Sequence Specific Interaction between Promoter DNA and Escherichia coli RNA Polymerase: Comparative Thermodynamic Analysis with One Immobilized Partner

Sequence specific interaction between DNA and protein molecules has been a subject of active investigation for decades now. Here, we have chosen single promoter containing bacteriophage Delta D-III T7 DNA and Escherichia coli RNA polymerase and followed their recognition at the air-water interface by using the surface plasmon resonance (SPR) technique, where the movement of one of the reacting species is restricted by way of arraying them on an immobilized support. For the Langmuir monolayer studies, we used a RNA polymerase with a histidine tag attached to one of its subunits, thus making it an xcellent substrate for Ni(II) ions, while the SPR Studies were done using biotin-labeled DNA immobilized on a streptavidin-coated chip. Detailed analysis of the thermodynamic parameters as a function of concentration and temperature revealed that the interaction of RNA polymerase with T7 DNA is largely entropy driven (83 (+/- 12) kcal mol(-1)) with a positive enthalpy of 13.6 (+/- 3.6) kcal mol(-1), The free energy of reaction determined by SPR and Langmuir-Blodgett technique was -11 (+/- 2) and -15.6 kcal mol(-1), respectively. The ability of these methods to retain the specificity of the recognition process was also established.

Effect of surfactants on the fluorescence spectra of water-soluble MEHPPV derivatives having grafted polyelectrolyte chains

Poly(2-methoxy-5-[2'-ethylhexyoxy]-1,4-phenylenevinylene) (MEHPPV) derivatives with polyacrylic acid (PAA) chains grafted onto their backbone were found to be water soluble, and they exhibited a dramatic increase in their fluorescence intensity in the presence of a variety of surfactants, even at concentrations far below their critical micelle concentrations (CMC). This increase was accompanied by a blue-shift in the emission maximum. These observations are rationalized based on the postulate that the backbone conformation of the conjugated polymer is modulated upon interaction of the surfactant molecules with the polyelectrolytic tethers, which in turn results in a significant depletion of intra-chain interchromophore interactions that are known to cause red-shifted emission bands with significantly lower emission yields.

Hydrophobic Peptide Channels and Encapsulated Water Wires

Peptide nanotubes with filled and empty pores and close-packed structures are formed in closely related pentapeptides. Enantiomorphic sequences, Boc-(D)Pro-Aib-Xxx-Aib-Val-OMe (Xxx = Leu, 1; Val, 2; Ala, 3; Phe, 4) and Boc-Pro-Aib-(D)Xxx-Aib-(D)Val-OMe ((XXX)-X-D = (D)Leu, 5; (D)Val, 6; (D)Ala, 7; (D)Phe, 8), yield molecular structures with a very similar backbone conformation but varied packing patterns in crystals. Peptides 1, 2, 5, and 6 show tubular structures with the molecules self-assembling along the crystallographic six-fold axis (c-axis) and revealing a honeycomb arrangement laterally (ab plane). Two forms of entrapped water wires have been characterized in 2: 2a with d(O center dot center dot center dot O) = 2.6 angstrom and 2b with d(O center dot center dot center dot O) = 3.5 angstrom. The latter is observed in 6 (6a) also. A polymorphic form of 6 (6b), grown from a solution of methanol-water, was observed to crystallize in a monoclinic system as a close-packed structure. Single-file water wire arrangements encapsulated inside hydrophobic channels formed by peptide nanotubes could be established by modeling the published structures in the cases of a cyclic peptide and a dipeptide. In all the entrapped water wires, each water molecule is involved in a hydrogen bond with a previous and succeeding water molecule. The O-H group of the water not involved in any hydrogen bond does not seem to be involved in an energetically significant interaction with the nanotube interior, a general feature of the one-dimensional water wires encapsulated in hydrophobic environements. Water wires in hydrophobic channels are contrasted with the single-file arrangements in amphipathic channels formed by aquaporins.

