De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex.

The de novo design of membrane proteins remains difficult despite recent advances in understanding the factors that drive membrane protein folding and association. We have designed a membrane protein PRIME (PoRphyrins In MEmbrane) that positions two non-natural iron diphenylporphyrins (Fe(III)DPP's) sufficiently close to provide a multicentered pathway for transmembrane electron transfer. Computational methods previously used for the design of multiporphyrin water-soluble helical proteins were extended to this membrane target. Four helices were arranged in a D(2)-symmetrical bundle to bind two Fe(II/III) diphenylporphyrins in a bis-His geometry further stabilized by second-shell hydrogen bonds. UV-vis absorbance, CD spectroscopy, analytical ultracentrifugation, redox potentiometry, and EPR demonstrate that PRIME binds the cofactor with high affinity and specificity in the expected geometry.

Water exchange rates of water-soluble manganese(III) porphyrins of therapeutical potential.

The activation parameters and the rate constants of the water-exchange reactions of Mn(III)TE-2-PyP(5+) (meso-tetrakis(N-ethylpyridinium-2-yl)porphyrin) as cationic, Mn(III)TnHex-2-PyP(5+) (meso-tetrakis(N-n-hexylpyridinium-2-yl)porphyrin) as sterically shielded cationic, and Mn(III)TSPP(3-) (meso-tetrakis(4-sulfonatophenyl)porphyrin) as anionic manganese(iii) porphyrins were determined from the temperature dependence of (17)O NMR relaxation rates. The rate constants at 298 K were obtained as 4.12 x 10(6) s(-1), 5.73 x 10(6) s(-1), and 2.74 x 10(7) s(-1), respectively. On the basis of the determined entropies of activation, an interchange-dissociative mechanism (I(d)) was proposed for the cationic complexes (DeltaS(double dagger) = approximately 0 J mol(-1) K(-1)) whereas a limiting dissociative mechanism (D) was proposed for Mn(III)TSPP(3-) complex (DeltaS(double dagger) = +79 J mol(-1) K(-1)). The obtained water exchange rate of Mn(III)TSPP(3-) corresponded well to the previously assumed value used by Koenig et al. (S. H. Koenig, R. D. Brown and M. Spiller, Magn. Reson. Med., 1987, 4, 52-260) to simulate the (1)H NMRD curves, therefore the measured value supports the theory developed for explaining the anomalous relaxivity of Mn(III)TSPP(3-) complex. A magnitude of the obtained water-exchange rate constants further confirms the suggested inner sphere electron transfer mechanism for the reactions of the two positively charged Mn(iii) porphyrins with the various biologically important oxygen and nitrogen reactive species. Due to the high biological and clinical relevance of the reactions that occur at the metal site of the studied Mn(iii) porphyrins, the determination of water exchange rates advanced our insight into their efficacy and mechanism of action, and in turn should impact their further development for both diagnostic (imaging) and therapeutic purposes.

Photophysics of bifunctional Ru(II) complexes bearing an aminoquinoline organic unit. Potential new photoprobes and photoreagents of DNA

