Purification and characterization of assimilatory nitrite reductase from Candida utilis

Nitrate assimilation in many plants, algae, yeasts and bacteria is mediated by two enzymes, nitrate reductase (EC 1.6.6.2) and nitrite reductase (EC 1.7.7.1). They catalyse the stepwise reduction of nitrate to nitrite and nitrite to ammonia respectively. The nitrite reductase from an industrially important yeast, Candida utilis, has been purified to homogeneity. Purified nitrite reductase is a heterodimer and the molecular masses of the two subunits are 58 and 66 kDa. The native enzyme exhibits a molecular mass of 126 kDa as analysed by gel filtration. The identify of the two subunits of nitrite reductase was confirmed by immunoblotting using antibody for Cucurbita pepo leaf nitrite reductase. The presence of two different sized transcripts coding for the two subunits was confirmed by (a) in vitro translation of mRNA from nitrate-induced C. utilis followed by immunoprecipitation of the in vitro translated products with heterologous nitrite reductase antibody and (b) Northern-blot analysis. The 66 kDa subunit is acidic in nature which is probably due to its phosphorylated status. The enzyme is stable over a range of temperatures. Both subunits can catalyse nitrite reduction, and the reconstituted enzyme, at a higher protein concentration, shows an activity similar to that of the purified enzyme. Each of these subunits has been shown to contain a few unique peptides in addition to a large number of common peptides. Reduced Methyl Viologen has been found to be as effective an electron donor as NADPH in the catalytic process, a phenomenon not commonly seen for nitrite reductases from other systems.

Effect of soil variability on the bearing capacity of clay and in slope stability problems

Site-specific geotechnical data are always random and variable in space. In the present study, a procedure for quantifying the variability in geotechnical characterization and design parameters is discussed using the site-specific cone tip resistance data (qc) obtained from static cone penetration test (SCPT). The parameters for the spatial variability modeling of geotechnical parameters i.e. (i) existing trend function in the in situ qc data; (ii) second moment statistics i.e. analysis of mean, variance, and auto-correlation structure of the soil strength and stiffness parameters; and (iii) inputs from the spatial correlation analysis, are utilized in the numerical modeling procedures using the finite difference numerical code FLAC 5.0. The influence of consideration of spatially variable soil parameters on the reliability-based geotechnical deign is studied for the two cases i.e. (a) bearing capacity analysis of a shallow foundation resting on a clayey soil, and (b) analysis of stability and deformation pattern of a cohesive-frictional soil slope. The study highlights the procedure for conducting a site-specific study using field test data such as SCPT in geotechnical analysis and demonstrates that a few additional computations involving soil variability provide a better insight into the role of variability in designs.

Two highly unsymmetrical tetradentate (N3O) Schiff base copper(II) complexes: Template synthesis, structural characterization, magnetic and computational studies

Two new copper(II) complexes, [Cu-2(L-1)(2)](ClO4)(2) (1) and [Cu(L-2)(ClO4)] (2), of the highly unsymmetrical tetradentate (N3O) Schiff base ligands HL1 and HL2 (where HL1 = N-(2-hydroxyacetophenone)-bis-3-aminopropylamine and HL2 = N-(salicyldehydine)-bis-3-aminopropylamine) have been synthesised using a template method. Their single crystal X-ray structures show that in complex 1 two independent copper(II) centers are doubly bridged through sphenoxo-O atoms (O1A and O1B) of the two ligands and each copper atom is five-coordinated with a distorted square pyramidal geometry. The asymmetric unit of complex 2 consists of two crystallographically independe N-(salicylidene) bis(aminopropyl)amine-copper(II) molecules, A and B, with similar square pyramidal geometries. Cryomagnetic susceptibility measurements (5-300 K) on complex 1 reveal a distinct antiferromagnetic interaction with J=-23.6 cm(-1), which is substantiated by a DFT calculation (J=-27.6 cm(-1)) using the B3LYP functional. Complex 1, immobilized over highly ordered hexagonal mesoporous silica, shows moderate catalytic activity for the epoxidation of cyclohexene and styrene in the presence of TBHP as an oxidant.

