The role of lysine-256 in the structure and function of sheep liver recombinant serine hydroxymethyltransferase

The active site lysine residue, K256, involved in Schiffs base linkage with pyridoxal-5'-phosphate (PEP) in sheep liver recombinant serine hydroxymethyltransferase (rSHMT) was changed to glutamine or arginine by site-directed mutagenesis. The purified K256Q and K256R SHMTs had less than 0.1% of catalytic activity with serine and H(4)folate as substrates compared to rSHMT. The mutant enzymes also failed to exhibit the characteristic visible absorbance spectrum (lambda(max) 425 nm) and did not produce the quinonoid intermediate (lambda(max) 495 nm) upon the addition of glycine and H(4)folate. The mutant enzymes were unable to catalyze aldol cleavage of beta-phenylserine and transamination of D-alanine. These results suggested that the mutation of the lysine had resulted in the inability of the enzyme to bind to the cofactor. Therefore, the K256Q SHMT was isolated as a dimer and the K256R SHMT as a mixture of dimers and tetramers which were converted to dimers slowly. On the other hand, rSHMT was stable as a tetramer for several months, further confirming the role of PLP in maintenance of oligomeric structure. The mutant enzymes also failed to exhibit the increased thermal stability upon the addition of serine, normally observed with rSHMT. The enhanced thermal stability has been attributed to a change in conformation of the enzyme from open to closed form leading to reaction specificity. The mutant enzymes were unable to undergo this conformational change probably because of the absence of bound cofactor.

Chiral synthons from carvone, Part 56. Enantiospecific synthesis of (-)-4-thiocyanatoneopupukeanane

Enantiospecific total synthesis of the natural enantiomer of the marine sesquiterpene (-)-4-thiocyanatoneopupukeanane (6) is described. The bicyclo[2.2.2]octanonecarboxylate 11, obtained from (R)-carvone and methyl methacrylate via Michael-Michael reaction, was transformed into bicyclo[2.2.2]octenecarboxylic acid 8. Intramolecular cyclopropanation reaction of the diazo ketone 7, derived from the acid 8, followed by regioselective reductive cyclopropane ring cleavage generated neopupukeanol 20, which was transformed into (-)-4-thiocyanatoneopupukeanane 6.

Constraint loss under dynamic loading in rate independent plastic solids

The objectives of this paper are to examine the loss of crack tip constraint in dynamically loaded fracture specimens and to assess whether it can lead to enhancement in the fracture toughness at high loading rates which has been observed in several experimental studies. To this end, 2-D plane strain finite element analyses of single edge notched (tension) specimen and three point bend specimen subjected to time varying loads are performed. The material is assumed to obey the small strain J(2) flow theory of plasticity with rate independent behaviour. The results demonstrate that a valid J-Q field exists under dynamic loading irrespective of the crack length and specimen geometry. Further, the constraint parameter Q becomes strongly negative at high loading rates, particularly in deeply cracked specimens. The variation of dynamic fracture toughness K-dc with stress intensity rate K for cleavage cracking is predicted using a simple critical stress criterion. It is found that inertia-driven constraint loss can substantially enhance K-dc for (K) over dot > 10(5) MPa rootm/s.

Determination of the reactivity ratios for the oxidative copolymerizations of indene with methyl, ethyl and butyl acrylates

Full Paper: The copolyperoxides of various compositions of indene with methyl acrylate, ethyl acrylate and butyl acrylate have been synthesized by the free-radical-initiated oxidative copolymerization. The compositions of copolyperoxide obtained from H-1 and C-13 NMR spectra have been used to determine the reactivity ratios of the monomers. The copolyperoxides contain a greater proportion of the indene units in random placement. The NMR studies have shown irregularities in the copolyperoxide chain due to the cleavage reactions of the propagating peroxide radical. The thermal analysis by differential scanning calorimetry suggests alternating peroxide units in the copolyperoxide chain. From the activation energy for the thermal degradation, it was inferred that degradation occurs via the dissociation of the peroxide (O-O) bonds of the copolyperoxide chain. The flexibility of the polyperoxides in terms of glass transition temperature (T-g) has also been examined.