[Ru(BPY)2POQ-Nmet]2+ and [Ru(TAP)2POQ-Nmet]2+ (1 and 3) are bifunctional complexes composed of a metallic unit linked by a flexible chain to an organic unit. They have been prepared as photoprobes or photoreagents of DNA. In this work, the spectroscopic properties of these bifunctional complexes in the absence of DNA are compared with those of the monofunctional analogues [Ru(BPY)2Phen]2+, [Ru-(BPY)2acPhen]2+, [Ru(TAP)2Phen]2+, and [Ru(TAP)2acPhen]2+ (2 and 4). The electrospray mass spectrometry and absorption data show that the quinoline moiety exists in the protonated and nonprotonated form. Although the bifunctional complex containing 2,2′-bipyridine (BPY) ligands exhibits photophysical properties similar to those of the monofunctional compounds, the bifunctional complex with 1,4,5,8-tetraazaphenanthrene (TAP) ligands behaves quite differently. It has weaker relative emission quantum yields and shorter luminescence lifetimes than the monofunctional TAP analogue when the quinoline unit is nonprotonated. This indicates an efficient intramolecular quenching of the 3MLCT (metal to ligand charge transfer) excited state of the TAP metallic moiety. When the organic unit is protonated, there is no internal quenching. In organic solvent, the nonquenched excited metallic unit (bearing a protonated quinoline) and the quenched one (bearing a nonprotonated organic unit) are in slow equilibrium as compared to the lifetime of the two emitters. In aqueous solution this equilibrium is faster and is catalysed by the presence of phosphate buffer. Flash photolysis experiments suggest that the intramolecular quenching process originates from a photoinduced electron transfer from the nonprotonated quinoline to the excited Ru(TAP)2 2+ moiety.

Synthesis of N3- and 2-NH2-substituted 6,7-diphenylpterins and their use as intermediates for the preparation of oligonucleotide conjugates designed to target photooxidative damage on single-stranded DNA representing the bcr-abl chimeric gene

Two 17-mer oligodeoxynucleotide-5'-linked-(6,7-diphenylpterin) conjugates, 2 and 3, were prepared as photosensitisers for targeting photooxidative damage to a 34-mer DNA oligodeoxynucleotide (ODN) fragment 1 representing the chimeric bcr-abl gene that is implicated in the pathogenesis of chronic myeloid leukaemia (CML). The base sequence in the 17-mer was 3'G G T A G T T A T T C C T T C T T5'. In the first of these ODN conjugates (2) the pterin was attached at its N3 atom, via a -(CH2)3OPO(OH)- linker, to the 5'-OH group of the ODN. Conjugate 2 was prepared from 2-amino-3-(3-hydroxypropyl)-6,7-diphenyl-4(3H)-pteridinone 10, using phosphoramidite methodology. Starting material 10 was prepared from 5-amino-7-methylthiofurazano[3,4-d]pyrimidine 4 via an unusual highly resonance stabilised cation 8, incorporating the rare 2H,6H-pyrimido[6,1-b][1,3]oxazine ring system. In the characterisation of 10 two pteridine phosphazenes, 15 and 29, were obtained, as well as new products containing two uncommon tricyclic ring systems, namely pyrimido[2,1-b]pteridine (20 and 24) and pyrimido[1,2-c]pteridine (27). In the second ODN conjugate the linker was -(CH2)5CONH(CH2)6OPO(OH)- and was attached to the 2-amino group of the pterin. In the preparation of 3, the N-hydroxysuccinimide ester 37 of 2-(5-carboxypentylamino)-6,7-diphenyl-4(3H)-pteridinone was condensed with the hexylamino-modified 17-mer. Excitation of 36 with near UV light in the presence of the single-stranded target 34-mer, 5'T G A C C A T C A A T A A G14 G A A G18 A A G21 C C C T T C A G C G G C C3' 1 caused oxidative damage at guanine bases, leading to alkali-labile sites which were monitored by polyacrylamide gel electrophoresis. Cleavage was observed at all guanine sites with a marked preference for cleavage at G14. In contrast, excitation of ODN-pteridine conjugate 2 in the presence of 1 caused oxidation of the latter predominantly at G18, with a smaller extent of cleavage at G15 and G14 (in the double-stranded portion) and G21. These results contrast with our previous observation of specific cleavage at G21 with ruthenium polypyridyl sensitisers, and suggest that a different mechanism, probably one involving Type 1 photochemical electron transfer, is operative. Much lower yields were found with the ODN-pteridine conjugate 3, perhaps as a consequence of the longer linker between the ODN and the pteridine in this case.

