Purification of 3,5-Dichlorocatechol 1,2-Dioxygenase, a Nonheme Iron Dioxygenase and a Key Enzyme in the Biodegradation of a Herbicide, 2,4-Dichlorophenoxyacetic acid (2,4-D), from Pseudomonas cepacia CSV90

An enzyme which cleaves the benzene ring of 3,5-dichiorocatechol has been purified to homogeneity from Pseudomonas cepacia CSV90, grown with 2,4-dichlorophenoxyacetic acid (2,4-D) as the sole carbon source. The enzyme was a nonheme ferric dioxygenase and catalyzed the intradiol cleavage of all the examined catechol derivatives, 3,5-dichlorocatechol having the highest specificity constant of 7.3 μM−1 s−1 in an air-saturated buffer. No extradiol-cleaving activity was observed. Thus, the enzyme was designated as 3,5-dichlorocatechol 1,2-dioxygenase. The molecular weight of the native enzyme was ascertained to be 56,000 by light scattering method, while the Mr value of the enzyme denatured with 6 M guanidine-HCl or sodium dodecyl sulfate was 29,000 or 31,600, respectively, suggesting that the enzyme was a homodimer. The iron content was estimated to be 0.89 mol per mole of enzyme. The enzyme was deep red and exhibited a broad absorption spectrum with a maximum at around 425 nm, which was bleached by sodium dithionite, and shifted to 515 nm upon anaerobic 3,5-dichlorocatechol binding. The catalytic constant and the Km values for 3,5-dichlorocatechol and oxygen were 34.7 s−1 and 4.4 and 652 μM, respectively, at pH 8 and 25°C. Some heavy metal ions, chelating agents and sulfhydryl reagents inhibited the activity. The NH2-terminal sequence was determined up to 44 amino acid residues and compared with those of the other catechol dioxygenases previously reported.

Solubility of sulfur dioxide at low partial pressures in dilute sulfuric acid solutions

Equilibrium of dissolution of sulfur dioxide at ppm levels in aqueous solutions of dilute sulfuric acid is analyzed, and a general expression is derived relating the total concentration of sulfur dioxide in the liquid phase to the partial pressure of SO2 in the gas and to the concentration of sulfuric acid in the solution. The equation is simplified for zero and high concentrations of the acid. Experiments at high concentrations of sulfuric acid have enabled the direct determination of Henry’s constant and its dependency on temperature. Heat of dissolution is -31.47 kJ/mol. Experiments in the absence of sulfuric acid and the related simplified expression have led to the determination of the equilibrium constant of the hydrolysis of aqueous sulfur dioxide and its temperature dependency.The heat of hydrolysis is 15.69 kJ/mol. The model equation with these parameters predicts the experimental data of the present work as well as the reported data very well.

Structure of Sesbania Mosaic Virus at 4·7 Å Resolution and Partial Sequence of the Coat Protein

Sesbania mosaic virus (SMV) is a plant virus infecting Sesbania grandiflora plants in Andhra Pradesh, India. Amino acid sequence of the tryptic peptides of SMV coat protein were determined using a gas phase sequenator. These sequences showed identical amino acids at 69% of the positions when aligned with the corresponding residues of southern bean mosaic virus (SBMV).Crystals diffracting to better than 3 Å resolution were obtained by precipitating the virus with ammonium sulphate. The crystals belonged to rhombohedral space group R3 with α = 291·4 Å and α = 61·9°. Three-dimensional X-ray diffraction data on these crystals were collected to a resolution of 4·7 Å, using a Siemens-Nicolet area detector system. Self-rotation function studies revealed the icosahedral symmetry of the virus particles, as well as their precise orientation in the unit cell. Cross-rotation function and modelling studies with SBMV showed that it is a valid starting model for SMV structure determination. Low resolution phases computed using a polyalanine model of SBMV were subjected to refinement and extension by real-space electron density averaging and solvent flattening. The final electron density map revealed a polypeptide fold similar to SBMV. The single disulphide bridge of SBMV coat protein is retained in SMV. Four icosahedrally independent cation binding sites have been tentatively identified. Three of these sites, related by a quasi threefold axis, are also found in SBMV. The fourth site is situated on the quasi threefold axis. Aspartic acid residues, which replace Ile218 of SBMV from the quasi threefold-related subunits are suitable ligands to the cation at this site

Functional Analysis of an Acid Adaptive DNA Adenine Methyltransferase from Helicobacter pylori 26695