Optimizing a piezometric network in the estimation of the groundwater budget: a case study from a crystalline-rock watershed in southern India

An estimate of the groundwater budget at the catchment scale is extremely important for the sustainable management of available water resources. Water resources are generally subjected to over-exploitation for agricultural and domestic purposes in agrarian economies like India. The double water-table fluctuation method is a reliable method for calculating the water budget in semi-arid crystalline rock areas. Extensive measurements of water levels from a dense network before and after the monsoon rainfall were made in a 53 km(2)atershed in southern India and various components of the water balance were then calculated. Later, water level data underwent geostatistical analyses to determine the priority and/or redundancy of each measurement point using a cross-validation method. An optimal network evolved from these analyses. The network was then used in re-calculation of the water-balance components. It was established that such an optimized network provides far fewer measurement points without considerably changing the conclusions regarding groundwater budget. This exercise is helpful in reducing the time and expenditure involved in exhaustive piezometric surveys and also in determining the water budget for large watersheds (watersheds greater than 50 km(2)).

Interaction of heterocyclic thiols/thiones eliminated from cephalosporins with iodine and its biological implications

Hydrolysis of beta-lactam antibiotics by beta-lactamases (e. g., metallo-beta-lactamase, m beta l) is one of the major bacterial defense systems. These enzymes can catalyze the hydrolysis of a variety of antibiotics including the latest generation of cephalosporins, cephamycins and imipenem. It is shown in this paper that the thiol/thione moieties eliminated from certain cephalosporins by m beta l-mediated hydrolysis readily react with molecular iodine to produce ionic compounds having S-I bonds. While the reaction of MTT with iodine produced the corresponding disulfide, MDT and DMETT produced the charge-transfer complexes MDT-I-2 and DMETT-I-2, respectively. Addition of two equivalents of I-2 to MDT produced a novel cationic complex having an almost linear S-I+-S moiety and I-5(-) counter anion.However, this reaction appears to be highly solvent dependent. When the reaction of MDT with I2 was carried out in water, the reaction produced a monocation having I-5(-), indicating the reactivity of MDT toward I2 is very similar to that of the most commonly used antithyroid drug methimazole (MMI). In contrast to MMI, MDT and DMETT, the triazine-based compound MTDT acts as a weak donor toward iodine. (C)2010 Elsevier Ltd. All rights reserved.

Contribution of different physical forces to the disjoining pressure of a thin water film being pressed by an oil droplet

With an objective to understand the nature of forces which contribute to the disjoining pressure of a thin water film on a steel substrate being pressed by an oil droplet, two independent sets of experiments were done. (i) A spherical silica probe approaches the three substrates; mica, PTFE and steel, in a 10 mM electrolyte solution at two different pHs (3 and 10). (ii) The silica probe with and without a smeared oil film approaches the same three substrates in water (pH = 6). The surface potential of the oil film/water was measured using a dynamic light scattering experiment. Assuming the capacity of a substrate for ion exchange the total interaction force for each experiment was estimated to include the Derjaguin-Landau-Verwey-Overbeek (DLVO) force, hydration repulsion, hydrophobic attraction and oil-capillary attraction. The best fit of these estimates to the force-displacement characteristics obtained from the two sets of experiment gives the appropriate surface potentials of the substrates. The procedure allows an assessment of the relevance of a specific physical interaction to an experimental configuration. Two of the principal observations of this work are: (i) The presence of a surface at constant charge, as in the presence of an oil film on the probe, significantly enhances the counterion density over what is achieved when both the surfaces allow ion exchange. This raises the corresponding repulsion barrier greatly. (ii) When the substrate surface is wettable by oil, oil-capillary attraction contributes substantially to the total interaction. If it is not wettable the oil film is deformed and squeezed out. (C) 2010 Elsevier Inc. All rights reserved.