A comparison of mitochondrial and nuclear DNA status in testicular sperm from fertile men and those with obstructive azoospermia

Background: Mitochondria are vital to sperm as their motility powerhouses. They are also the only animal organelles with their own unique genome; encoding subunits for the complexes required for the electron transfer chain. Methods: A modified long PCR technique was used to study mitochondrial DNA (mtDNA) in ejaculated and testicular sperm samples from fertile men (n=11) and testicular sperm from men with obstructive azoospermia (n=25). Nuclear DNA fragmentation was measured by an alkaline single cell gel electrophoresis (COMET) assay. Results: Wild-type mtDNA was detected in only 60% of fertile mens�??�?�¢?? testicular sperm, 50% of their ejaculated sperm and 46% of testicular sperm from men with obstructive azoospermia. The incidence of mitochondrial deletions in testicular sperm of fertile and infertile men was not significantly different but the mean size of the deletions was significantly less in testicular sperm from fertile men compared with men with obstructive azoospermia (p<0.02). Nuclear DNA fragmentation in testicular sperm from fertile men and men with obstructive azoospermia was not significantly different. Conclusion: Multiple mtDNA deletions are common in testicular and ejaculated sperm from both fertile and infertile men. However, in males with obstructive azoospermia the mtDNA deletions in testicular sperm are of a larger scale.

Catalytic Role of Metal Oxides in Gold-Based Catalysts: A First Principles Study of CO Oxidation on TiO2 Supported Au

CO oxidation on TiO2 supported Au has been studied using density functional theory calculations. Important catalytic roles of the oxide have been identified: (i) CO oxidation occurs at the interface between Au and the oxide with a very small barrier; and (ii) O-2 adsorption at the interface is the key step in the reaction. The physical origin of the oxide promotion effect has been further investigated: The oxide enhances electron transfer from the Au to the antibonding states of O-2, giving rise to (i) strong ionic bonding between the adsorbed O-2, Au, and the Ti cation; and (ii) a significant activation of O-2 towards CO oxidation.

On the low-frequency electrical polarization of bacterial cells in sands

We performed electrical measurements on sands flushed with bacterial suspensions of varying concentration. The first experiment was conducted with Shewanella putrefaciens (biomass 0â??0.5 mg/L) and the second with Escherichia coli (biomass 0â??42 mg/L). We measured a biomass-dependent low-frequency (10 Hz) polarization. At cell density 12 mg/L polarization increased (up to 15%). We attribute the decrease in polarization at low cell density to alteration of the mineral-fluid interface due to mineral-cell interactions. The polarization enhancement at higher cell density is possibly a pore throat mechanism resulting from decreased ionic mobility and/or electron transfer due to cell accumulation in pores.

Electrochemical reduction of benzoic acid and substituted benzoic acids in some room temperature ionic liquids

Using cyclic voltammetry, the electrochemical reduction of benzoic acid (BZA) has been studied at Pt and Au microelectrodes (10 and 2 mu m diameter) in six room temperature ionic liquids (RTILs), namely [C(2)mim][NTf2], [C(4)mim][NTf2], [C(4)mpyrr][NTf2], [C(4)mim][BF4], [C(4)mim][NO3], and [C(4)mim][PF6] (where [C(n)mim](+) = 1-alkyl-3-methylimidazolium, [NTf2](-) = bis(trifluoromethylsulfonyl)imide, [C(4)mpyrr](+) = N-butyl-N-methylpyrrolidinium, [BF4](-) = tetrafluoroborate, [NO3](-) = nitrate, and [PF6](-) = hexafluorophosphate). In all cases, a main reduction peak was observed, assigned to the reduction of BZA in a CE mechanism, where dissociation of the acid takes place before electron transfer to the dissociated proton. One anodic peak was observed on the reverse sweep, assigned to the oxidation of adsorbed hydrogen, and a reductive

Oxidation of several p-phenylenediamines in room temperature ionic liquids: Estimation of transport and electrode kinetic parameters

