Deciphering the Distinct Role for the Metal Coordination Motif in the Catalytic Activity of Mycobacterium smegmatis Topoisomerase I

Mycobacterium smegmatis topoisomerase I (Mstopol) is distinct from typical type IA topoisomerases. The enzyme binds to both single- and double-stranded DNA with high affinity, making specific contacts. The enzyme comprises conserved regions similar to type IA topoisomerases from Escherichia coli and other eubacteria but lacks the typically found zinc fingers in the carboxy-terminal domain. The enzyme can perform DNA cleavage m the absence of Mg2+ but religation needs exogenously added Mg2+. One molecule of Mg2+ tightly bound to the enzyme has no role in DNA cleavage but is needed only for the religation reaction. The toprim. (topoisomerase-primase) domain in MstopoI comprising the Mg2+ binding pocket, conserved in both type IA and type II topoisomerases, was subjected to mutagenesis to understand the role of Mg2+, in different steps of the reaction. The residues D108, D110, and E112 of the enzyme, which form the acidic triad in the DXDXE motif, were changed to alanines. D108A mutation resulted in an enzyme that is Mg2+ dependent for DNA cleavage unlike Mstopol and exhibited enhanced DNA cleavage property and reduced religation activity. The mutant was toxic for cell growth, most likely due to the imbalance in cleavage-religation equilibrium. In contrast, the E112A mutant behaved like wild-type enzyme, cleaving DNA in a Mg2+-independent fashion, albeit to a reduced extent. Intra- and intermolecular religation assays indicated specific roles for D108 and E112 residues during the reaction. Together, these results indicate that the D108 residue has a major role during cleavage and religation, while E112 is important for enhancing the efficiency of cleavage. Thus, although architecturally and mechanistically similar to topoisomerase I from E. coli, the metal coordination pattern of the mycobacterial enzyme is distinct, opening up avenues to exploit the enzyme to develop inhibitors.

Novel organic-inorganic composite polymer-electrolyte membranes for DMFCs

Organic-inorganic composite membranes comprising Nation with inorganic materials such as silica, mesoporous zirconium phosphate (MZP) and mesoporous titanium phosphate (MTP) are fabricated and evaluated as proton-exchange-membrane electrolytes for direct methanol fuel cells (DMFCs). For Nation-silica composite membrane, silica is impregnated into Nation matrix as a sol by a novel water hydrolysis process precluding the external use of an acid. Instead, the acidic nature of Nation facilitates in situ polymerization reaction with Nation leading to a uniform composite membrane. The rapid hydrolysis and polymerization reaction while preparing zirconia and titania sols leads to uncontrolled thickness and volume reduction in the composite membranes, and hence is not conducive for casting membranes. Nafion-MZP and Nafion-MTP composite membranes are prepared by mixing pre-formed porous MZP and MTP with Nation matrix. MZP and MTP are synthesised by co-assembly of a tri-block co-polymer, namely pluronic-F127, as a structure-directing agent, and a mixture of zirconium butoxide/titanium isopropoxide and phosphorous trichloride as inorganic precursors. Methanol release kinetics is studied by volume-localized NMR spectroscopy (employing ``point resolved spectroscopy'', PRESS), the results clearly demonstrating that the incorporation of inorganic fillers in Nation retards the methanol release kinetics under osmotic drag. Appreciable proton conductivity with reduced methanol permeability across the composite membranes leads to improved performance of DMFCs in relation to commercially available Nafion-117 membrane.

Nucleotide sequence and expression inE. coli of the complete P4 type VP4 from a G2 serotype human rotavirus

The complete sequence of a P4 type VP4 gene from a G2 serotype human rotavirus, IS2, isolated in India has been determined. Although the IS2 VP4 is highly homologous to the other P4 type alleles, it contained acidic amino acid substitutions at several positions that make it acidic among the P4 type alleles that are basic. Moreover, comparative sequence analysis revealed unusual polymorphism in members of the P4 type at amino acid position 393 which is highly conserved in members of other VP4 types. To date, expression of complete VP4 inE. coli has not been achieved. In this study we present successful expression inE. coli of the complete VP4 as well as VP8* and VP5* cleavage subunits in soluble form as fusion proteins of the maltose-binding protein (MBP) and their purification by single-step affinity chromatography. The hemagglutinating activity exhibited by the recombinant protein was specifically inhibited by the antiserum raised against it. Availability of pure VP4 proteins should facilitate development of polyclonal and monoclonal antibodies (MAbs) for P serotyping of rotaviruses.

Formation of a novel surface structure encoded by Salmonella Pathogenicity Island 2.