DNA topoisomerase I from mycobacteria - A potential drug target

DNA topoisomerases are ubiquitous group of enzymes altering the topology of DNA by concerted breakage and rejoining of the phosphodiester backbone of DNA. The enzymes are classified based on the pattern of DNA cleavage. Type IA enzymes found in all bacteria nick the DNA and attach themselves covalently to the 5' side of the nick during the first transesterification reaction. Most of the information on this group of enzymes comes from studies with E. coli topoisomerase I and III. Members of type IA group are single subunit Zn++ metalloenzymes recognizing single stranded DNA without high degree of sequence specificity during relaxation reaction of negatively super coiled DNA. So far no inhibitors are known for this group of enzymes inspite of their important role in maintaining homeostasis of DNA topology. Molecular characterization of DNA topoisomerase I from mycobacteria has revealed some of the important features of type IA enzymes hitherto unknown and provide scope for identifying novel inhibitors. The present review describes the recent developments in the area summarizing the distinctive features of mycobacterial topoisomerase I. The enzyme has several properties not shared by either type IA or 113 enzymes with respect to DNA binding, recognition, sequence specificity and interaction pattern. The physiological basis of the unusual features is discussed. The unique properties described would aid in developing the enzyme as a target molecule in pharmaceutical design. In addition, the findings lead to address some fundamental questions on the intracellular role of topoisomerase I in the biology of mycobacteria which are one of the most formidable group of pathogenic organisms.

Remarkable photocytotoxicity in hypoxic HeLa cells by a dipyridophenazine copper(II) Schiff base thiolate

Copper(II) complexes Cu(satp)(L)] (1-3) of a Schiff base thiolate (salicylidene-2-aminothiophenol, H(2)satP) and phenanthroline bases (L), viz. 1,10-phenanthroline (phen in 1), dipyrido3,2-d:2',3'-f]quinoxaline (dpq in 2) and dipyrido3,2-a:2',3'-c]phenazine (dppz in 3), were prepared, characterized and their anaerobic DNA photocleavage activity and hypoxic photocytotoxicity studied. The redox active complexes show the Cu(II)-Cu(I) couple near -0.5 V for 1 and near 0.0 V vs. SCE (saturated calomel electrode) for 2 and 3. The one-electron paramagnetic complexes (similar to 1.85 mu(B)) are avid DNA binders giving K(b) values within 1.0 x 10(5) - 8.0 x 10(5) M(-1). Thermal melting and viscosity data along with molecular docking calculations suggest DNA groove and/or partial intercalative binding of the complexes. The complexes show anaerobic DNA cleavage activity in red light under argon via type-I pathway, while DNA photocleavage in air proceeds via hydroxyl radical pathway. The DFT (density functional theory) calculations reveal a thyil radical pathway for the anaerobic DNA photocleavage activity and suggest the possibility of generation of a transient copper(I) species due to bond breakage between the copper and sulfur to generate the thyil radical. An oxidation of the copper(I) species is likely by oxygen in an aerobic medium or by the buffer medium in an anaerobic condition. Complex 3 exhibits significant photocytotoxicity in HeLa cells (IC(50) = 8.3(+/- 1.0) mu M) in visible light, while showing lower dark toxicity (IC(50) = 17.2(+/- 1.0) mu M). A significant reduction in the dark toxicity is observed under hypoxic cellular conditions (IC(50) = 30.0(+/- 1.0) mu M in dark), while retaining its photocytotoxicity (IC(50) = 8.0(+/- 1.0) mu M). (C) 2011 Elsevier Inc. All rights reserved.

A convenient enantiospecific methodology for (-)-(1R,5S)-1,5-dimethylbicyclo[3.3.0]octa-2,7-dione: A formal total synthesis of (-)-ceratopicanol

An enantiospecific formal total synthesis of (-)-ceratopicanol starting from the readily and abundantly available monoterpene (R)-limonene is described. A combination of Claisen rearrangement-intramolecular diazo-ketone cyclopropanation-regiospecific reductive cyclopropane cleavage reactions are employed for the stereo- and regiospecific generation of the two vicinal ring junction quaternary carbon atoms.

Efficient visible light induced nuclease activity of a ternary mono-1,10-phenanthroline copper(II) complex containing 2-(methylthio)ethylsalicylaidimine

Ternary Schiff base copper(II) complex [CuL(phen)](ClO4), where HL is 2-(methylthio)ethylsalicylaldimine and phen is 1,10-phenanthroline, has been prepared and structurally characterized by X-ray crystallography. The complex shows a CuN3OS coordination in a square-pyramidal (4 + 1) geometry with the sulfur as an equatorial ligand. The complex is an avid binder to double-stranded DNA in the minor groove and exhibits both photonuclease and chemical nuclease activity. When exposed to UV light of 312 nm (96 W) or visible light of 532 nm (125 W) under aerobic conditions, the complex causes significant cleavage of supercoiled pUC19 DNA in the absence of any externally added reducing agent or H2O2.