Photocytotoxic Oxovanadium(IV) Complexes Showing Light-Induced DNA and Protein Cleavage Activity

Oxovanadium(IV) complexes [VO(L)(B)]Cl-2 (1-3), where L is bis(2-benzimidazolylmethyl)amine and B is 1,10-phenanthroline(phen),dipyrido[3,2-d:2',3'-f]quinoxaline(dpq) or dipyrido[3,2-a:2',3'-c]phenazine (dppz), have been prepared, characterized, and their photo-induced DNA and protein cleavage activity studied. The photocytotoxicity of complex 3 has been studied using adenocarcinoma A549 cells, The phen complex 1, structurally characterized by single-crystal X-ray crystallography, shows the presence of a vanadyl group in six-coordinate VON5 coordination geometry. The ligands L and phen display tridentate and bidentate N-donor chelating binding modes, respectively. The complexes exhibit a d-d band near 740 nm in 15% DMF-Tris-HCl buffer (pH 7.2). The phen and dpq complexes display an irreversible cathodic cyclic voltammetric response near -0.8 V in 20% DMF-Tris-HCl buffer having 0.1 M KCl as supporting electrolyte. The dppz complex 3 exhibits a quasi-reversible voltammogram near -0.6 V (vs SCE) that is assignable to the V(IV)-V(III)couple. The complexes bind to calf thymus DNA giving binding constant values in the range of 6.6 x 10(4)-2.9 x 10(5) M-1. The binding site size, thermal melting and viscosity binding data suggest DNA surface and/or groove binding nature of the complexes. The complexes show poor ``chemical nuclease'' activity in dark in the presence of 3-mercaptopropionic acid or hydrogen peroxide. The dpq and dppz complexes are efficient photocleavers of plasmid DNA in UV-A light of 365 nm via a mechanistic pathway that involves formation of both singlet oxygen and hydroxyl radicals. The complexes show significant photocleavage of DNA in near-IR light (>750 nm) via hydroxyl radical pathway. Among the three complexes, the dppz complex 3 shows significant BSA and lysozyme protein cleavage activity in UV-A light of 365 nm via hydroxyl radical pathway. The dppz complex 3 also exhibits photocytotoxicity in non-small cell lung carcinoma/human lung adenocarcinoma A549 cells giving IC50 value of 17 mu M in visible light(IC50 = 175 mu M in dark).

Understanding solvent effects on structure and reactivity of organic intermediates: a Raman study

The effect of solvent on chemical reactivity has generally been explained on the basis of the dielectric constant and viscosity. However a number of spectroscopic studies, including UV-VIS, IR and Raman, has led to numerous empirical parameters to define solvent effect based on either solvating ability or polarity scale. These parameters include solvent polarizability, dipolarity, Lewis acidity and Lewis basicity, E-T(30), pi*, alpha, beta etc. However, from a structural point of view, we can separate solvation as static and dynamic processes. The static solvation basically relates to stabilization of the molecular structure by the solvent to attain the equilibrium structure, both in the intermediate and ground state. Dynamic solvation relates to solvent reorganization-induced dynamics prior to the structural reorganization to reach the equilibrium state. In this paper, we present (a) structural distortions induced by the solvent due to preferential solvation of the triplet excited state, and (b) the importance of dynamic solvation induced by vibronic coupling (pseudo-Jahn-Teller coupling). The examples include the effect of solvent on structure and reactivity of excited states of 2,2,2-trifluoroacetophenone (TFA). Based on the comparison of time resolved resonance Raman (TR3) data of TFA and other substituted acetophenone systems, it was found that change in solvent polarity indeed results in electronic state switching and structural changes in the excited state, which explains the trend in reactivity. Further, a TR3 study of fluoranil (FA) in the triplet excited state in solvents of varying polarities indicates that the structure of FA in the triplet excited state is determined by vibronic coupling effects and thus distorted structure. These experimental results have been well supported by density functional theoretical computational studies.