The type III secretion system (T3SS) encoded by Salmonella Pathogenicity Island 2 (SPI2) is essential for virulence and intracellular proliferation of Salmonella enterica. We have previously identified SPI2-encoded proteins that are secreted and function as a translocon for the injection of effector proteins. Here, we describe the formation of a novel SPI2-dependent appendage structure in vitro as well as on the surface of bacteria that reside inside a vacuole of infected host cells. In contrast to the T3SS of other pathogens, the translocon encoded by SPI2 is only present singly or in few copies at one pole of the bacterial cell. Under in vitro conditions, appendages are composed of a filamentous needle-like structure with a diameter of 10 nm that was sheathed with secreted protein. The formation of the appendage in vitro is dependent on acidic media conditions. We analyzed SPI2-encoded appendages in infected cells and observed that acidic vacuolar pH was not required for induction of SPI2 gene expression, but was essential for the assembly of these structures and their function as translocon for delivery of effector proteins.

Expression, purification and X-ray analysis of 1,3-propanediol dehydrogenase (Aq_1145) from Aquifex aeolicus VF5

1,3-Propanediol dehydrogenase is an enzyme that catalyzes the oxidation of 1,3-propanediol to 3-hydroxypropanal with the simultaneous reduction of NADP(+) to NADPH. SeMet-labelled 1,3-propanediol dehydrogenase protein from the hyperthermophilic bacterium Aquifex aeolicus VF5 was overexpressed in Escherichia coli and purified to homogeneity. Crystals of this protein were grown from an acidic buffer with ammonium sulfate as the precipitant. Single-wavelength data were collected at the selenium peak to a resolution of 2.4 angstrom. The crystal belonged to space group P3(2), with unit-cell parameters a = b = 142.19, c = 123.34 angstrom. The structure contained two dimers in the asymmetric unit and was solved by the MR-SAD approach.

Aqueous colloidal stability evaluated by zeta potential measurement and resultant TiO2 for superior photovoltaic performance

Controlling the morphological structure of titanium dioxide (TiO 2) is crucial for obtaining superior power conversion efficiency for dye-sensitized solar cells. Although the sol-gel-based process has been developed for this purpose, there has been limited success in resisting the aggregation of nanostructured TiO2, which could act as an obstacle for mass production. Herein, we report a simple approach to improve the efficiency of dye-sensitized solar cells (DSSC) by controlling the degree of aggregation and particle surface charge through zeta potential analysis. We found that different aqueous colloidal conditions, i.e., potential of hydrogen (pH), water/titanium alkoxide (titanium isopropoxide) ratio, and surface charge, obviously led to different particle sizes in the range of 10-500 nm. We have also shown that particles prepared under acidic conditions are more effective for DSSC application regarding the modification of surface charges to improve dye loading and electron injection rate properties. Power conversion efficiency of 6.54%, open-circuit voltage of 0.73 V, short-circuit current density of 15.32 mA/cm2, and fill factor of 0.73 were obtained using anatase TiO 2 optimized to 10-20 nm in size, as well as by the use of a compact TiO2 blocking layer.

Identification and thermodynamic characterization of molten globule states of periplasmic binding proteins

Molten globule-like intermediates have been shown to occur during protein folding and are thought to be involved in protein translocation and membrane insertion. However, the determinants of molten globule stability and the extent of specific packing in molten globules is currently unclear. Using far- and near-UV CD and intrinsic and ANS fluorescence, we show that four periplasmic binding proteins (LBP, LIVBP, MBP, and RBP) form molten globules at acidic pH values ranging from 3.0 to 3.4. Only two of these (LBP and LIVBP) have similar sequences, but all four proteins adopt similar three-dimensional structures. We found that each of the four molten globules binds to its corresponding ligand without conversion to the native state. Ligand binding affinity measured by isothermal titration calorimetry for the molten globule state of LIVBP was found to be comparable to that of the corresponding native state, whereas for LBP, MBP, and RBP, the molten globules bound ligand with approximately 5-30-fold lower affinity than the corresponding native states. All four molten globule states exhibited cooperative thermal unfolding assayed by DSC. Estimated values of Delta C-p of unfolding show that these molten globule states contain 28-67% of buried surface area relative to the native states. The data suggest that molten globules of these periplasmic binding proteins retain a considerable degree of long range order. The ability of these sequentially unrelated proteins to form highly ordered molten globules may be related to their large size as well as an intrinsic property of periplasmic binding protein folds.