Single-File Diffusion of Water Inside Narrow Carbon Nanorings

We use atomistic molecular dynamics (MD) simulations to study the diffusion of water molecules confined inside narrow (6,6) carbon nanorings. The water molecules form two oppositely polarized chains. It is shown that the effective interaction between these two chains is repulsive in nature. The computed mean-squared displacement (MSD) clearly shows a scaling with time similar to t(1/2), which is consistent with single-file diffusion (SFD). The time up to which the water molecules undergo SFD is shown to be the lifetime of the water molecules inside these chains. Simulations of "uncharged" water molecules inside the nanoring show the formation of several water chains and yield SFD. These observations conclusively prove that the diffusion is Fickian when there is a single chain of water and SFD is observed only when two or more chains are present.

X-Ray structure of a ternary complex, copper(II)–lnosine 5-monophosphate–benzimidazole. The first example for the absence of direct metal–nucleotide interaction

The unprecedented absence of direct metal–nucleotide interaction has been observed in the X-ray structure of the ternary metal nucleotide system [Cu(bzim)(H2O)5]2+[IMP]2–·3H2O [IMP = inosine 5-monophosphate(2–), bzim = benzimidazole). The complex crystallizes in the space group P21 with a= 7.013(2), b= 13.179(9), c= 14.565(9)Å, = 94.82(4)°, and Z= 2. The structure was solved by the heavy-atom method and refined by full-matrix least squares on the basis of 1 761 observed (I? 3i) reflections to final R and R values of 0.034 and 0.036 respectively. The CuII has a distorted octahedral co-ordination with a nitrogen of the bzim ligand [Cu–N 1.947(5)Å] and three oxygens of water molecules in the basal plane [mean Cu–O 2.017(3)Å] and two more water oxygens at axial positions [Cu–O 2.194(6) and 2.732(5)Å]. The nucleotide base stacks with the bzim ligand at an average distance of 3.5 Å and an angle of 22°. In the lattice, N(7) of the base is linked to a lattice water through a hydrogen bond, while all the phosphate oxygens are involved in hydrogen bonds with co-ordinated as well as lattice water molecules. The co-ordination behaviour of IMP to CuII is compared in structures containing different -aromatic amines in order to assess the influence of the ternary ligand in complex formation. The present results indicate that, apart from the commonly observed phosphate binding, other modes of co-ordination are possible, these being influenced mainly by the -accepting properties of the ternary ligand.

Interaction between the Z-type DNA duplex and 1,3-propanediamine:crystal structure of d(CACGTG)(2) at 1.2 angstrom resolution

The crystal structure of a hexamer duplex d(CACGTG)(2) has been determined and refined to an R-factor of 18.3% using X-ray data up to 1.2 angstrom resolution. The sequence crystallizes as a left-handed Z-form double helix with Watson-Crick base pairing. There is one hexamer duplex, a spermine molecule, 71 water molecules, and an unexpected diamine (Z-5, 1,3-propanediamine, C3H10N2)) in the asymmetric unit. This is the high-resolution non-disordered structure of a Z-DNA hexamer containing two AT base pairs in the interior of a duplex with no modifications such as bromination or methylation on cytosine bases. This structure does not possess multivalent cations such as cobalt hexaammine that are known to stabilize Z-DNA. The overall duplex structure and its crystal interactions are similar to those of the pure-spermine form of the d(CGCGCG)(2) structure. The spine of hydration in the minor groove is intact except in the vicinity of the T5A8 base pair. The binding of the Z-5 molecule in the minor grove of the d(CACGTG)(2) duplex appears to have a profound effect in conferring stability to a Z-DNA conformation via electrostatic complementarity and hydrogen bonding interactions. The successive base stacking geometry in d(CACGTG)(2) is similar to the corresponding steps in d(CG)(3). These results suggest that specific polyamines such as Z-5 could serve as powerful inducers of Z-type conformation in unmodified DNA sequences with AT base pairs. This structure provides a molecular basis for stabilizing AT base pairs incorporated into an alternating d(CG) sequence.

