Sb + O alloys equilibrium with Sb2O3 has been measured by a solid state cell using a fully stabilized CaO.ZrO2 electrolyte. The cell was designed to contain the Sb + Sb2O3 mixture in a closed volume, that the vaporization of the oxide can be minimized and true equilibrium attained. The Gibbs free energy of the reaction 2 Sb(s) + 3/2 O2 = Sb2O3(s) is Delta G deg = --719560 + 274.51 T( plus/minus 500) and Sb(l) + 3/2 O2 = Sb2O3(l), Delta G deg = --704711 + ( plus/minus 500) ( Delta G deg in J/mole, T in deg K). The combination of these results with Sieverts' law yields the standard free energy of solution of oxygen in liquid antimony according to the reaction 1/2 O2 = \O\Sb,at.% as Delta G deg = --129620 + 14.23 T ( plus/minus 950). The standard enthalopy and entropy of the solution of oxygen in Sb are compared with values for other metal- oyxgen systems, and with the standard enthalpies of formation of corresponding oxides. The resulting correlations permit the estimation of the standard free energy of solution of oxygen in pure metals for which experimental information is lacking. 24 ref.--AA

Impact of metal on the DNA photocleavage activity and cytotoxicity of ferrocenyl terpyridine 3d metal complexes

Ferrocenyl terpyridine 3d metal complexes and their analogues, viz. [M(Fc-tpy)(2)](ClO(4))(2) (1-4), [Zn(Ph-tpy)(2)](ClO(4))(2) (5) and [Zn(Fc-dpa)(2)]X(2) (X = ClO(4), 6; PF6, 6a), where M = Fe(II) in 1, Co(II) in 2, Cu(II) in 3 and Zn(II) in 4, Fc-tpy is 4'-ferrocenyl-2,2': 6', 2 `'-terpyridine, Ph-tpy is 4'-phenyl-2,2': 6', 2 `'-terpyridine and Fc-dpa is ferrocenyl-N,N-dipicolylmethanamine, are prepared and their DNA binding and photocleavage activity in visible light studied. Complexes 2, 4, 5 and 6a that are structurally characterized by X-ray crystallography show distorted octahedral geometry with the terpyridyl ligands binding to the metal in a meridional fashion, with Fc-dpa in 6a showing a facial binding mode. The Fc-tpy complexes display a charge transfer band in the visible region. The ferrocenyl (Fc) complexes show a quasi-reversible Fc(+)-Fc redox couple within 0.48 to 0.66 V vs. SCE in DMF-0.1 M TBAP. The DNA binding constants of the complexes are similar to 10(4) M(-1). Thermal denaturation and viscometric data suggest DNA surface binding through electrostatic interaction by the positively charged complexes. Barring the Cu(II) complex 3, the complexes do not show any chemical nuclease activity in the presence of glutathione. Complexes 1-4 exhibit significant plasmid DNA photocleavage activity in visible light via a photoredox pathway. Complex 5, without the Fc moiety, does not show any DNA photocleavage activity. The Zn(II) complex 4 shows a significant PDT effect in HeLa cancer cells giving an IC(50) value of 7.5 mu M in visible light, while being less toxic in the dark (IC(50) = 49 mu M).

Solubility and activity of oxygen in liquid manganese

The oxygen concentration of liquid manganese in equilibrium with MnAl2+2xO4+3x and α−Al2O3 has been determined in the temperature range 1520 to 1875 K. The oxygen content of quenched samples, wrapped in oxygen-free nickel foil, was determined by an inert gas fusion technique. The results are combined with accurate data now available on the Gibbs energies of formation of MnO and Al2O3−saturated MnAl2+2xO4+3x to derive the oxygen content of liquid manganese in equilibrium with MnO and the Gibbs energy of solution of diatomic oxygen gas in liquid manganese. The enthalpy and entropy of solution of oxygen in manganese are compared with similar data on other metal-oxygen systems.

Three phase equilibria for activity determinations: system Co Mn

A solid state e.m.f. cell with yttria-doped thoria as the electrolyte and a mixture of Cr + Cr sub 2 O sub 3 as the reference electrode, was employed for the measurement of the activity of manganese in the Co--Mn system at 1760 deg K, for 0.3 > X sub Mn > 0.05. The liquid alloy was contained in an alumina crucible and saturated with MnAl sub 2+2x O sub 4+3x . The cell can be represented by Pt, W, (Co--Mn) + MnAl sub 2+2x O sub 4+3x + Al sub 2 O sub 3 /ThO sub 2 --Y sub 2 O sub 3 /Cr + Cr sub 2 O sub 3 , Pt. The activity of manganese shows negative deviations from Raoult's law. The activities in the Co--Mn system are intermediate between those in the Fe--Mn and Ni--Mn systems. The Gibbs' energies of mixing in these systems follow the trends given by Miedema's model. 14 ref.--AA.