N,N′-Bis(aryl)pyridine-2,6-dicarboxamide complexes of ruthenium: Synthesis, structure and redox properties

Reaction of five N,N′-bis(aryl)pyridine-2,6-dicarboxamides (H2L-R, where H2 denotes the two acidic protons and R (R = OCH3, CH3, H, Cl and NO2) the para substituent in the aryl fragment) with [Ru(trpy)Cl3](trpy = 2,2′,2″-terpyridine) in refluxing ethanol in the presence of a base (NEt3) affords a group of complexes of the type [RuII(trpy)(L-R)], each of which contains an amide ligand coordinated to the metal center as a dianionic tridentate N,N,N-donor along with a terpyridine ligand. Structure of the [RuII(trpy)(L-Cl)] complex has been determined by X-ray crystallography. All the Ru(II) complexes are diamagnetic, and show characteristic 1H NMR signals and intense MLCT transitions in the visible region. Cyclic voltammetry on the [RuII(trpy)(L-R)] complexes shows a Ru(II)–Ru(III) oxidation within 0.16–0.33 V versus SCE. An oxidation of the coordinated amide ligand is also observed within 0.94–1.33 V versus SCE and a reduction of coordinated terpyridine ligand within −1.10 to −1.15 V versus SCE. Constant potential coulometric oxidation of the [RuII(trpy)(L-R)] complexes produces the corresponding [RuIII(trpy)(L-R)]+ complexes, which have been isolated as the perchlorate salts. Structure of the [RuIII(trpy)(L-CH3)]ClO4 complex has been determined by X-ray crystallography. All the Ru(III) complexes are one-electron paramagnetic, and show anisotropic ESR spectra at 77 K and intense LMCT transitions in the visible region. A weak ligand-field band has also been shown by all the [RuIII(trpy)(L-R)]ClO4 complexes near 1600 nm.

Propargyloxycarbonyl as a protecting group for the side chains of serine, threonine and tyrosine

Propargyloxycarbonyl group is used as a protecting group for the hydroxyl groups of serine, threonine and tyrosine. The propargyloxycarbonyl derivatives of these hydroxy amino acids are stable to acidic and basic reagents commonly employed in peptide synthesis. The deprotection of the O-Poc derivatives using tetrathiomolybdate does not affect commonly used protecting groups such as N-Boc, N-Cbz, N-Fmoc, methyl and benzyl esters. The di-and tripeptides synthesized using O-Poc derivatives of serine, threonine and tyrosine are stable, isolable compounds and give the hydroxy peptides in good yields when treated with tetrathiomolybdate.

Three-dimensional structure of heat shock protein 90 from Plasmodium falciparum: molecular modelling approach to rational drug design against malaria

We have recently implicated heat shock protein 90 from Plasmodium falciparum (PfHsp90) as a potential drug target against malaria. Using inhibitors specific to the nucleotide binding domain of Hsp90, we have shown potent growth inhibitory effects on development of malarial parasite in human erythrocytes. To gain better understanding of the vital role played by PfHsp90 in parasite growth, we have modeled its three dimensional structure using recently described full length structure of yeast Hsp90. Sequence similarity found between PfHsp90 and yeast Hsp90 allowed us to model the core structure with high confidence. The superimposition of the predicted structure with that of the template yeast Hsp90 structure reveals an RMSD of 3.31 angstrom. The N-terminal and middle domains showed the least RMSD (1.76 angstrom) while the more divergent C-terminus showed a greater RMSD (2.84 angstrom) with respect to the template. The structure shows overall conservation of domains involved in nucleotide binding, ATPase activity, co-chaperone binding as well as inter-subunit interactions. Important co-chaperones known to modulate Hsp90 function in other eukaryotes are conserved in malarial parasite as well. An acidic stretch of amino acids found in the linker region, which is uniquely extended in PfHsp90 could not be modeled in this structure suggesting a flexible conformation. Our results provide a basis to compare the overall structure and functional pathways dependent on PfHsp90 in malarial parasite. Further analysis of differences found between human and parasite Hsp90 may make it possible to design inhibitors targeted specifically against malaria.

Localized agglutinin staining in muscle capillaries from normal and very old atrophic human muscle using winged bean ( Psophocarpus tetragonolobus ) lectin

The winged bean (Psophocarpus tetragonolobus) agglutinin (total lectin) and its basic (WBA I) and acidic isoform (WBA II) were used to analyze capillaries in sections from human muscle. The microvessels were clearly labeled after incubation with the lectins in both normal muscle and in old muscles with age-related type II atrophy or muscle fiber grouping. Muscle fibers, nerves, and connective tissue remained unstained. The total lectin detected muscle capillaries from all blood group AB0 individuals. The isoform WBA I reacted only with blood vessels in blood group A and B individuals, while the blood vessels in blood group 0 individuals were demonstrated with WBA II. WBA I staining was inhibited by p-nitrophenyl α-galactopyranoside and N-acetylgalactosamine, whereas 2′-fucosyllactose and preincubation with an antibody against type-1 chain H abolished capillary staining with WBA II. The study demonstrates the usefulness of WBA as a marker of capillaries in human muscle.