Interaction of metal ions with 6-oxopurine nucleotides. Part 1. X-Ray structures of ternary cobalt(III) complexes with inosine 5'-monophosphate or guanosine 5'-monophosphate

The crystal structures of two ternary metal nucleotide complexes of cobalt, [Co(en)2(H2O)2]-[Co(5?-IMP)2(H2O)4]Cl2·4H2O (1) and [Co(en)2(H2O)2][Co(5?-GMP)2(H2O)4]Cl2·4H2O (2), have been analysed by X-ray diffraction (en = ethylenediamine, 5?-IMP = inosine 5?-monophosphate, and 5?-GMP = guanosine 5?-monophosphate). Both complexes crystallize in the orthorhombic space group C2221 with a= 8.725(1), b= 25.891(5), c= 21.212(5)Å, Z= 4 for (1) and a= 8.733(2), b= 26.169(4), c= 21.288(4)Å, Z= 4 for (2). The structure of (1) was solved by the heavy-atom method, while that of (2) was deduced from (1). The structures were refined to R values of 0.09 and 0.10 for 1 546 and 1 572 reflections for (1) and (2) respectively. The two structures are isomorphous. A novel feature is that the chelate ligand en and the nucleotide are not co-ordinated to the same metal ion. One of the metal ions lying on the two-fold a axis is octahedrally co-ordinated by two chelating en molecules and two water oxygens, while the other on the two-fold b axis is octahedrally co-ordinated by two N(7) atoms of symmetry-related nucleotides in a cis position and four water oxygens. The conformations of the nucleotides are C(2?)-endo, anti, and gauche�gauche. In both (1) and (2) the charge-neutralising chloride ions are disordered in the vacant space between the molecules. These structures bear similarities to the mode of nucleotide co-ordination to PtII complexes of 6-oxopurine nucleotides, which are the proposed models for intrastrand cross-linking in DNA by a metal complex.

Support-Dependent Activity of Noble Metal Substituted Oxide Catalysts for the Water Gas Shift Reaction

The water gas shift reaction was carried out over noble metal ion substituted nanocrystalline oxide catalysts with different supports. Spectroscopic studies of the catalysts before and after the reaction showed different surface phenomena occurring over the catalysts. Reaction mechanisms were proposed based upon the surface processes and intermediates formed. The dual site mechanism utilizing the oxide ion vacancies for water dissociation and metal ions for CO adsorption was proposed to describe the kinetics of the reaction over the reducible oxides like CeO2. A mechanism based on the interaction of adsorbed CO and the hydroxyl group was proposed for the reaction over ZrO2. A hybrid mechanism based on oxide ion vacancies and surface hydroxyl groups was proposed for the reaction over TiO2. The deactivation of the catalysts was also found to be support dependent. Kinetic models for both activation and deactivation were proposed. (C) 2010 American Institute of Chemical Engineers AIChE J, 56: 2662-2676, 2010

Sonochemical synthesis of Ce1-xFexO2-delta (0 <= x <= 0.45) and Ce0.65Fe0.33Pd0.02O2-delta nanocrystallites: oxygen storage material, CO oxidation and water gas shift catalyst

Nanocrystalline Ce1-xFexO2-delta (0 <= x <= 0.45) and Ce0.65Fe0.33Pd0.02O2-delta of similar to 4 nm sizes were synthesized by a sonochemical method using diethyletriamine (DETA) as a complexing agent. Compounds were characterized by powder X-ray diffraction (XRD), X-ray photo-electron spectroscopy (XPS) and transmission electron microscopy (TEM). Ce1-xFexO2-delta (0 <= x <= 0.45) and Ce0.65Fe0.33Pd0.02O2-delta crystallize in fluorite structure where Fe is in +3, Ce is in +4 and Pd is in +2 oxidation state. Due to substitution of smaller Fe3+ ion in CeO2, lattice oxygen is activated and 33% Fe substituted CeO2 i.e. Ce0.67Fe0.33O1.835 reversibly releases 0.31O] up to 600 degrees C which is higher or comparable to the oxygen storage capacity of CeO2-ZrO2 based solid solutions (Catal. Today 2002, 74, 225-234). Due to interaction of redox potentials of Pd2+/0(0.89 V) and Fe3+/2+ (0.77 V) with Ce4+/3+ (1.61 V), Pd ion accelerates the electron transfer from Fe2+ to Ce4+ in Ce0.65Fe0.33Pd0.02O1.815, making it a high oxygen storage material as well as a highly active catalyst for CO oxidation and water gas shift reaction. The activation energy for CO oxidation with Ce0.65Fe0.33Pd0.02O1.815 is found to be as low as 38 kJ mol(-1). Ce0.67Fe0.33O1.835 and Ce0.65Fe0.33Pd0.02O1.815 have also shown high activity for the water gas shift reaction. CO conversion to CO2 is 100% H-2 specific with these catalysts and conversion rate was found to be as high 27.2 mu moles g(-1) s(-1) and the activation energy was found to be 46.4 kJ mol(-1) for Ce0.65Fe0.33Pd0.02O1.815.

