Functional characterization of the precursor and spliced forms of RecA protein of Mycobacterium tuberculosis

The recA locus of pathogenic mycobacteria differs from that of nonpathogenic species because it contains large intervening sequences nested in the RecA homology region that are excised by an unusual protein-splicing reaction. In vivo assays indicated that Mycobacterium tuberculosis recA partially complemented Escherichia coli recA mutants for recombination and mutagenesis. Further, splicing of the 85 kDa precursor to 38 kDa MtRecA protein was necessary for the display of its activity, in vivo. To gain insights into the molecular basis for partial and lack of complementation by MtRecA and 85 kDa proteins, respectively, we purified both of them to homogeneity. MtRecA protein, but not the 85 kDa form, bound stoichiometrically to single-stranded DNA in the presence of ATP. MtRecA protein was cross-linked to 8-azidoadenosine 5'-triphosphate with reduced efficiency, and kinetic analysis of ATPase activity suggested that it is due to decreased affinity for ATP. In contrast, the 85 kDa form was unable to bind ATP, in the presence or absence of ssDNA and, consequently, was entirely devoid of ATPase activity. Molecular modeling studies suggested that the decreased affinity of MtRecA protein for ATP and the reduced efficiency of its hydrolysis might be due to the widening of the cleft which alters the hydrogen bonds and the contact area between the enzyme and the substrate and changes in the disposition of the amino acid residues around the magnesium ion and the gamma-phosphate. The formation of joint molecules promoted by MtRecA protein was stimulated by SSB when the former was added first. The probability of an association between the lack and partial levels of biological activity of RecA protein(s) to that of illegitimate recombination in pathogenic mycobacteria is considered.

Multivalent ligand presentation as a central concept to study intricate carbohydrate-protein interactions

Studying the weak binding affinities between carbohydrates and proteins has been a central theme in sustained efforts to uncover intricate details of this class of biomolecular interaction. The amphiphilic nature of most carbohydrates, the competing nature of the surrounding water molecules to a given protein receptor site and the receptor binding site characteristics led to the realization that carbohydrates are required to exert favorable interactions, primarily through clustering of the ligands. The clustering of sugar ligands has been augmented using many different innovative molecular scaffolds. The synthesis of clustered ligands also facilitates fine-tuning of the spatial and topological proximities between the ligands, so as to allow the identification of optimal molecular features for significant binding affinity enhancements. The kinetic and thermodynamic parameters have been delineated in many instances, thereby allowing an ability to correlate the multivalent presentation and the observed ligand-receptor interaction profiles. This critical review presents various multivalent ligands, synthetic and semisynthetic, and mechanisms by which the weak binding affinities are overcome, and the ligand-receptor complexation leads to significantly enhanced binding affinities (157 references).

The Role of UPF0157 in the Folding of M-tuberculosis Dephosphocoenzyme A Kinase and the Regulation of the Latter by CTP

Background: Targeting the biosynthetic pathway of Coenzyme A (CoA) for drug development will compromise multiple cellular functions of the tubercular pathogen simultaneously. Structural divergence in the organization of the penultimate and final enzymes of CoA biosynthesis in the host and pathogen and the differences in their regulation mark out the final enzyme, dephosphocoenzyme A kinase (CoaE) as a potential drug target. Methodology/Principal Findings: We report here a complete biochemical and biophysical characterization of the M. tuberculosis CoaE, an enzyme essential for the pathogen's survival, elucidating for the first time the interactions of a dephosphocoenzyme A kinase with its substrates, dephosphocoenzyme A and ATP; its product, CoA and an intrinsic yet novel inhibitor, CTP, which helps modulate the enzyme's kinetic capabilities providing interesting insights into the regulation of CoaE activity. We show that the mycobacterial enzyme is almost 21 times more catalytically proficient than its counterparts in other prokaryotes. ITC measurements illustrate that the enzyme follows an ordered mechanism of substrate addition with DCoA as the leading substrate and ATP following in tow. Kinetic and ITC experiments demonstrate that though CTP binds strongly to the enzyme, it is unable to participate in DCoA phosphorylation. We report that CTP actually inhibits the enzyme by decreasing its Vmax. Not surprisingly, a structural homology search for the modeled mycobacterial CoaE picks up cytidylmonophosphate kinases, deoxycytidine kinases, and cytidylate kinases as close homologs. Docking of DCoA and CTP to CoaE shows that both ligands bind at the same site, their interactions being stabilized by 26 and 28 hydrogen bonds respectively. We have also assigned a role for the universal Unknown Protein Family 0157 (UPF0157) domain in the mycobacterial CoaE in the proper folding of the full length enzyme. Conclusions/Significance: In view of the evidence presented, it is imperative to assign a greater role to the last enzyme of Coenzyme A biosynthesis in metabolite flow regulation through this critical biosynthetic pathway.

