Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease

The role of invariant water molecules in the activity of plant cysteine protease is ubiquitous in nature. On analysing the 11 different Protein DataBank (PDB) structures of plant thiol proteases, the two invariant water molecules W I and W2 (W220 and W222 in the template 1PPN structure) were observed to form H-bonds with the Ob atom of Asn 175. Extensive energy minimization and molecular dynamics simulation studies up to 2 ns on all the PDB and solvated structures clearly revealed the involvement of the H-bonding association of the two water molecules in fixing the orientation of the asparagine residue of the catalytic triad. From this study, it is suggested that H-bonding of the water molecule at the W1 invariant site better stabilizes the Asn residue at the active site of the catalytic triad.

Mechanism of catalytic activity of metal oxides and chromites on ammonium perchlorate pyrolysis

This study investigates the mechanism of action of transition metal chromites on the decomposition of ammonium perchlorate.

Ultrafine powders of SrTiO3 from the hydrothermal preparation and their catalytic activity in the photolysis of water

Ultrafine powders of SrTiO3 are prepared at 100–150°C by the hydrothermal method, starting from TiO2·xH2O gel and Sr(OH)2 and H2O-isopropanol mixed solvent as the medium, The X-ray diffractograms of the powder show line broadening. The minimum crystallite size obtained ranges from 5 to 20nm with 20% H2O-80% C3H7OH as the reaction medium, as estimated from X-ray half-peak widths and TEM studies. The electron diffraction results indicate high concentration of lattice defects in these crystallites. The optical spectra of the particle suspensions in water show that the absorption around the band gap is considerably broadened, together with the appearance of maxima in the far ultraviolet. Aqueous suspensions of SrTiO3 powders, as such, do not produce H2 or O2 on UV irradiation. After coating with rhodium, H2 and O2 are evolved on illumination. However, the turn over number of O2 is lower than the stoichiometrically expected values from the corresponding values of H2. No correlation of the photocatalytic activity with surface area is observed. The activity of Rh-SrTiO3 slowly deteriorates with extended period of irradiation.

Structures of mannose-6-phosphate isomerase from Salmonella typhimurium bound to metal atoms and substrate: implications for catalytic mechanism

Mannose-6-phosphate isomerase (MPI) catalyzes the inter-conversion of mannose 6-phosphate and fructose 6-phosphate. X-ray crystal structures of MPI from Salmonella typhimurium in the apo form (with no metal bound) and in the holo form (with bound Zn2+) and two other structures with yttrium bound at an inhibitory site and complexed with Zn2+ and fructose 6-phosphate (F6P) were determined in order to gain insights into the structure and the isomerization mechanism. Isomerization involves acid/base catalysis with proton transfer between the C1 and C2 atoms of the substrate. His99, Lys132, His131 and Asp270 are close to the substrate and are likely to be the residues involved in proton transfer. The interactions observed at the active site suggest that the ring-opening step is probably catalyzed by His99 and Asp270. An active-site loop consisting of residues 130-133 undergoes conformational changes upon substrate binding. Zn2+ binding induces structural order in the loop consisting of residues 50-54. The metal atom appears to play a role in substrate binding and is probably also important for maintaining the architecture of the active site. Isomerization probably follows the previously suggested cis-enediol mechanism.

Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase.The role of conserved residues and complementary mutations

The active site of triosephosphate isomerase (TIM, EC: 5.3.1.1), a dimeric enzyme, lies very close to the subunit interface. Attempts to engineer monomeric enzymes have yielded well-folded proteins with dramatically reduced activity. The role of dimer interface residues in the stability and activity of the Plasmodium falciparum enzyme, PfTIM, has been probed by analysis of mutational effects at residue 74. The PfTIM triple mutant W11F/W168F/Y74W (Y74W*) has been shown to dissociate at low protein concentrations, and exhibits considerably reduced stability in the presence of denaturants, urea and guanidinium chloride. The Y74W* mutant exhibits concentration-dependent activity, with an approximately 22-fold enhancement of kcat over a concentration range of 2.5–40 μm, suggesting that dimerization is obligatory for enzyme activity. The Y74W* mutant shows an approximately 20-fold reduction in activity compared to the control enzyme (PfTIM WT*, W11F/W168F). Careful inspection of the available crystal structures of the enzyme, together with 412 unique protein sequences, revealed the importance of conserved residues in the vicinity of the active site that serve to position the functional K12 residue. The network of key interactions spans the interacting subunits. The Y74W* mutation can perturb orientations of the active site residues, due to steric clashes with proximal aromatic residues in PfTIM. The available crystal structures of the enzyme from Giardia lamblia, which contains a Trp residue at the structurally equivalent position, establishes the need for complementary mutations and maintenance of weak interactions in order to accommodate the bulky side chain and preserve active site integrity.

Analysis of proteins with the `hot dog' fold: Prediction of function and identification of catalytic residues of hypothetical proteins

Background: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme A-binding enzymes with a variety of substrates located at their active sites. Results: We have analyzed the structural features and sequences of proteins having the hot dog fold. This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization. Segments with certain conserved sequence motifs seem to play crucial structural and functional roles in various classes of these proteins. Conclusion: The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects.