Isoperimetric Problem and Meta-fibonacci Sequences

Let G = (V,E) be a simple, finite, undirected graph. For S ⊆ V, let $\delta(S,G) = \{ (u,v) \in E : u \in S \mbox { and } v \in V-S \}$ and $\phi(S,G) = \{ v \in V -S: \exists u \in S$ , such that (u,v) ∈ E} be the edge and vertex boundary of S, respectively. Given an integer i, 1 ≤ i ≤ ∣ V ∣, the edge and vertex isoperimetric value at i is defined as b e (i,G) =  min S ⊆ V; |S| = i |δ(S,G)| and b v (i,G) =  min S ⊆ V; |S| = i |φ(S,G)|, respectively. The edge (vertex) isoperimetric problem is to determine the value of b e (i, G) (b v (i, G)) for each i, 1 ≤ i ≤ |V|. If we have the further restriction that the set S should induce a connected subgraph of G, then the corresponding variation of the isoperimetric problem is known as the connected isoperimetric problem. The connected edge (vertex) isoperimetric values are defined in a corresponding way. It turns out that the connected edge isoperimetric and the connected vertex isoperimetric values are equal at each i, 1 ≤ i ≤ |V|, if G is a tree. Therefore we use the notation b c (i, T) to denote the connected edge (vertex) isoperimetric value of T at i. Hofstadter had introduced the interesting concept of meta-fibonacci sequences in his famous book “Gödel, Escher, Bach. An Eternal Golden Braid”. The sequence he introduced is known as the Hofstadter sequences and most of the problems he raised regarding this sequence is still open. Since then mathematicians studied many other closely related meta-fibonacci sequences such as Tanny sequences, Conway sequences, Conolly sequences etc. Let T 2 be an infinite complete binary tree. In this paper we related the connected isoperimetric problem on T 2 with the Tanny sequences which is defined by the recurrence relation a(i) = a(i − 1 − a(i − 1)) + a(i − 2 − a(i − 2)), a(0) = a(1) = a(2) = 1. In particular, we show that b c (i, T 2) = i + 2 − 2a(i), for each i ≥ 1. We also propose efficient polynomial time algorithms to find vertex isoperimetric values at i of bounded pathwidth and bounded treewidth graphs.

Conformation of the flexible bent helix of Leu1-zervamicin in crystal C and a possible gating action for ion passage

The membrane channel-forming polypeptide, Leu(1)-zervamicin, Ac-Leu-Ile-Gln-Iva-Ile(5)-Thr-Aib-Leu-Aib-Hyp(10) -Gln-Aib-Hyp-Aib-Pro(15)-Phol (Aib: alpha-aminoisobutyric acid; Iva: isovaline; Hyp: 4-hydroxyproline; Phol: phenylalininol) has been analyzed by x-ray diffraction in a third crystal form. Although the bent helix is quite similar to the conformations found in crystals A and B, the amount of bending is more severe with a bending angle approximate to 47 degrees, The water channel formed by the convex polar faces of neighboring helices is larger at the mouth than in crystals A and B, and the water sites have become disordered. The channel is interrupted in the middle by a hydrogen bond between the OH of Hyp(10) and the NH2 of the Gln(11) of a neighboring molecule. The side chain of Gln(11) is wrapped around the helix backbone in an unusual fashion in order that it can augment the polar side of the helix. In the present crystal C there appears to be an additional conformation for the Gln(11) side chain (with approximate to 20% occupancy) that opens the channel for possible ion passage. Structure parameters for C85H140N18O22.xH(2)O.C2H5OH are space group P2(1)2(1)2(1), a = 10.337 (2) Angstrom, b = 28.387 (7) Angstrom, c = 39.864 (11) Angstrom, Z = 4, agreement factor R = 12.99% for 3250 data observed > 3 sigma(F), resolution = 1.2 Angstrom. (C) 1994 John Wiley & Sons, Inc.

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.

Topography of the combining region of a Thomsen-Friedenreich-antigen-specific lectin jacalin (Artocarpus integrifolia agglutinin). A thermodynamic and circular-dichroism spectroscopic study

Thermodynamic analysis of carbohydrate binding by Artocarpus integrifolia (jackfruit) agglutinin (jacalin) shows that, among monosaccharides, Me alpha GalNAc (methyl-alpha-N-acetylgalactosamine) is the strongest binding ligand. Despite its strong affinity for Me alpha GalNAc and Me alpha Gal, the lectin binds very poorly when Gal and GalNAc are in alpha-linkage with other sugars such as in A- and B-blood-group trisaccharides, Gal alpha 1-3Gal and Gal alpha 1-4Gal. These binding properties are explained by considering the thermodynamic parameters in conjunction with the minimum energy conformations of these sugars. It binds to Gal beta 1-3GalNAc alpha Me with 2800-fold stronger affinity over Gal beta 1-3GalNAc beta Me. It does not bind to asialo-GM1 (monosialoganglioside) oligosaccharide. Moreover, it binds to Gal beta 1-3GalNAc alpha Ser, the authentic T (Thomsen-Friedenreich)-antigen, with about 2.5-fold greater affinity as compared with Gal beta 1-3GalNAc. Asialoglycophorin A was found to be about 169,333 times stronger an inhibitor than Gal beta 1-3GalNAc. The present study thus reveals the exquisite specificity of A. integrifolia lectin for the T-antigen. Appreciable binding of disaccharides Glc beta 1-3GalNAc and GlcNAc beta 1-3Gal and the very poor binding of beta-linked disaccharides, which instead of Gal and GalNAc contain other sugars at the reducing end, underscore the important contribution made by Gal and GalNAc at the reducing end for recognition by the lectin. The ligand-structure-dependent alterations of the c.d. spectrum in the tertiary structural region of the protein allows the placement of various sugar units in the combining region of the lectin. These studies suggest that the primary subsite (subsite A) can accommodate only Gal or GalNAc or alpha-linked Gal or GalNAc, whereas the secondary subsite (subsite B) can associate either with GalNAc beta Me or Gal beta Me. Considering these factors a likely arrangement for various disaccharides in the binding site of the lectin is proposed. Its exquisite specificity for the authentic T-antigen, Gal beta 1-3GalNAc alpha Ser, together with its virtual non-binding to A- and B-blood-group antigens, Gal beta 1-3GalNAc beta Me and asialo-GM1 should make A. integrifolia lectin a valuable probe for monitoring the expression of T-antigen on cell surfaces.