Ions in water: Role of attractive interactions in size dependent diffusivity maximum

A molecular dynamics study of model ions in water is reported. The van der Waals diameter of both the cations and anions is varied. We have carried out two sets of simulations-with and without dispersion interaction-between the ion and water. Self-diffusivity of the ions exhibits an anomalous maximum as a function of the van der Waals diameter for both these sets. This existence of a maximum in self-diffusivity when there is no dispersion interaction between the ion and the water is attributed to the attractive term from electrostatic interactions. Detailed analysis of this effect shows that the solvent shell is more strongly defined in the presence of dispersion interactions. A smaller ion exhibits biexponential decay while a single exponential decay is seen for the ion with maximum diffusivity in the self-part of the intermediate scattering function. The solvent structure around the ion appears to determine much of the dynamics of the ion. Interesting trends are seen in the activation energies and these can be understood in terms of the levitation effect. (C) 2010 American Institute of Physics. doi:10.1063/1.3481656]

Ab initio molecular orbital calculations on ion-molecule and ion pair-molecule complexes of the water-lithium cyanide system

Ab initio molecular orbital (MO) calculations with the 3-21G and 6-31G basis sets were performed on a series of ion-molecule and ion pair-molecule complexes for the H2O + LiCN system. Stabilisation energies (with counter-poise corrections), geometrical parameters, internal force constants and harmonic vibrational frequencies were evaluated for 16 structures of interest. Although the interaction energies are smaller, the geometries and relative stabilities of the monohydrated contact ion pair are reminiscent of those computed for the complexes of the individual ions. Thus, interaction of the oxygen lone pair with lithium leads to a highly stabilised C2v structure, while the coordination of water to the cyanide ion involves a slightly non-linear hydrogen bond. Symmetrical bifurcated structures are computed to be saddle points on the potential energy surface, and to have an imaginary frequency for the rocking mode of the water molecule. On optimisation the geometries of the solvent shared ion pair structures (e.g. Li+cdots, three dots, centered OH2cdots, three dots, centered CN−) revealed a proton transfer from the water molecule leading to hydrogen bonded forms such as Li-O-Hcdots, three dots, centered HCN. The variation in the force constants and harmonic frequencies in the various structures considered are discussed in terms of ion-molecular and ion pair-molecule interactions.

Ab initio molecular orbital calculations on ion pair-water complexes of metal halides and oxides

Ab initio MO calculations are performed on a series of ion-molecular and ion pair-molecular complexes of H2O + MX (MX = LiF, LiCl, NaCl, BeO and MgO) systems. BSSE-corrected stabilization energies, optimized geometrical parameters, internal force constants and harmonic vibrational frequencies have been evaluated for all the structures of interest. The trends observed in the geometrical parameters and other properties calculated for the mono-hydrated contact ion pair complexes parallel those computed for the complexes of the individual ions. The bifurcated structures are found to be saddle points with an imaginary frequency corresponding to the rocking mode of water molecules. The solvent-shared ion pair complexes have high interaction energies. Trends in the internal force constant and harmonic frequency values are discussed in terms of ion-molecular and ion-pair molecular interactions.