Solubility and activity of oxygen in liquid nickel in equilibrium with -Al2O3 and NiO.(1+x)Al2O3

The limiting solubility of oxygen in liquid nickel in equilibrium withα-alumina and nickel aluminate has been measured by inert gas fusion analysis of suction samples in the temperature range 1730 to 1975 K. The corresponding oxygen potential has been monitored by a solid electrolyte cell consisting of calcia stabilized zirconia as the electrolyte and Mo + MoO2 as the reference electrode. The results can be summarized by the following equations: log(at. pct O) = \frac - 10,005T + 4.944 ( ±0.015)log(atpctO)=T−10005+4944(0015) % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn DmO2 /4.606RT = log P O2 1/2 = \frac - 13,550T + 4.411 ( ±0.009)O24606RT=logPO212=T−13550+4411(0009) From simultaneous measurements of the potential and concentration of oxygen in melts, not in thermodynamic equilibrium with alumina and aluminate phases, information on the composition dependence of the activity coefficient and the standard free energy of solution of oxygen is obtained. For the reaction, $\frac{1}{2} O_2 \to \underset{\raise0.3em\hbox{$Missing close brace ΔG o = -72,930 - 7.11T (±840) J gr.at.–1 = + 0.216 at. pct OlogfO=T−500+0216atpctO where the standard state for dissolved oxygen is that which makes the value of activity equal to the concentration (in at. pct) in the limit as concentration approaches zero. The oxygen solubility in liquid nickel in equilibrium with solid NiO, evaluated from thermodynamic data, is compared with information reported in the literature. Implications of the results to the deoxidation equilibria of aluminum in nickel are discussed.

Tie lines and activities in the system CoO MgO SiO2 at 1373 K

The tie lines between (CoXMg1−X)O solid solution with rock salt structure and orthosilicate solid solution (CoYMg1−Y)-Si0.5O2, and between orthosilicate and metasilicate (CoZMg1-Z)SiO3 crystalline solutions, have been determined experimentally at 1373 K. The compositions of coexisting phases have been determined by electron probe microanalysis (EPMA) and lattice parameter measurement on equilibrated samples. The metasilicate solid solution exists only for 0 > Z > 0.213. The activity of CoO in the rock salt solid solution was determined as a function of composition and temperature in the range of 1023 to 1373 K using a solid-state galvanic cell: Pt, (CoXMg1−X)O+Co|(Y2O3)ZrO2|Co+CoO, Pt The free energy of mixing of (CoXMg1−X)O crystalline solution can be expressed by the equation ΔGE=X(1 −X)[(6048 − 2.146T)X+ (8745 − 3.09T)(1 −X)] J·mol−1 The thermodynamic data for the rock salt phase is combined with information on interphase partitioning of Co and Mg to generate the mixing properties for the ortho- and metasilicate solid solutions. For the orthosilicate solution (CoYMg1 −Y)Si0.5O2 at 1373 K, the excess Gibbs free energy of mixing is given by the relation ΔGE=Y(1 −Y)[2805Y+ 3261(1 −Y)] J·mol−1 For the metasilicate solution (CoZMg1 −Z)SiO3 at the same temperature, the excess free energy can be expressed by the relation ΔGE=Z(1 −Z)[2570Z+ 3627(1 −Z)] J·mol−1

Activity of TiO2 in the System ZrO2-TiO2 and Gibbs Energy of Formation of ZrTiO4

The activity of Ti02 in single and two··phase regions of ihe system ZrOrTi02 has heen measured lIsing solid state cells based on yttria··doped tho ria (YDT) as the solid electrolyte at 1373 K. The cells used can be represented as: Pt, Tio.07PtO.Y3 + Zrj.,Tix0 2 / YDT / Ti02 + Tio.07Pto.93, Pt Pt, Tio.07Pto.93 + ZrJ.xTix02 + ZrTi04 / YDT / Ti02+ Tio.07PtO.93, Pt In each cell the composition of Pt-Ti alloy was identical at hoth electrodes. The emf of the cell is therefore directly related to the activity of Ti02 in oxide phase or oxide phase mixture: aTiO~ :;: cxp (-4FE/RT). The activity coefficient of Ti02 in th~ zirconia-rich solid solution with monoclinic structure (CUl2 2" XTi02 2" 0) can be expressed as:In the zirconia-rich solid solution with tetragonal structure (0.085 2" X ri02 2" 0.03), the activity coefficient is given by:In YTi02 (± 0.012) = 2.354 (1-XTiO? )2 +0.064 The standard Gibbs energy of formation of ZrTi04 is -5650 (± 200) J/mol at 1373 K .

