Structural and kinetic studies on the activators of succinate dehydrogenase

1. 1. Diverse classes of compounds such as dicarboxylates, pyrophosphates, quinols and nitrophenols are known to activate mitochondrial succinate dehydrogenase (EC 1.3.99.1). Examples in each class — malonate, pyrophosphate, ubiquinol and 2,4-dinitrophenol — are selected for comparative studies on the kinetic constants and structural relationship. 2. 2. The activated forms of the enzyme obtained on preincubating mitochondria with the effectors exhibited Michaelian kinetics and gave doublereciprocal plots which are nearly parallel to that of the basal form. On activation, Km for the substrate also increased along with V. The effectors activated the enzyme at low concentrations and inhibited, in a competitive fashion, at high concentrations. The binding constant for activation was lower than that for inhibition for each effector. 3. 3. These compounds possess ionizable twin oxygens separated by a distance of Image and having fractional charges in the range of −0.26 to −0.74 e. The common twin-oxygen feature of the substrate and the effectors suggested the presence of corresponding counter charges in the binding domain. The competitive nature of effectors with the substrate for inhibition further indicated the close structural resemblance of the activation and catalytic sites.

Studies in terpenoids. Part XXXI. Synthesis of pyrocurzerenone, a furosesquiterpenoid from Curcuma zedoaria

7-Acetonyloxy-5-methyl--tetralone (Vc) was cyclodehydrated to 7,8-dihydro-1,5-dimethylnaphtho[2,1-b]furan-9(6H)-one (VIa), the structure of which was established by an independent synthesis from methyl 4-(4-acetonyloxy-2-methylphenyl)butyrate (IXd). Similarly, 7-acetonyloxy-2,5-dimethyl--tetralone (Vf), synthesized via 4-(5-isopropyl-4-methoxy-2-methylphenyl)-2-methylbutyric acid (XIIb) and 7-methoxy-2,5-dimethyl--tetralone (Vd), was cyclodehydrated to 7,8-dihydro-1,5,8-trimethylnaphtho[2,1-b]furan-9(6H)-one (VIb), which on reduction and dehydration furnished pyrocurzerenone (6,7-dihydro-1,5,8-trimethylnaphtho[2,1-b]furan)(I). The deisopropylation and cyclodehydration of (XIIb) to (Vd) were effected in one step by treatment with polyphosphoric acid.

Studies in terpenoids. Part XXX. Synthesis of pterosin E, a sesquiter-penoid from bracken

Pterosin E (2,5,7-trimethyl-1-oxoindan-6-ylacetic acid)(Ia), a naturally occurring sesquiterpenoid has been synthesized starting from -bromomesitylene (IIIa). Alkylation of diethyl methylmalonate with (IIIa) gave the diester (IIIb) which was converted into the cyanomethyl diester (IVb). Hydrolysis of (IVb) to the dicarboxylic acid (V) followed by its cyclodehydration gave pterosin E.

Studies on transport phenomena during solidification of an aluminum alloy in the presence of linear electromagnetic stirring

Numerical and experimental studies on transport phenomena during solidification of an aluminum alloy in the presence of linear electromagnetic stirring are performed. The alloy is electromagnetically stirred to produce semisolid slurry in a cylindrical graphite mould placed in the annulus of a linear electromagnetic stirrer. The mould is cooled at the bottom, such that solidification progresses from the bottom to the top of the cylindrical mould. A numerical model is developed for simulating the transport phenomena associated with the solidification process using a set of single-phase governing equations of mass. momentum, energy. and species conservation. The viscosity variation of the slurry, used in the model, is determined experimentally using a rotary viscometer. The set of governing equations is solved using a pressure-based finite volume technique, along with an enthalpy based phase change algorithm. The numerical study involves prediction of temperature, velocity, species and solid fraction distribution in the mould. Corresponding solidification experiments are performed, with time-temperature history recorded at key locations. The microstructures at various temperature measurement locations in the solidified billet are analyzed. The numerical predictions of temperature variations are in good agreement with experiments, and the predicted flow field evolution correlates well with the microstructures observed at various locations.