The Isolation and Characterization of β-N-Oxalyl-L-α,β-Diaminopropionic Acid: A Neurotoxin from the Seeds of Lathyrus sativus

A neurotoxic compound has been isolated from the seeds of Lathyrus sativus in 0.5% yield and characterized as β-N-oxalyl-L-α,β-diaminopropionic acid. The compound is highly acidic in character and forms oxalic acid and diaminopropionic acid on acid hydrolysis. The compound has a specific rotation of -36.9° and has apparent pK values in the order of 1.95, 2.95, and 9.25, corresponding to the two carboxyl and one amino functions, respectively. The compound has been synthesized by reacting an aqueous methanolic solution of the copper complex of L-α,β-diaminopropionic acid prepared at pH 4.5-5.0 with dimethyl oxalate under controlled pH conditions and isolating the compound by chromatography on a Dowex 50-H+ column after precipitating the copper. The compound induced severe neurological symptoms in day-old chicks at the level of 20 mg/chick, but not in rats or mice. It also inhibited the growth of several microorganisms and of the insect larva Corcyra cephalonica Staint. L-Homoarginine had no neural action in chicks. It is suggested that the neurotoxic compound is species specific in its action and may be related to "neurolathyrism" associated with the human consumption of L. sativus seeds.

Enzymatic cross-linking of β-casein and its impact on digestibility and allergenicity

Protein modification via enzymatic cross-linking is an attractive way for altering food structure so as to create products with increased quality and nutritional value. These modifications are expected to affect not only the structure and physico-chemical properties of proteins but also their physiological characteristics, such as digestibility in the GI-tract and allergenicity. Protein cross-linking enzymes such as transglutaminases are currently commercially available, but also other types of cross-linking enzymes are being explored intensively. In this study, enzymatic cross-linking of β-casein, the most abundant bovine milk protein, was studied. Enzymatic cross-linking reactions were performed by fungal Trichoderma reesei tyrosinase (TrTyr) and the performance of the enzyme was compared to that of transglutaminase from Streptoverticillium mobaraense (Tgase). Enzymatic cross-linking reactions were followed by different analytical techniques, such as size exclusion chromatography -Ultra violet/Visible multi angle light scattering (SEC-UV/Vis-MALLS), phosphorus nuclear magnetic resonance spectroscopy (31P-NMR), atomic force (AFM) and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF MS). The research results showed that in both cases cross-linking of β-casein resulted in the formation of high molecular mass (MM ca. 1 350 kg mol-1), disk-shaped nanoparticles when the highest enzyme dosage and longest incubation times were used. According to SEC-UV/Vis-MALLS data, commercial β-casein was cross-linked almost completely when TrTyr and Tgase were used as cross-linking enzymes. In the case of TrTyr, high degree of cross-linking was confirmed by 31P-NMR where it was shown that 91 % of the tyrosine side-chains were involved in the cross-linking. The impact of enzymatic cross-linking of β-casein on in vitro digestibility by pepsin was followed by various analytical techniques. The research results demonstrated that enzymatically cross-linked β-casein was stable under the acidic conditions present in the stomach. Furthermore, it was found that cross-linked β-casein was more resistant to pepsin digestion when compared to that of non modified β-casein. The effects of enzymatic cross-linking of β-casein on allergenicity were also studied by different biochemical test methods. On the basis of the research results, enzymatic cross-linking decreased allergenicity of native β-casein by 14 % when cross-linked by TrTyr and by 6 % after treatment by Tgase. It can be concluded that in addition to the basic understanding of the reaction mechanism of TrTyr on protein matrix, the research results obtained in this study can have high impact on various applications like food, cosmetic, medical, textile and packing sectors.