Mutational analysis of active-site residues in the Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease: Asp(122) and Asp(193) are crucial to the double-stranded DNA cleavage activity whereas Asp(218) is not

Mycobacterium leprae recA harbors an in-frame insertion sequence that encodes an intein homing endonuclease (PI-MleI). Most inteins (intein endonucleases) possess two conserved LAGLIDADG (DOD) motifs at their ctive center. A common feature of LAGLIDADG-type homing endonucleases is that they recognize and cleave the same or very similar DNA sequences. However, PI-MleI is distinctive from other members of the family of LAGLIDADG-type HEases for its modular structure with functionally separable domains for DNA-binding and cleavage, each with distinct sequence preferences. Sequence alignment analyses of PI-MleI revealed three putative LAGLIDADG motifs; however, there is conflicting bioinformatics data in regard to their identity and specific location within the intein polypeptide. To resolve this conflict and to determine the active-site residues essential for DNA target site recognition and double-stranded DNA cleavage, we performed site-directed mutagenesis of presumptive catalytic residues in the LAGLIDADG motifs. Analysis of target DNA recognition and kinetic parameters of the wild-type PI-MleI and its variants disclosed that the two amino acid residues, Asp(122) (in Block C) and Asp(193) (in functional Block E), are crucial to the double-stranded DNA endonuclease activity, whereas Asp(218) (in pseudo-Block E) is not. However, despite the reduced catalytic activity, the PI-MleI variants, like the wild-type PI-MleI, generated a footprint of the same length around the insertion site. The D122T variant showed significantly reduced catalytic activity, and D122A and D193A mutations although failed to affect their DNA-binding affinities, but abolished the double-stranded DNA cleavage activity. On the other hand, D122C variant showed approximately twofold higher double-stranded DNA cleavage activity, compared with the wild-type PI-MleI. These results provide compelling evidence that Asp(122) and Asp(193) in DOD motif I and II, respectively, are bona fide active-site residues essential for DNA cleavage activity. The implications of these results are discussed in this report.

The RecA intein of Mycobacterium tuberculosis promotes cleavage of ectopic DNA sites. Implications for the dispersal of inteins in natural populations

The RecA intein of Mycobacterium tuberculosis, a novel double-stranded DNA endonuclease, requires both Mn(2+) and ATP for efficient cleavage of the inteinless recA allele. In this study, we show that Mg(2+) alone was sufficient to stimulate PI-MtuI to cleave double-stranded DNA at ectopic sites. In the absence of Mg(2+), PI-MtuI formed complexes with topologically different forms of DNA containing ectopic recognition sequences with equal affinity but failed to cleave DNA. We observed that PI-MtuI was able to inflict double-strand breaks robustly within the ectopic recognition sequence to generate either a blunt end or 1-2-nucleotide 3'-hydroxyl overhangs. Mutational analyses of the presumptive metal ion-binding ligands (Asp(122), Asp(222), and Glu(220)) together with immunoprecipitation assays provided compelling evidence to link both the Mg(2+)- and Mn(2+) and ATP-dependent endonuclease activities to PI-MtuI. The kinetic mechanism of PI-MtuI promoted cleavage of ectopic DNA sites proceeded through a sequential mechanism with transient accumulation of nicked circular duplex DNA as an intermediate. Together, these data suggest that PI-MtuI, like group II introns, might mediate ectopic DNA transposition and hence its lateral transfer in natural populations.