Synthesis based on cyclohexadienes Part 36: an efficient methodology for the construction of spiro[4.5]decanes: a formal synthesis of acorone

An efficient strategy for the contruction of spiro[4.5] decanes is described and involves a bridgehead substitution of a methoxyl group by a methyl group followed by an oxidative cleavage of the tricyclo[5.2.2.0(1,5)] undecane 25 to produce the spiro[4.5] decanes 31 & 32 which are intermediates in the synthesis of acorone. A novel one-pot conversion of alpha-methoxy carboxylic acid to alpha-methyl carboxylic acid is described.

The effect of T-stress on plane strain dynamic crack growth in elastic-plastic materials

In this paper, the effects of T -stress on steady, dynamic crack growth in an elastic-plastic material are examined using a modified boundary layer formulation. The analyses are carried out under mode I, plane strain conditions by employing a special finite element procedure based on moving crack tip coordinates. The material is assumed to obey the J (2) flow theory of plasticity with isotropic power law hardening. The results show that the crack opening profile as well as the opening stress at a finite distance from the tip are strongly affected by the magnitude and sign of the T -stress at any given crack speed. Further, it is found that the fracture toughness predicted by the analyses enhances significantly with negative T -stress for both ductile and cleavage mode of crack growth.

Dicopper(II) complexes showing DNA hydrolase activity and monomeric adduct formation with bis(4-nitrophenyl)phosphate

Ferromagnetic dicopper(II) complexes [Cu(2)(mu-O(2)CCH(3))(mu-OH)(L)(2)(mu-L(1))](PF(6))(2), where L = 1,10-phenanthroline (phen), L(1) = H(2)O in 1 and L = dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), L(1) = CH(3)CN in 2, are prepared and structurally characterized. Crystals of 1 and 2 belong to the monoclinic space group of P2(1)/n and P2(1)/m, respectively. The copper(II) centers display distorted square-pyramidal geometry having a phenanthroline base and two oxygen atoms of the bridging hydroxo and acetate group in the basal plane. The fifth coordination site has weak axially bound bridging solvent molecule H(2)O in 1 and CH(3)CN in 2. The Cu center dot center dot center dot Cu distances are 3.034 and 3.046 angstrom in 1 and 2, respectively. The complexes show efficient hydrolytic cleavage of supercoiled pUC19 DNA as evidenced from the mechanistic studies that include T4 DNA ligase experiments. The binuclear complexes form monomeric copper(II) adducts [Cu(L)(2)(BNPP)](PF(6)) (L = phen, 3; dpq, 4) with bis(4-nitrophenyl)phosphate (BNPP) as a model phosphodiester. The crystal structures of 3 and 4 reveal distorted trigonal bipyramidal geometry in which BNPP binds through the oxygen atom of the phosphate. The kinetic data of the DNA cleavage reactions of the binuclear complexes under pseudo- and true-Michaelis-Menten conditions indicate remarkable enhancement in the DNA hydrolysis rate in comparison to the control data. (C) 2011 Elsevier B.V. All rights reserved.

Identification and characterization of cysteine proteinases of Trypanosoma evansi

Trypanosoma evansi is a causative agent of `surra', a common haemoprotozoan disease of livestock in India causing high morbidity and mortality in disease endemic areas. The proteinases released by live and dead trypanosomes entail immunosuppression in the infected host, which immensely contribute in disease pathogenesis. Cysteine proteinases are identified in the infectious cycle of trypanosomes such as cruzain from Trypanosoma cruzi, rhodesain or brucipain from Trypanosoma brucei rhodesiense and congopain from Trypanosoma congelense. These enzymes localised in lysosome-like organelles, flagellar pocket and on cell surface, which play a critical role in the life cycle of protozoan parasites, viz. in host invasion, nutrition and alteration of the host immune response. The paper describes the identification of cysteine proteinases of T. evansi lysate, activity profile at different pH optima and inhibition pattern using a specific inhibitor, besides the polypeptide profile of an antigen. Eight proteinases of T. evansi were identified in the molecular weight (MW) ranges of 28-170 kDa using gelatin substrate-polyacrylamide gel electrophoresis (GS-PAGE), and of these proteinases, six were cysteine proteinases, as they were inhibited by L-3-carboxy-2,3-transepoxypropionyl-lecuylamido (4-guanidino)-butane (E-64), a specific inhibitor. These proteolytic enzymes were most reactive in acidic pH between 3.0 and 5.5 in the presence of dithiothreitol and completely inactive at alkaline pH 10.0. Similarly, the GS-PAGE profile of the serum samples of rats infected with T. evansi revealed strong proteolytic activity only at the 28-kDa zone at pH 5.5, while no proteolytic activity was observed in serum samples of uninfected rats. Further, the other zones of clearance, which were evident in T. evansi antigen zymogram, could not be observed in the serum samples of rats infected with T. evansi. The polypeptide pattern of the whole cell lysate antigen revealed 12-15 polypeptide bands ranging from 28 to 81 kDa along with five predominant polypeptides bands (MW of 81, 66, 62, 55 and 45 kDa), which were immunoreactive with hyperimmune serum (HIS) and serum of experimentally infected rabbits with T. evansi infection. The immunoblot recognised antibodies in experimentally infected rabbits and against HIS as well, corresponding to the zone of clearances at lower MW ranges (28-41 kDa), which may be attributed to the potential of these proteinases in the diagnosis of T. evansi infection. Since these thiol-dependent enzymes are most active in acidic pH and considering their inhibition characteristics, these data suggest that they resemble to the mammalian lysosomal cathepsin B and L.

Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides

Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical `b-ion' series, exhibiting initial backbone cleavage explicitly at the beta-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the `b' or/and the `y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the beta-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the `y-type'. Complementary NMR data showed that, while all metal ions were located around the beta-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent beta-hydroxy acid residue in isariins and the cis peptide bond in isaridins.

Ferrocene-Conjugated L-Tryptophan Copper(II) Complexes of Phenanthroline Bases Showing DNA Photocleavage Activity and Cytotoxicity

Ferrocene-conjugated L-tryptophan (L-Trp) reduced Schiff base (Fc-TrpH) copper(II) complexes [Cu(Fc-Trp)(L)](ClO(4)) of phenanthroline bases (L), viz. 2,2'-bipyridine (bpy in 1), 1,10-phenanthroline (phen in 2), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq in 3), and dipyrido[3,2-a:2',3'-c]phenazine (dppz in 4), were prepared and characterized and their photocytotoxicity studied. Cationic reduced Schiff base (Ph-TrpH) complexes [Cu(Ph-Trp)(L)(H(2)O)] (ClO(4)) (L = phen in 5; dppz in 6) having the ferrocenyl moiety replaced by a phenyl group and the Zn(II) analogue (7) of complex 4 were prepared and used as control species. The crystal structures of 1 and 5 with respective square-planar CuN(3)O and square-pyramidal CuN(3)O(2) coordination geometry show significantly different core structures. Complexes 1-4 exhibit a Cu(II)-Cu(I) redox couple near -0.1 V and the Fc(+)-Fc couple at similar to 0.5 V vs SCE in DMF-0.1 M [Bu(4)(n)N] (ClO(4)) (Fc = ferrocenyl moiety). The complexes display a copper(II)-based d-d band near 600 nm and a Fc-centered band at similar to 450 nm in DMF-Tris-HCl buffer. The complexes are efficient binders to calf thymus DNA. They are synthetic chemical nucleases in the presence of thiol or H(2)O(2), forming hydroxyl radicals. The photoactive complexes are cleavers of pUC19 DNA in visible light, forming hydroxyl radicals. Complexes 2-6 show photocytotoxicity in HeLa cancer cells, giving IC(50) values of 4.7, 10.2, 1.3, 4.8, and 4.3 mu M, respectively, in visible light with the appearance of apoptotic bodies. The complexes also show photocytotoxicity in MCF-7 cancer cells. Nuclear chromatin cleavage has been observed with acridine orange/ethidium bromide (AO/EB) dual staining with complex 4 in visible light. The complexes induce caspase-independent apoptosis in the HeLa cells.

Interplay between NS3 protease and human La protein regulates translation-replication switch of Hepatitis C virus

HCV NS3 protein plays a central role in viral polyprotein processing and RNA replication. We demonstrate that the NS3 protease (NS3(pro)) domain alone can specifically bind to HCV-IRES RNA, predominantly in the SLIV region. The cleavage activity of the NS3 protease domain is reduced upon HCV-RNA binding. More importantly, NS3(pro) binding to the SLIV hinders the interaction of La protein, a cellular IRES-trans acting factor required for HCV IRES-mediated translation, resulting in inhibition of HCV-IRES activity. Although overexpression of both NS3(pro) as well as the full length NS3 protein decreased the level of HCV IRES mediated translation, replication of HCV replicon RNA was enhanced significantly. These observations suggest that the NS3(pro) binding to HCV IRES reduces translation in favor of RNA replication. The competition between the host factor (La) and the viral protein (NS3) for binding to HCV IRES might regulate the molecular switch from translation to replication of HCV.