Syntheses of the trans,meso- and racemic C11 acids, degradation products of diterpene acids

Syntheses of the isomers of the C11 acid, 1(a),3(a)- dimethylcyclohexane-1 (e),2(e),3(e)-tricarboxylic acid (A) and 1(a),3(e)-dimethylcyclohexane-1(e),2(e),3(a)-tricarboxylic acid (B), the latter by two different routes, are reported. Two of the four possible isomers of the precursor triester, trimethyl 1-methylcyclohexane-1,2,3-tricarboxylate, on individual methylation followed by hydrolysis, gave the trans,meso-acid (A), identified by comparison with an authentic sample, and the cis,trans-form (B) whose structure and configuration were proved by comparison with a specimen obtained by the unambiguous and highly stereoselective second synthesis. This demonstrated that methylation of the triester isomers occurs stereospecifically and exclusively at C-3. In the second sequence, it has been possible to assign definite conformations to four key intermediates and the final product, directly from n.m.r. spectra, from changes in these spectra accompanying specific steps, and from chemical evidence. Comparison of the n.m.r. spectra of the isomeric triesters (A) and (B) has provided unequivocal proof of the accepted trans,meso configuration for the abietic acid degradation product (A).

The interaction of glycoxylate with cysteine and its application to the assay of isocitritase and of transaminases involving glyoxylate

An interesting interaction between glyoxylate and cystein takes place in phosphate buffer (pH 7.0) to form a product which is resistant to hydrolysis at ordinary temperatures. The reaction product is broken up by acid hydrolysis at elevated temperatures under controlled conditions, giving a quantitive yield of glyoxylate. Other keto acids, such as α-ketoglutarate, pyruvate and oxaloacetate, do not interact with cysteine under similar conditions. Methods based on these findings are described for(a) direct estimation of other keto acids in the presence of glyoxylate, and (b) assay of isocitritase and glyoxylate transaminase.

Saturated liquid densities of cryogenic liquids and refrigerants

The saturated liquid density, varrholr, data along the liquid vapour coexistence curve published in the literature for several cryogenic liquids, hydrocarbons and halocarbon refrigerants are fitted to a generalized equation of the following form varrholr = 1 + A(1 − Tr + B(1 − Tr)β The values of β, the index in phase density differences power law, have been obtained by means of two approaches namely statistical treatment of saturated fluid phase density difference data and the existence of a maximum in T(varrho1 − varrhov) along the saturation curve. Values of the constants A and B are determined utilizing the fact that Tvarrho1 has a maximum at a characteristic temperature T. Values of A, B and β are tabulated for Ne, Ar, Kr, Xe, N2, O2, methane, ethane, propane, iso-butane, n-butane, propylene, ethylene, CO2, water, ammonia, refrigerants-11, 12, 12B1, 13, 13B1, 14, 21, 22, 23, 32, 40, 113, 114, 115, 142b, 152a, 216, 245 and azeotropes R-500, 502, 503, 504. The average error of prediction is less than 2%.