Abatement of fluoride from water using manganese dioxide-coated activated alumina

Batch adsorption of fluoride onto manganese dioxide-coated activated alumina (MCAA) has been studied. Adsorption experiments were carried out at various pH (3–9), time interval (0–6 h), adsorbent dose (1–16 g/l), initial fluoride concentration (1–25 mg/l) and in the presence of different anions. Adsorption isotherms have been modeled using Freundlich, Langmuir and Dubinin–Raduskevich isotherms and adsorption followed Langmuir isotherm model. Kinetic studies revealed that the adsorption followed second-order rate kinetics. MCAA could remove fluoride effectively (up to 0.2 mg/l) at pH 7 in 3 h with 8 g/l adsorbent dose when 10 mg/l of fluoride was present in 50 ml of water. In the presence of other anions, the adsorption of fluoride was retared. The mechanism of fluoride uptake by MCAA is due to physical adsorption as well as through intraparticle diffusion which was confirmed by kinetics, Dubinin–Raduskevich isotherm, zeta-potential measurements and mapping studies of energy-dispersive analysis of X-ray.

Characterization of hot deformation behavior of Zr-1Nb-1Sn alloy

The hot deformation behavior of beta-quenched Zr-1 Nb-1Sn was studied in the temperature range 650-1050 degrees C and strain rate range 0.001-100 s(-1) using processing maps. These maps revealed three different domains: a domain of dynamic recovery at temperatures <700 degrees C and at strain rates <3 x 10(-3) s(-1), a domain of dynamic recrystallization in the temperature range 750-950 C-degrees and at strain rates <10(-2) S-1 with a peak at 910 degrees C and 10(-3) S-1 (in alpha + beta phase field), and a domain of large-grain superplasticity in the beta phase field at strain rates <10(-2) s(-1). In order to identify the rate controlling mechanisms involved in these domains, kinetic analysis was carried out to determine the various activation parameters. In addition, the processing maps showed a regime of flow instability spanning both alpha + beta and beta phase fields. The hot deformation behavior of Zr 1Nb-1Sn was compared with that of Zr, Zr-2.5Nb and Zircaloy-2 to bring out the effects of alloy additions. (C) 2006 Elsevier BN. All rights reserved.

Kinetics of photocatalytic reduction of NO by CO with Pd2+-Ion-Substituted Nano-TiO2

The objective of the present study is to develop the reaction mechanism and kinetics of photoreduction of NO by CO. For this purpose, the reactions were conducted in the presence of Pd-ion-substituted nano-TiO2, Ti1-xPdxO2-delta, which was synthesized via a solution combustion method. The photocatalytic activity was investigated with unsubstituted TiO2, 1% Pd/TiO2(imp), and Ti1-xPdxO2-delta (where x = 0.05-0.3). No appreciable NO conversion was observed over unsubstituted TiO2, although, despite competitive adsorption of NO and CO on the Pd2+ sites, there was a significant reduction of NO over Ti1-xPdxO2-delta. The kinetic model showed that the enhanced catalytic activity is due to the NO photodissociation at the oxide-ion vacancy.