Synthesis and Structure-Activity Correlation Studies of Secondary- and Tertiary-Amine-Based Glutathione Peroxidase Mimics

In this study, a series of seeondary- and tertiary-amino-substituted diaryl diselenides were synthesized and studied for their glutathione peroxidase (GPx) like antioxidant activities with H2O2, cumene hydroperoxide, or tBuOOH as substrates and with PhSH or glutathione (GSH) as thiol cosubstrates. This study reveals that replacement of the tert-amino groups in benzylamine-based diselenides by sec-amino moieties drastically enhances the catalytic activities in both the aromatic thiol (PhSH) and GSH assay systems. Particularly, the N-propyl- and N-isopropylamino-substituted diselenides are 8-18 times more active than the corresponding N,N-dipropyl- and N,N-diisopropylamine-based compounds in all three peroxide systems when GSH is used as the thiol cosubstrate. Although the catalytic mechanism of sec-amino-substituted disclenides is similar to that of the tert-amine-based compounds, differences in the stability and reactivity of some of the key intermediates account for the differences in the GPx-like activities. it is observed that the sec-amino groups are better than the tert-amino moieties for generating the catalytically active selenols. This is due to the absence of any significant thiol-exchange reactions in the selenenyl sulfides derived from sec-amine-based diselenides. Furthermore, the seleninic acids (RSeO2H) derived from the sec-amine-based compounds are more stable toward further reactions with peroxides than their tert-amine-based analogues.

Conformational Choices for the Stereochemically Constrained gamma-Amino Acid Residue Gabapentin: Theoretical Studies and Correlation With Experimental Results

Gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn) is an achiral, conformationally constrained gamma amino acid residue. A survey of available crystal structures of Gpn peptides reveals that the torsion angles about the C-gamma-C-beta (theta(1)) and C-beta-C-alpha(theta(2)) bonds are overwhelmingly limited to gauche, gauche (g(+)g(+)/g(-)g(-)) conformations. The Gpn residue forms C-7 and C-9 hydrogen bonds in which the donor and acceptor atoms come from the flanking peptide units. In combination with alpha amino acid residues alpha gamma and gamma alpha segments can adopt C-12 hydrogen bonded structures. The conformational choices available to the Gpn residue have been probed using energy calculations, adopting a grid search strategy. Ramachandran phi-psi maps have been constructed for fixed values of theta(1) and theta(2), corresponding to the gauche and trans conformations. The sterically allowed and energetically favorable regions of conformational space have been defined and experimental observations compared. C-7 and C-9 hydrogen bonded conformational families have been identified using a grid search approach in which theta(1) and theta(2) values are varied over a range of +/- 10 degrees about ideal values at 1 degrees intervals. The theoretical analysis together with experimental observations for 59 Gpn residues from 35 crystal structures permits definition of the limited range of conformational possibilities at this gamma amino acid residue. .

New structural insights and molecular-modelling studies of 4-methyl-5-beta-hydroxyethylthiazole kinase from Pyrococcus horikoshii OT3 (PhThiK)

4-Methyl-5-beta-hydroxyethylthiazole kinase (ThiK) catalyses the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole. This work reports the first crystal structure of an archaeal ThiK: that from Pyrococcus horikoshii OT3 (PhThiK) at 1.85 angstrom resolution with a phosphate ion occupying the position of the beta-phosphate of the nucleotide. The topology of this enzyme shows the typical ribokinase fold of an alpha/beta protein. The overall structure of PhThiK is similar to those of Bacillus subtilis ThiK (BsThiK) and Enterococcus faecalis V583 ThiK (EfThiK). Sequence analysis of ThiK enzymes from various sources indicated that three-quarters of the residues involved in interfacial regions are conserved. It also revealed that the amino-acid residues in the nucleotide-binding, magnesium ion-binding and substrate-binding sites are conserved. Binding of the nucleotide and substrate to the ThiK enzyme do not influence the quaternary association (trimer) as revealed by the crystal structure of PhThiK.