Photocytotoxicity and DNA cleavage activity of L-arg and L-lys Schiff base oxovanadium(IV) complexes having phenanthroline bases

Oxovanadium(IV) complexes [VO(sal-argH)(B)] Cl (1-3) and [VO(sal-lysH)(B)] Cl (4-6), where sal-argH2 and sal-lysH(2) are N-salicylidene-L-arginine and N-salicylidene-L-lysine Schiff bases and B is a phenanthroline base, viz. 1,10-phenanthroline (phen in 1 and 4); dipyrido[3,2-d: 2', 3'-f] quinoxaline (dpq in 2 and 5) and dipyrido[3,2-a: 2', 3'-c] phenazine (dppz in 3 and 6), have been prepared, characterized and their DNA photocleavage activity studied. Complex 1, characterized by X-ray crystallography, shows the presence of a vanadyl group in VIVO3N3 coordination geometry with a tridentate Schiff base having a pendant guanidinium moiety and bidentate phen ligand. The complexes exhibit a d-d band at similar to 715 nm in 20% DMF-Tris-HCl buffer. The complexes are redox active showing cathodic and anodic responses near -1.0 V and 0.85 V (vs. SCE) for the V(IV)-V(III) and V(V)-V(IV) couples, respectively, in DMF-Tris-HCl buffer. The complexes bind to calf thymus DNA giving Kb values in the range of 3.8 x 10(4) to 1.6 x 10(5) M-1. Thermal denaturation and viscosity data suggest DNA groove binding nature of the complexes. The complexes do not show any `chemical nuclease'' activity in dark in the presence of 3-mercaptopropionic acid or H2O2. The dpq and dppz complexes are efficient photocleavers of plasmid DNA in UV-A (365 nm) and red light (676 nm) via singlet oxygen pathway. The dppz complexes exhibit photocytotoxicity in HeLa cancer cells giving IC50 values of 15.4 mu M for 3 and 17.5 mu M for 6 in visible light while being non-toxic in dark giving IC50 values of > 100 mu M.

A self-consistent formulation for analysis and generation of non-uniform DNA structure

A fully self-consistent formulation is described here for the analysis and generation of base-pairs in non-uniform DNA structures, in terms of various local parameters. It is shown that the internal "wedge parameters" are mathematically related to the parameters describing the base-pair orientation with respect to an external helix axis. Hence any one set of three translation and three rotation parameters are necessary and sufficient to completely describe the relative orientation of the base-pairs comprising a step (or doublet). A general procedure is outlined for obtaining an average or global helix axis from the local helix axes for each step. A graphical representation of the local helix axes in the form of a polar plot is also shown and its application for estimating the curvature of oligonucleotide structures is illustrated, with examples of both A and B type structures.

Ferrocene-Promoted Photoactivated DNA Cleavage and Anticancer Activity of Terpyridyl Copper(II) Phenanthroline Complexes

Ferrocene-appended copper(II) complexes [Cu( Fc-tpy)(B)](ClO4)(2) (1-3) and [Cu(Ph-tpy)(dppz)](ClO4)(2) (4) as control, where Fc-tpy is 4'-ferroceny1-2,2':6',2 ''-terpyridine, Ph-tpy is 4'-pheny1-2,2':6',2 ''-terpyridine, and B is a phenanthroline base, viz., 1,10-phenanthroline (phen, 1), dipyridoquinoxaline (dpq, 2), and dipyridophenazine (dppz, 3), were prepared and structurally characterized, and their DNA binding, photoactivated DNA cleavage activity, and cytotoxic properties were studied [Fe = (eta(5)-C5H4)Fe-11(eta(5)-C5H5)]. Complexes 1 and 3 as hexafluorophosphate salts were structurally characterized by X-ray crystallography. Molecular structures of [Cu(Fc-tpy)(phen)](PF6)(2) (1a) and [Cu(Fc-tpy)(dppz)](PF6)(2)center dot MeCN (3a center dot MeCN) show a distorted square-pyramidal geometry at copper(II), with the Fc-tpy ligand and the phenanthroline base showing respective tridentate and bidentate binding modes. The phenanthroline base exhibits axial-equatorial bonding, while the Fc-tpy ligand binds at the basal plane. The complexes showed quasi-reversible cyclic voltammetric responses near 0.45 and -0.3 V vs SCE in aqueous DMF-0.1 M KCl assignable to the Fc(+)-Fc and Cu(II) Cu(1) redox couples, respectively. The complexes bind to DNA, giving K-b values of 1.4 x 10(4) to 5.6 x 10(5) M-1 in the order 4 similar to 3 > 2 > 1. Thermal denaturation and viscometric titration data suggest groove and/or partial intercalative mode of DNA binding of the complexes. The complexes showed chemical nuclease activity in the presence of 3-mercaptopropionic acid (0.5 mM) or H2O2 (0.25 mM). Complexes 2-4 showed plasmid DNA cleavage activity in visible light, forming (OH)-O-center dot radicals. The Fc-tpy complex 3 showed better DNA photocleavage activity than its Ph-tpy analogue. The ferrocene moiety in the dppz complex 3 makes it more photocytotoxic than the Ph-tpy analogue 4 in HeLa cells.