Enhanced adsorption capacity of activated alumina by impregnation with alum for removal of As(V) from water

Alum-impregnated activated alumina (AIAA) was investigated in the present work as an adsorbent for the removal of As(V) from water by batch mode. Adsorption study at different pH values shows that the efficiency of AIAA is much higher than as such activated alumina and is suitable for treatment of drinking water. The adsorption isotherm experiments indicated that the uptake of As(V) increased with increasing As(V) concentration from 1 to 25 mg/l and followed Langmuir-type adsorption isotherm. Speciation diagram shows that in the pH range of 2.8–11.5, arsenate predominantly exists as H2AsO4− and HAsO42− species and hence it is presumed that these are the major species being adsorbed on the surface of AIAA. Intraparticle diffusion and kinetic studies revealed that adsorption of As(V) was due to physical adsorption as well as through intraparticle diffusion. Effect of interfering ions revealed that As(V) sorption is strongly influenced by the presence of phosphate ion. The presence of arsenic on AIAA is depicted from zeta potential measurement, scanning electron microscopy (SEM) and energy-dispersive analysis of X-ray (EDAX) mapping study. Alum-impregnated activated alumina successfully removed As(V) to below 40 ppb (within the permissible limit set by WHO) from water, when the initial concentration of As(V) is 10 mg/l.

Lifting the singular nature of a model for peeling of an adhesive tape

We investigate the dynamics of peeling of an adhesive tape subjected to a constant pull speed. Due to the constraint between the pull force, peel angle and the peel force, the equations of motion derived earlier fall into the category of differential-algebraic equations (DAE) requiring an appropriate algorithm for its numerical solution. By including the kinetic energy arising from the stretched part of the tape in the Lagrangian, we derive equations of motion that support stick-slip jumps as a natural consequence of the inherent dynamics itself, thus circumventing the need to use any special algorithm. In the low mass limit, these equations reproduce solutions obtained using a differential-algebraic algorithm introduced for the earlier singular equations. We find that mass has a strong influence on the dynamics of the model rendering periodic solutions to chaotic and vice versa. Apart from the rich dynamics, the model reproduces several qualitative features of the different waveforms of the peel force function as also the decreasing nature of force drop magnitudes.

Rheology of dense sheared granular flows

Rapid granular flows are defined as flows in which the time scales for the particle interactions are small compared to the inverse of the strain rate, so that the particle interactions can be treated as instantaneous collisions. We first show, using Discrete Element simulations, that even very dense flows of sand or glass beads with volume fraction between 0.5 and 0.6 are rapid granular flows. Since collisions are instantaneous, a kinetic theory approach for the constitutive relations is most appropriate, and we present kinetic theory results for different microscopic models for particle interaction. The significant difference between granular flows and normal fluids is that energy is not conserved in a granular flow. The differences in the hydrodynamic modes caused by the non-conserved nature of energy are discussed. Going beyond the Boltzmann equation, the effect of correlations is studied using the ring kinetic approximation, and it is shown that the divergences in the viscometric coefficients, which are present for elastic fluids, are not present for granular flows because energy is not conserved. The hydrodynamic model is applied to the flow down an inclined plane. Since energy is not a conserved variable, the hydrodynamic fields in the bulk of a granular flow are obtained from the mass and momentum conservation equations alone. Energy becomes a relevant variable only in thin 'boundary layers' at the boundaries of the flow where there is a balance between the rates of conduction and dissipation. We show that such a hydrodynamic model can predict the salient features of a chute flow, including the flow initiation when the angle of inclination is increased above the 'friction angle', the striking lack of observable variation of the volume fraction with height, the observation of a steady flow only for certain restitution coefficients, and the density variations in the boundary layers.

One-dimensional zig-zag type coordination polymers of Ni(II) and Cu(II) containing 1,3-benzenedicarboxylate and 1,3-diaminopropane: Structural, spectral and thermal studies

Two coordination polymers [Ni(ipt)(dap)(2)](n) (1) and [Cu(ipt)(dap)H2O](n) center dot nH(2)O (2) with an overall one-dimensional arrangement and having isophthalate (ipt) as bridging moieties and chelating 1,3-diaminopropane (dap) as structure modulating units have been prepared and characterized by crystallographic, spectroscopic and thermo-analytical studies. Both have an overall one-dimensional zig-zag nature but with a distorted octahedral NiN4O2 chromophore for 1 and a distorted square pyramidal CuN2O3 chromophore for 2. Even though the ipt units are acting as bridging units through mono-dentatively coordinating carboxylate functions in both polymers, compound 1 has the carboxylate oxygen linkages at the trans positions, while in 2 the oxygen linkages occur at the cis positions leading to a different type of zig-zag arrangement. Relevant spectral and bonding parameters also could be evaluated for the compounds using UV-Vis and EPR spectra. Thermal stability and possible structural modifications on thermal treatment of the compounds were also investigated and the relevant thermodynamic and kinetic parameters evaluated from the thermal data. (C) 2007 Elsevier B.V. All rights reserved.