The electrochemical oxidation of N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) has been studied by cyclic voltammetry and potential step chronoamperometry at 303 K in five ionic liquids, namely [C(2)mim] [NTf2], [C(4)mim] [NTf2] [C(4)mpyrr] [NTf2] [C(4)mim] [BF4], and [C(4)mim] [PF6] (where [C(n)mim](+) = 1-alkyl-3-methylimidazolium, [C(4)mpyrr](+) = N-butyl-N-methylpyrrolidinium, [NTf2](-) = bis(trifluoromethylsulfonyl)imide, [BF4](-) = tetrafluoroborate, and [PF6](-) = hexafluorophosphate). Diffusion coefficients, D, of 4.87, 3.32, 2.05, 1.74, and 1.34 x 10(-11) m(2) s(-1) and heterogeneous electron-transfer rate constants, k(0), of 0.0109, 0.0103, 0.0079, 0.0066, and 0.0059 cm s(-1) were calculated for TMPD in [C(2)mim] [NTf2], [C(4)mim] [NTf2], [C(4)mpyrr] [NTf2], [C(4)mim] [BF4], and [C(4)mim] [PF6], respectively, at 303 K. The oxidation of TMPD in [C4mim][PF6] was also carried out at increasing temperatures from 303 to 343 K, with an activation energy for diffusion of 32.3 kJ mol(-1). k(0) was found to increase systematically with increasing temperature, and an activation energy of 31.4 kJ mol(-1) was calculated. The study was extended to six other p-phenylenediamines with alkyl/phenyl group substitutions. D and k(0) values were calculated for these compounds in [C(2)mim] [NTf2], and it was found that k(0) showed no obvious relationship with the hydrodynamic radius, r.

Electroreduction of oxygen in a series of room temperature ionic liquids composed of group 15-centered cations and anions

The electrochemical reduction of oxygen is reported in four room temperature ionic liquids (RTILs) based on quaternary alkyl -onium cations and heavily fluorinated anions in which the central atom is either nitrogen or phosphorus. Data were collected using cyclic voltammetry and potential step chronoamperometry at gold, platinum, and glassy carbon disk electrodes of micrometer dimension under water-free conditions at a controlled temperature. Analysis via fitting, to appropriate theoretical equations was then carried out to obtain kinetic and thermodynamic information pertaining to the electrochemical processes observed. In the quaternary ammonium electrolytes, reduction of oxygen was found to occur reversibly to give stable superoxide, in an analogous manner to that seen in conventional aprotic solvents such as dimethyl sufoxide and acetonitrile. The most significant difference is in the relative rate of diffusion; the diffusion coefficients of oxygen in the RTILs are an order of magnitude lower than in common organic solvents, and for superoxide these values are reduced by a further factor of 10. In the quaternary phosphonium ionic liquids, however, more complex voltammetry is observed, akin to that expected for the reduction of oxygen in acidified organic media. This is shown to be consistent with the occurrence of a proton abstraction reaction between the electrogenerated superoxide and quaternary alkyl phosphonium cations following the initial electron transfer.

Potential and kinetic sputtering of alkanethiol self-assembled monolayers by impact of highly charged ions

Highly charged ions have been used to study the sputtering of positive molecular fragments from mercaptoundecanoic acid and dodecanethiol self-assembled monolayers on gold surfaces. The samples were bombarded with Arq+ (42n⁺, and Cn+1O2H_{2n + 1}⁺ from mercaptoundecanoic and H+, CnH_2n⁺, and Cn+1H_{2n + 3}⁺ from dodecanethiol. The proton yields were increased with larger charge state q of the highly charged ion (HCI) in both samples, scaling as qgamma, with gamma~5. The charge state dependence is discussed in terms of electron transfer to the HCI. The final yield of protons depends on molecular functional group characteristics, orientation on the surface, and reneutralization phenomena.