Mycobacterium leprae RecA is structurally analogous but functionally distinct from Mycobacterium tuberculosis RecA protein

Mycobacterium leprae is closely related to Mycobacterium tuberculosis, yet causes a very different illness. Detailed genomic comparison between these two species of mycobacteria reveals that the decaying M. leprae genome contains less than half of the M. tuberculosis functional genes. The reduction of genome size and accumulation of pseudogenes in the M. leprae genome is thought to result from multiple recombination events between related repetitive sequences, which provided the impetus to investigate the recombination-like activities of RecA protein. In this study, we have cloned, over-expressed and purified M. leprae RecA and compared its activities with that of M. tuberculosis RecA. Both proteins, despite being 91% identical at the amino acid level, exhibit strikingly different binding profiles for single-stranded DNA with varying GC contents, in the ability to catalyze the formation of D-loops and to promote DNA strand exchange. The kinetics and the extent of single-stranded DNA-dependent ATPase and coprotease activities were nearly equivalent between these two recombinases. However, the degree of inhibition exerted by a range of ATP:ADP ratios was greater on strand exchange promoted by M. leprae RecA compared to its M. tuberculosis counterpart. Taken together, our results provide insights into the mechanistic aspects of homologous recombination and coprotease activity promoted by M. lepare RecA, and further suggests that it differs from the M. tuberculosis counterpart. These results are consistent with an emerging concept of DNA-sequence influenced structural differences in RecA nucleoprotein filaments and how these differences reflect on the multiple activities associated with RecA protein. (C) 2011 Elsevier B.V. All rights reserved.

Functional regulation of PVBV Nuclear Inclusion protein-a protease activity upon interaction with Viral Protein genome-linked and phosphorylation

Regulation of NIa-Pro is crucial for polyprotein processing and hence, for successful infection of potyviruses. We have examined two novel mechanisms that could regulate NIa-Pro activity. Firstly, the influence of VPg domain on the proteolytic activity of NIa-Pro was investigated. It was shown that the turnover number of the protease increases when these two domains interact (as: two-fold; trans: seven-fold) with each other. Secondly, the protease activity of NIa-Pro could also be modulated by phosphorylation at Ser129. A mutation of this residue either to aspartate (phosphorylation-mimic) or alanine (phosphorylation-deficient) drastically reduces the protease activity. Based on these observations and molecular modeling studies, we propose that interaction with VPg as well as phosphorylation of Ser129 could relay a signal through Trp143 present at the protein surface to the active site pocket by subtle conformational changes, thus modulating protease activity of NIa-Pro. (C) 2011 Elsevier Inc. All rights reserved.

Photo-induced DNA cleavage activity and remarkable photocytotoxicity of lanthanide(III) complexes of a polypyridyl ligand

Lanthanide(III) complexes [Ln(pyphen)(acac)(2)(NO3)] (1, 2), [Ln(pydppz)(acac)(2)(NO3)] (3, 4) and [La(pydppz)(anacac)(2)(NO3)] (5), where Ln is La(III) (in 1, 3, 5) and Gd(III) (in 2, 4), pyphen is 6-(2-pyridyl)-1,10-phenanthroline, pydppz is 6-(2-pyridyl)-dipyrido[3,2-a:2',3'-c] phenazine, anacac is anthracenylacetylacetonate and acac is acetylacetonate, were prepared, characterized and their DNA photocleavage activity and photocytotoxicity studied. The crystal structure of complex 2 displays a GdO6N3 coordination. The pydppz complexes 3-5 show an electronic spectral band at similar to 390 nm in DMF. The La(III) complexes are diamagnetic, while the Gd(III) complexes are paramagnetic with seven unpaired electrons. The molar conductivity data suggest 1 : 1 electrolytic nature of the complexes in aqueous DMF. They are avid binders to calf thymus DNA giving K-b in the range of 5.4 10(4)-1.2 x 10(6) M-1. Complexes 3-5 efficiently cleave supercoiled DNA to its nicked circular form in UV-A light of 365 nm via formation of singlet oxygen (O-1(2)) and hydroxyl radical (HO center dot) species. Complexes 3-5 also exhibit significant photocytotoxic effect in HeLa cancer cells giving respective IC50 value of 0.16(+/- 0.01), 0.15(+/- 0.01) and 0.26 +/-(0.02) mu M in UV-A light of 365 nm, while they are less toxic in dark with an IC50 value of >3 mu M. The presence of an additional pyridyl group makes the pydppz complexes more photocytotoxic than their dppz analogues. FACS analysis of the HeLa cells treated with complex 4 shows apoptosis as the major pathway of cell death. Nuclear localization of complex 5 having an anthracenyl moiety as a fluorophore is evidenced from the confocal microscopic studies.

Structure and Photocatalytic Activity of Ti 1- x M x O 2±δ (M = W, V, Ce, Zr, Fe, and Cu) Synthesized by Solution Combustion Method

The W, V, Ce, Zr, Fe, and Cu metal ion substituted nanocrystalline anatase TiO2 was prepared by solution combustion method and characterized by XRD, Raman, BET, EPR, XPS, IR TGA, UV absorption, and photoluminescence measurements. The structural studies indicate that the solid solution formation was limited to a narrow range of concentrations of the dopant ions. The photocatalytic degradation of 4-nitrophenol under UV and solar exposure was investigated with Ti1-xMxO2±δ. The degradation rates of 4-nitrophenol with these catalysts were lesser than the degradation rates of 4-nitrophenol with undoped TiO2 both with UV exposure and solar radiation. However, the photocatalytic activities of most metal ion doped TiO2 are higher than the activity of the commercial TiO2, Degussa P25. The decrease in photocatalytic activity is correlated with decrease in photoluminescence due to electron states of metal ions within the band gap of TiO2.