USING FLUORESCENT AND NON-FLUORESCENT STEROLS TO STUDY RAFTS AND INTRACELLULAR CHOLESTEROL TRANSPORT IN MAMMALIAN CELLS

Cholesterol is an essential component in the membranes of most eukaryotic cells, in which it mediates many functions including membrane fluidity, permeability and the formation of ordered membrane domains. In this work a fluorescent and a non-fluorescent cholesterol analog were characterized as tools to study cholesterol. Next, these analogs were used to study two specific cell biological processes that involve cholesterol, i.e. the structure and function of ordered membrane domains/rafts and intracellular cholesterol transport. The most common method for studying ordered membrane domains is by disrupting them by cholesterol depletion. Because cholesterol depletion affects many cellular functions besides those mediated by membrane domains, this procedure is highly unspecific. The cellular exchange of cholesterol by desmosterol as a tool to study ordered membrane domains was characterized. It turned out that the ability of desmosterol to form and stabilize membrane domains in vitro was weaker compared to cholesterol. This result was reinforced by atomistic scale simulations that indicated that desmosterol has a lower ordering effect on phospholipid acyl chains. Three procedures were established for exchanging cellular cholesterol by desmosterol. In cells in which desmosterol was the main sterol, insulin signaling was attenuated. The results suggest that this was caused by desmosterol destabilizing membrane rafts. Contrary to its effect on ordered membrane domains it was found that replacing cholesterol by desmosterol does not change cell growth/viability, subcellular sterol distribution, Golgi integrity, secretory pathway, phospholipid composition and membrane fluidity. Together these results suggest that exchanging cellular cholesterol by desmosterol provides a selective tool for perturbing rafts. Next, the importance of cholesterol for the structure and function of caveolae was analyzed by exchanging the cellular cholesterol by desmosterol. The sterol exchange reduced the stability of caveolae as determined by detergent resistance of caveolin-1 and heat resistance of caveolin-1 oligomers. Also the sterol exchange led to aberrations in the caveolar structure; the morphology of caveolae was altered and there was a larger variation in the amount of caveolin-1 molecules per caveola. These results demonstrate that cholesterol is important for caveolar stability and structural homogeneity. In the second part of this work a fluorescent cholesterol analog was characterized as a tool to study cholesterol transport. Tight control of the intracellular cholesterol distribution is essential for many cellular processes. An important mechanism by which cells regulate their membrane cholesterol content is by cholesterol traffic, mostly from the plasma membrane to lipid droplets. The fluorescent sterol probe BODIPY-cholesterol was characterized as a tool to analyze cholesterol transport between the plasma membrane, the endoplasmic reticulum (ER) and lipid droplets. The behavior of BODIPY-cholesterol was compared to that of natural sterols, using both biochemical and live-cell microcopy assays. The results show that the transport kinetics of BODIPY-cholesterol between the plasma membrane, the ER and lipid droplets is similar to that of unesterified cholesterol. Next, BODIPY-cholesterol was utilized to analyze the importance of oxysterol binding protein related proteins (ORPs) for cholesterol transport between the plasma membrane, the ER, and lipid droplets in mammalian cells. By overexpressing all human ORPs it turned out that especially ORP1S and ORP2 enhanced sterol transport from the plasma membrane to lipid droplets. Our results suggest that the increased sterol transport takes place between the plasma membrane and ER and not between the ER and lipid droplets. Simultaneous knockdown of ORP1S and ORP2 resulted in a moderate but significant inhibition of sterol traffic from the plasma membrane to ER and lipid droplets, suggesting a physiological role for these ORPs in this process. The two phenylalanines in an acidic tract (FFAT) motif in ORPs, which mediates interaction with vesicle associated membrane protein associated proteins (VAPs) in the ER, was not necessary for mediating sterol transport. However, VAP silencing slowed down sterol transport, most likely by destabilizing ORPs containing a FFAT motif.

Vapour phase synthesis of salol over solid acids via transesterification

The transesterification of methyl salicylate with phenol has been studied in vapour phase over solid acid catalysts such as ZrO2, MoO3 and SO42- or Mo(VI) ions modified zirconia. The catalytic materials were prepared and characterized for their total surface acidity, BET surface area and powder XRD patterns. The effect of mole-ratio of the reactants, catalyst bed temperature, catalyst weight, flow-rate of reactants, WHSV and time-on-stream on the conversion (%) of phenol and selectivity (%) of salol has been investigated. A good yield (up to 70%) of salol with 90% selectivity was observed when the reactions were carried out at a catalyst bed temperature of 200 degrees C and flow-rate of 10 mL/h in presence of Mo(VI)/ZrO2 as catalyst. The results have been interpreted based on the variation of acidic properties and powder XRD phases of zirconia on incorporation of SO42- or Mo(VI) ions. The effect of poisoning of acid sites of SO42- or Mo(VI) ions modified zirconia on total surface acidity, powder XRD phases and catalytic activity was also studied. Possible reaction mechanisms for the formation of salol and diphenyl ether over acid sites are proposed.