Structural studies of analgesics and their interactions. Part 4. Crystal structures of phenylbutazone and a 2 : 1 complex between phenylbutazone and piperazine

The X-ray crystal structures of 4-butyl-1,2-diphenylpyrazolidine-3,5-dione (phenylbutazone)(I). and its 2 : 1 complex (II) with piperazine have been determined by direct methods and the structures refined to R 0.096 (2 300 observed reflections measured by diffractometer) and 0.074 (2 494 observed reflections visuallyestimated). Crystals are monoclinic, space group P21/c; for (I)a= 21.695(4), b= 5.823(2), c= 27.881(4)Å, = 108.06 (10)°, Z= 8, and for (II)a= 8.048(4), b= 15.081(4), c= 15.583(7)Å, = 95.9(3)°, Z= 2. The two crystallographically independant molecules in the structure of (I) are similar except for the conformation of the butyl group, which is disordered in one of the molecules. In the pyrazolidinedione group, the two C–C bonds are single and the two C–O bonds double. The two nitrogen atoms in the five-membered ring are pyramidal with the attached phenyl groups lying on the opposite sides of the mean plane of the ring. The phenylbutazone molecule in (II) exists as a negative ion owing to deprotonation of C-4. C-4 is therefore trigonal and the orientation of the Bu group with respect to the pyrazolidinedione group is considerably different from that in (I); there is also considerable electron delocalization along the C–O and C–C bonds. These changes in geometry and electronic structure may relate to biological activity. The doubly charged cationic piperazine molecule exists in the chair form with the nitrogen atoms at the apices. The crystal structure of (II) is stabilized by ionic interactions and N–H O hydrogen bonds.

Conformational studies on cyclic dipeptides

An analysis of 11 crystal structures of cyclic dipeptides so far reported in the literature is made, with main reference to the internal parameters of these molecules. Preferred conformations of the side chains of cyclic dipeptides with different α-amino acid residues have been studied by classical energy calculations. The possible conformations of the DKP ring are also studied. The significance of the non-bonded interaction in deciding the pathway for conformational change has also been investigated. The agreement between theoretical results and experimental observations is quite good, both with respect to the conformation of these molecules as well as the enthalpy difference as estimated from n.m.r. studies between different conformers.

Flow Studies in Non Circular Tubes with Wall Injection

An analysis of inviscid incompressible flow in a tube of sinusoidally perturbed circular cross section with wall injection has been made. The velocity and pressure fields have been obtained. Measurements of axial velocity profiles and pressure distribution have been made in a simulated star shaped tube with wall injection. The static pressure at the star recess is found to be more than that at the star point, this feature being in conformity with the analytical result. Flow visualisation by photography of injected smoke seems to show simple diffusion rather than strong vortices in the recess.

Some Studies on Hydrogen-Oxygen Diffusion Flame

The opposed-jet diffusion flame has been considered with four step reaction kinetics for hydrogenoxygen system. The studies have revealed that the flame broadening reduces and maximum temperature increases as pressure increases. The relative importance of different reaction steps have been brought out in different regions (unstable, near extinction and equilibrium). The present studies have also led to the deduction of the oveall reaction rate constants of an equivalent single step reaction using matching of a certain overall set of parameters for four step reaction scheme and equivalent single step reaction.

Studies on the reduction of hematite by carbon

Single pellet experiments have been carried out in a nitrogen atmosphere to study the reduction of hematite by graphite in the temperature range 925 to 1060°C. The effect of variables such as c/Fe2O3 molar ratio, pellet size, and so forth, has been investigated. Gas analysis data show a continuous decrease in CO2/CO ratio during reduction, the values being far away from Fe/FeO equilibrium for wustite reduction by CO. The activation energies associated with different degrees of reduction appear to be widely different suggesting a possible changeover in reaction mechanism during the progress of reduction. X-ray diffraction studies confirm the stepwise nature of hematite reduction.

N. m. r. and infrared spectroscopic studies of hydrogen bonding in hindered alcohols. An instance of a true hydrogen bonded dimer in an alcohol

Hydrogen bonding in the highly hindered alcohol 2,4-dimethyl-3-ethyl-3-pentanol has been studied by proton n.m.r. and infrared spectroscopy. This alcohol associates to form a dimer but no higher hydrogen bonded species; hence the monomer–dimer equilibrium can be studied without interference from competing processes. Spectral and thermodynamic properties for the hydrogen bonding are reported.