Thermal Characteristics of SrO-2B(2)O(3) Glasses

Transparent SrO-2B(2)O(3) (SBO) glasses were fabricated via the conventional melt-quenching technique. X-ray diffraction (XRD) and differential thermal analysis (DTA) studies carried out on the as-quenched glasses confirmed their amorphous and glassy nature, respectively. The thermal parameters were evaluated for the as-quenched glass-plates using non-isothermal DTA experiments. The average values of the activation energies for the glass transition and crystallization of these glasses were 800 +/- 10 kJ/mol and 298 +/- 10 kJ/mol respectively. The values of the kinetic parameters that were obtained by different non-isothermal techniques were in close agreement.

Characterization of an N6 adenine methyltransferase from Helicobacter pylori strain 26695 which methylates adjacent adenines on the same strand

Genomic sequences of Helicobacter pylori strains 26695, J99, HPAGI and G27 have revealed an abundance of restriction and modification genes. hp0050, which encodes an N6 adenine DNA methyltransferase, was cloned, overexpressed and purified to near homogeneity. It recognizes the sequence 5'-GRRG-3' (where R is A or G) and, most intriguingly, methylates both adenines when R is A (5'-GAAG-3'). Kinetic analysis suggests a nonprocessive (repeated-hit) mechanism of methylation in which HP0050 methyltransferase methylates one adenine at a time in the sequence 5'-GAAG-3'. This is the first report of an N6 adenine DNA methyltransferase that methylates two adjacent residues on the same strand. Interestingly, HP0050 homologs from two clinical strains of H. pylori (PG227 and 128) methylate only 5'-GAGG-3' compared with 5'-GRRG-3' in strain 26695. HP0050 methyltransferase is highly conserved as it is present in more than 90% of H. pylori strains. Inactivation of hp0050 in strain PG227 resulted in poor growth, suggesting its role in the biology of H. pylori. Collectively, these findings provide impetus for exploring the role(s) of this conserved DNA methyltransferase in the cellular processes of H. pylori.

Modeling of formation of gold nanoparticles by citrate method

Properties of nanoparticles are size dependent, and a model to predict particle size is of importance. Gold nanoparticles are commonly synthesized by reducing tetrachloroauric acid with trisodium citrate, a method pioneered by Turkevich et al (Discuss. Faraday Soc. 1951, 11, 55). Data from several investigators that used this method show that when the ratio of initial concentrations of citrate to gold is varied from 0.4 to similar to 2, the final mean size of the particles formed varies by a factor of 7, while subsequent increases in the ratio hardly have any effect on the size. In this paper, a model is developed to explain this widely varying dependence. The steps that lead to the formation of particles are as follows: reduction of Au3+ in solution, disproportionation of Au+ to gold atoms and their nucleation, growth by disproportionation on particle surface, and coagulation. Oxidation of citrate results in the formation of dicarboxy acetone, which aids nucleation but also decomposes into side products. A detailed kinetic model is developed on the basis of these steps and is combined with population balance to predict particle-size distribution. The model shows that, unlike the usual balance between nucleation and growth that determines the particle size, it is the balance between rate of nucleation and degradation of dicarboxy acetone that determines the particle size in the citrate process. It is this feature that is able to explain the unusual dependence of the mean particle size on the ratio of citrate to gold salt concentration. It is also found that coagulation plays an important role in determining the particle size at high concentrations of citrate.