HP0593 DNA-(N-6-adenine)-methyltransferase (HP0593 MTase) is a member of a Type III restriction-modification system in Helicobacter pylori strain 26695. HP0593 MTase has been cloned, overexpressed and purified heterologously in Escherichia coli. The recognition sequence of the purified MTase was determined as 5'-GCAG-3' and the site of methylation was found to be adenine. The activity of HP0593 MTase was found to be optimal at pH 5.5. This is a unique property in context of natural adaptation of H. pylori in its acidic niche. Dot-blot assay using antibodies that react specifically with DNA containing m6A modification confirmed that HP0593 MTase is an adenine-specific MTase. HP0593 MTase occurred as both monomer and dimer in solution as determined by gel-filtration chromatography and chemical-crosslinking studies. The nonlinear dependence of methylation activity on enzyme concentration indicated that more than one molecule of enzyme was required for its activity. Analysis of initial velocity with AdoMet as a substrate showed that two molecules of AdoMet bind to HP0593 MTase, which is the first example in case of Type III MTases. Interestingly, metal ion cofactors such as Co2+, Mn2+, and also Mg2+ stimulated the HP0593 MTase activity. Preincubation and isotope partitioning analyses clearly indicated that HP0593 MTase-DNA complex is catalytically competent, and suggested that DNA binds to the MTase first followed by AdoMet. HP0593 MTase shows a distributive mechanism of methylation on DNA having more than one recognition site. Considering the occurrence of GCAG sequence in the potential promoter regions of physiologically important genes in H. pylori, our results provide impetus for exploring the role of this DNA MTase in the cellular processes of H. pylori.

Hybrid Polypeptides: Gabapentin as a Stereochemically Constrained gamma-Amino Acid Residue

The design of folded structures in peptides containing the higher homologues of alpha-amino acid residues requires the restriction of the range of local conformational choices In alpha-amino acids stereochemically constrained residues like alpha,alpha-dialkylated residue, aminoisobutyric acid (Aib), and D-Proline ((D)Pro) have proved extremely useful in the design of helices and hairpins in short peptides Extending this approach, backbone substitution and cyclization are anticipated to bc useful in generating conformationally constrained beta- and gamma-residues This brief review provides a survey of work on hybrid peptide sequences concerning the conformationally constrained gamma-amino acid residue 1-aminomethyl cyclohexane acetic acid, gabapentin (Gpn) This achiral, beta,beta-disubstituted, gamma-residue strongly favors gauche-gauche conformations about the C-alpha-C-beta (0(2)) and C-alpha-C-gamma (0(1)) bonds, facilitating local folding The Gpn residue can adopt both C-7 (NH1 -> CO1) and C-9 (CO1 (I)<- NH1+I) hydrogen bonds which are analogous to the C-5 and C7 (gamma-turn) conformations at alpha-residues In conjunction with adjacent residues, Gpn may be used in ay and gamma alpha segments to generate C-12 hydrogen bonded conformations which may be considered as expanded analogs of conventional beta-turns The structural characterization of C-12 helices, C-12/C-10 helices with mixed hydrogen bond directionalities and beta-hairpins incorporating Gpn residues at the turn segment is illustrated (C) 2010 Wiley Periodicals, Inc Biopolymers (Pept Sci) 94 733-741 2010

Cement stabilised rammed earth. Part A: compaction characteristics and physical properties of compacted cement stabilised soils

Rammed earth is used for load bearing walls of buildings and there is growing interest in this low carbon building material. This paper is focused on understanding the compaction characteristics and physical properties of compacted cement stabilised soil mixtures and cement stabilised rammed earth (CSRE). This experimental study addresses (a) influence of soil composition, cement content, time lag on compaction characteristics of stabilised soils and CSRE and (b) effect of moulding water content and density on compressive strength and water absorption of compacted cement stabilised soil mixes. Salient conclusions of the study are (a) compaction characteristics of soils are not affected by the addition of cement, (b) there is 50% fall in strength of CSRE for 10 h time lag, (c) compressive strength of compacted cement stabilised soil increases with increase in density irrespective of moulding moisture content and cement content, and (d) compressive strength increases with the increase in moulding water content and compaction of CSRE on the wet side of OMC is beneficial in terms of strength.

An Approach Toward Homocalystegines and Silyl-homocalystegines. Acid-Mediated Migrations of Acetates in Seven-Membered Ring Systems