Investigating the Mechanism and Electrode Kinetics of the Oxygen vertical bar Superoxide (O-2 vertical bar O-2(center dot-)) Couple in Various Room-Temperature Ionic Liquids at Gold and Platinum Electrodes in the Temperature Range 298-318 K

The reduction of oxygen was studied over a range of temperatures (298-318 K) in n-hexyltriethylammonium bis(trifluoromethanesulfonyl)imide, [N-6,N-2,N-2,N-2][NTf2], and 1-butyl-2,3-methylimidazolium bis(trifluoromethanesulfonyl)imide, [C(4)dmim][NTf2] on both gold and platinum microdisk electrodes, and the mechanism and electrode kinetics of the reaction investigated. Three different models were used to simulate the CVs, based on a simple electron transfer ('E'), an electron transfer coupled with a reversible homogeneous chemical step ('ECrev') and an electron transfer followed by adsorption of the reduction product ('EC(ads)'), and where appropriate, best fit parameters deduced, including the heterogeneous rate constant, formal electrode potential, transfer coefficient, and homogeneous rate constants for the ECrev mechanism, and adsorption/desorption rate constants for the EC(ads) mechanism. It was concluded from the good simulation fits on gold that a simple E process operates for the reduction of oxygen in [N-6,N-2,N-2,N-2][NTf2], and an ECrev process for [C(4)dmim][NTf2], with the chemical step involving the reversible formation of the O-2(center dot-)center dot center dot center dot [C(4)dmim](+) ion-pair. The E mechanism was found to loosely describe the reduction of oxygen in [N-6,N-2,N-2,N-2][NTf2] on platinum as the simulation fits were reasonable although not perfect, especially for the reverse wave. The electrochemical kinetics are slower on Pt, and observed broadening of the oxidation peak is likely due to the adsorption of superoxide on the electrode surface in a process more complex than simple Langmuirian. In [C(4)dmim][NTf2] the O-2(center dot-) predominantly ion-pairs with the solvent rather than adsorbs on the surface, and an ECrev quantitatively describes the reduction of oxygen on Pt also.

Measuring the solubility of benzoic acid in room temperature ionic liquids using chronoamperometric techniques

The electrochemical reduction of benzoic acid (BZA) has been studied at platinum micro-electrodes (10 and 2 mu m diameters) in acetonitrile (MeCN) and six room temperature ionic liquids (RTILs): [C(2)mim][NTf2], [C(4)min][NTf2], [C(4)mpyrr][NTf2], [C(4)mim][BF4], [C(4)mim][NO3] and [C(4)mim][PF6] (where [C(n)mim](+)=1-alkyl-3-methylimidazolium, [NTf2](-)=bis(trifluoromethylsulphonyl)imide, [C(4)mpyrr](+)=N-butyl-N-methylpyrrolidinium, [BF4](-)=tetrafluoroborate, [NO3](-)=nitrate and [PF6] = hexafluorophosphate). Based on the theoretical fitting to experimental chronoamperometric transients in [C4mpyrr][NTf2] and MeCN at several concentrations and on different size electrodes, it is suggested that a fast chemical step preceeds the electron transfer step in a CE mechanism (given below) in both RTILs and MeCN, leading to the appearance of a simple one-electron transfer mechanism.

The proton pumping stoichiometry of purified mitochondrial complex I reconstituted into proteoliposomes

NADH:ubiquinone oxidoreductase (complex I) is the largest and most complicated enzyme of aerobic electron transfer. The mechanism how it uses redox energy to pump protons across the bioenergetic membrane is still not understood. Here we determined the pumping stoichiometry of mitochondrial complex I from the strictly aerobic yeast Yarrowia lipolytica. With intact mitochondria, the measured value of 3.8H(->+)/2e(-) indicated that four protons are pumped per NADH oxidized. For purified complex I reconstituted into proteoliposomes we measured a very similar pumping stoichiometry of 3.6H(->+)/2e(-). This is the first demonstration that the proton pump of complex I stayed fully functional after purification of the enzyme. (c) 2006 Elsevier B.V. All rights reserved.