Effectiveness factor for zeroth-order catalytic reactions with volume change and nonuniform catalyst activity profiles

Analytical solutions are presented for the effectiveness factor of a zeroth-order reaction with volume change and nonuniform catalyst activity profile in slab, cylinder and spherical pellets. The possibility of shape normalization is considered for a variety of activity profiles and pellet shapes. When the catalyst activity at the external surface of the pellet is non-zero, shape normalization is obtained, which makes the asymptotic behavior of the effectiveness factor identical for small and large values of Thiele modulus, however, the normalization can lead to significant errors, particularly for the case of activity profiles decreasing towards the outer surface of the catalyst.

Evaluation of rumen fatty acid hydrogenation intermediates and differences in bacterial communities after feeding wheat- or corn-based dried distillers grains to feedlot cattle

The effect of partially replacing rolled barley (86.6% of control diet) with 20% wheat dried distillers grains plus solubles (DDGS), 40% wheat DDGS, 20% corn DDGS, or 40% corn DDGS (dietary DM basis) on rumen fluid fatty acid (FA) composition and some rumen bacterial communities was evaluated using 100 steers (20 per treatment). Wheat DDGS increased the 11t-to 10t-18:1 ratio (P < 0.05) in rumen fluid and there was evidence that the conversion of trans-18:1 to 18:0 was reduced in the control and wheat DDGS diets but not in the corn DDGS diet. Bacterial community profiles obtained using denaturing gradient gel electrophoresis and evaluated by Pearson correlation similarity matrices were not consistent for diet and, therefore, these could not be linked to different specific rumen FA. This inconsistency may be related to the nature of diets fed (dominant effect of barley), limited change in dietary composition as the result of DDGS inclusion, large animal-to-animal variation, and possibly additional stress as a result of transport just before slaughter. Ruminal densities of a key fiber-digesting bacteria specie that produces 11t-18:1 from linoleic and linolenic acids (Butyrivibrio fibrisolvens), and a lactate producer originally thought responsible for production of 10t, 12c-18:2 (Megasphaera elsdenii) were not influenced by diet (P > 0.05).

Conformational effects in the hydrogenation of hemimellitic and cyclohex-1-ene-1,2,3-tricarboxylic acids

The three possible isomers of cyclohexane-1,2,3-tricarboxylic acid were synthesised and separated in order to study the regiospecificity and stereoselectivity of the α-C alkylation of their trimethyl esters. No definitive conclusions could be reached on this aspect for reasons which became apparent in the course of the work. However, the three independent methods adopted for the synthesis of the isomeric tricarboxylic acids have given dramatically different isomer compositions. The reasons are explored in this paper.

Allosteric serine hydroxymethyltransferase from monkey liver: Correlation of conformational changes caused by denaturants with the alterations in catalytic activity

The far-ultraviolet region circular dichroic spectrumof serine hydroxymethyltransferase from monkey liver showed that the protein is in an α-helical conformation. The near ultraviolet circular dichoric spectrum revealed two negative bands originating from the tertiary conformational environment of the aromatic amino acid residues. Addition of urea or guanidinium chloride perturbed the characteristic fluorescence and far ultraviolet circular dichroic spectrum of the enzyme. The decrease in (θ)222 and enzyme activity followed identical patterns with increasing concentrations of urea, whereas with guanidinium chloride, the loss of enzyme activity preceded the loss of secondary structure. 2-Chloroethanol, trifluoroethanol and sodium dodecyl sulphate enhanced the mean residue ellipticity values. In addition, sodium dodecyl sulphate also caused a perturbation of the fluorescence emission spectrum of the enzyme. Extremes of pH decreased the – (θ)222 value. Plots of –(θ)222and enzyme activity as a function of pH showed maximal values at pH 7.4-7.5. These results suggested the prevalence of "conformational flexibility" in the structure of serine hydroxymethyltransferase.

Experimental investigation of catalytic and non-catalytic surface reactions on SiO2 thin films with shock heated oxygen gas

The present study is to investigate the interaction of strong shock heated oxygen on the surface of SiO2 thin film. The thermally excited oxygen undergoes a three-body recombination reaction on the surface of silicon dioxide film. The different oxidation states of silicon species on the surface of the shock-exposed SiO2 film are discussed based on X-ray Photoelectron Spectroscopy (XPS) results. The surface morphology of the shock wave induced damage at the cross section of SiO2 film and structure modification of these materials are analyzed using scanning electron microscopy and ion microscopy. Whether the surface reaction of oxygen on SiO2 film is catalytic or non-catalytic is discussed in this paper.

Liquid phase hydrogenation of aniline in a trickle bed reactor

A rate equation is developed for the liquid phase hydrogenation of aniline over cylindrical catalyst pellets of 30% nickel deposited on clay in a trickle bed reactor. The equation takes into account external and internal diffusional limitations, and describes the experimental data adequately. The hydrogenation reaction is first order with respect to hydrogen and zero order with respect to aniline. Effectiveness factors are in the range 0.003-0.03. Apparent activation energy of the reaction is 12.7 kcal/mol and true activation energy is 39.6 kcal/mol.