A short access to homocalystegine analogues silylated at C7 is described. The synthesis involves the desymmetrization of a (phenyldimethylsilyl)methylcycloheptatriene using osmium-mediated dihydroxylation, followed by the diol protection and a cycloaddition involving the remaining diene moiety and an acylnitroso reagent. Additions of the osmium and acylnitroso reagents were shown, through X-ray diffraction studies of the resulting major isomers, to occur anti and syn, respectively, relative to the SiCH2 substituent. N-O bond cleavage on the resulting cycloadduct then produces the aminopolyol having a silylmethyl substituent. Oxidation of the C-Si bond also afforded an access to unusual amino-heptitols having five contiguous stereogenic centers. In the course of this work, we finally observed a unusual rearrangement taking place on cycloheptanone 18 substituted by two acetyl groups and a neighboring Boc-protected amine. A profound reorganization of the substituents on the seven-membered ring effectively took place under acidic conditions (TFA) leading to the thermodynamically more stable homocalystegine-type compound., DFT calculations of the conformational energy of isomeric silyl homocalystegines indicated that the product observed upon the acid-mediated rearrangement was the most stable of a series of analogues with various distributions of substituents along the seven-membered ring backbone. A tentative mechanism is proposed to rationalize the acetate migrations and inversions of the stereochemistry at various stereocenters.

Amino acid selective unlabeling for sequence specific resonance assignments in proteins

Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective `unlabeling' or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly C-13/N-15 labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {(CO)-C-12 (i) -N-15 (i+1)}-filtered HSQC, which aids in linking the H-1(N)/N-15 resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i - 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to H-2 labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of N-14 at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies.

A β,β,β-trialkoxyethyllithium stable towards fragmentation: a carboxyl protected acetic acid dianion equivalent

The novel alkyllithium 1b is not only intriguingly stable towards fragmentation, but also a synthetically useful reagent, complementing current carboxylic ester enolate methodology. Its design is based on interesting mechanistic principles, and harnesses the known stability of the 2,4,10-trioxaadamantane framework.

Analysis of the effects of amino-acid-sequence on the structure of proteins

The conformation of amino acid side chains as observed in well-determined structures of globular proteins has earlier been extensively investigated. In contrast, the structural features of the polypeptide backbone that result from the occurrence of specific amino acids along the polypeptide have not been analysed. In this article, we present the statistically significant features in the backbone geometry that appear to be a consequence of the occurrence of rotamers of different amino acid side chains by analysing 102 well-refined structures that form a random collection of proteins. It is found that the persistence of helical segments around each residue is influenced by the residue type. Several residues exert asymmetrical influence between the carboxyl and amino terminal polypeptide segments. The degree to which secondary structures depart from an average geometry also appears to depend on residue type. These departures are correlated to the corresponding Chou and Fasman parameters of amino acid residues. The frequency distribution of the side chain rotamers is influenced by polypeptide secondary structure. In turn, the rotamer conformation of side chain affects the extension of the secondary structure of the backbone. The strongest correlation is found between the occurrence of g+ conformation and helix propagation on the carboxyl side of many residues.

Generalized State Parameter for Partly Saturated Soils

Studies on compressibility and shear strength aspects are the concern of many investigators concerned with partly saturated soils. In soil engineering connected with partly saturated soils, there are no approaches connecting soil states and stress conditions. The present investigation is essentially a step in this direction. A generalized state parameter, identified with regard to material states is shown to be related to the compressibility and shear strength. The involved parameters are simple and normally determined in routine investigations. The advantage of this approach is that changes in soil states due to external stress conditions and the associated changes in strength can be examined particularly when different types of soils are involved.

Liquid-Liquid Interphase (Biphasic) as the Reaction Medium in the Assembly of a Hierarchy of Structures of 4,4 `-Azodibenzoic Acid with Zinc and Cadmium

The compounds Zn(C12H8N2)](2)C12N2H8(COO)(2)](2)center dot(C6H12O)center dot(H2O), I, Zn(C12H8N2)]C12N2H8(COO)(2)], II, Cd(C12H8N2)(H2O)]C12N2H8(COO)(2)]center dot(H2O), III, Zn(C10N2H8)]C12N2H8(COO)(2)]center dot 0.5(C10N2H8), IV, Cd(C12N2H8(COO)(2)center dot H2O], V, and Zn-3(mu(2)-O)(mu(3)-O)(3)]C12N2H8(COO)(2)], VI, have been synthesized by using a biphasic approach (I, III, V, VI) or regular hydrothermal method (II, IV). The compounds exhibit one (I and II), two (In), and three dimensionally (IV, V, VI) extended structures. The flexible azodibenzoate ligand gives rise to a 3-fold interpenetration (IV) when the synthesis was carried out using normal hydrothermal methods. The biphasic approach forms structures without any interpenetrations, especially in the three-dimensional structures of V and VI. Formation of Cd2O2 dimers in V and extended M-O(H)-M two-dimensional layers in VI suggests the subtle structural control achieved by the biphasic method. Transformation studies indicate that it is possible to transform I to II. Lewis acid catalytic studies have been performed to evaluate the role of the coordination environment in such reactions. All the compounds have been characterized by a variety of techniques that includes powder X-ray diffraction, infrared, thermogravitric analysis, UV-vis, photoluminescence studies.