Importance of tyrosine residues of Bacillus stearothermophilus serine hydroxymethyltransferase in cofactor binding and l-allo-Thr cleavage

Serine hydroxymethyltransferase (SHMT) from Bacillus stearothermophilus (bsSHMT) is a pyridoxal 5'-phosphate-dependent enzyme that catalyses the conversion of l-serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. In addition, the enzyme catalyses the tetrahydrofolate-independent cleavage of 3-hydroxy amino acids and transamination. In this article, we have examined the mechanism of the tetrahydrofolate-independent cleavage of 3-hydroxy amino acids by SHMT. The three-dimensional structure and biochemical properties of Y51F and Y61A bsSHMTs and their complexes with substrates, especially l-allo-Thr, show that the cleavage of 3-hydroxy amino acids could proceed via Cα proton abstraction rather than hydroxyl proton removal. Both mutations result in a complete loss of tetrahydrofolate-dependent and tetrahydrofolate-independent activities. The mutation of Y51 to F strongly affects the binding of pyridoxal 5'-phosphate, possibly as a consequence of a change in the orientation of the phenyl ring in Y51F bsSHMT. The mutant enzyme could be completely reconstituted with pyridoxal 5'-phosphate. However, there was an alteration in the λmax value of the internal aldimine (396 nm), a decrease in the rate of reduction with NaCNBH3 and a loss of the intermediate in the interaction with methoxyamine (MA). The mutation of Y61 to A results in the loss of interaction with Cα and Cβ of the substrates. X-Ray structure and visible CD studies show that the mutant is capable of forming an external aldimine. However, the formation of the quinonoid intermediate is hindered. It is suggested that Y61 is involved in the abstraction of the Cα proton from 3-hydroxy amino acids. A new mechanism for the cleavage of 3-hydroxy amino acids via Cα proton abstraction by SHMT is proposed.

Structure formation in short designed peptides probed by proteolytic cleavage

The formation of local structure, in short peptides has been probed by examining cleavage patterns and rates of proteolysis of designed sequences with a high tendency to form β-hairpin structures. Three model sequences which bear fluorescence donor and acceptor groups have been investigated: Dab-Gaba-Lys-Pro-Leu-Gly-Lys-Val-Xxx-Yyy-Glu-Val-Ala-Ala-Cys-Lys-NH2 ï EDANS Xxx-Yyy: Peptide 1=DPro-LPro, Peptide 2=DPro-Gly, Peptide 3=Leu-Ala Fluorescence resonance energy transfer (FRET) provides a convenient probe for peptide cleavage. MALDI mass spectrometry has been used to probe sites of cleavage and CD spectroscopy to access the overall backbone conformation using analog sequences, which lack strongly absorbing donor and acceptor groups. The proteases trypsin, subtilisin, collagenase, elastase, proteinase K and thermolysin were used for proteolysis and the rates of cleavage determined. Peptide 3 is the most susceptible to cleavage by all the enzymes except thermolysin, which cleaves all three peptides at comparable rates. Peptides 1 and 2 are completely resistant to the action of trypsin, suggesting that β-turn formation acts as a deterrent to proteolytic cleavage.

Suppression of spinel formation to induce reversible thermal behavior in the layered double hydroxides (LDHs) of Co with Al, Fe, Ga, and In

The layered double hydroxides (LDHs) of Co with trivalent cations decompose irreversibly to yield oxides with the spinel structure. Spinel formation is aided by the oxidation of Co(II) to Co(III) in the ambient atmosphere. When the decomposition is carried out under N-2, the oxidation of Co(II) is suppressed, and the resulting oxide has the rock salt structure. Thus, the Co-Al-CO32-/Cl- LDHs yield oxides of the type Co1- Al-x(2x/3)rectangle O-x/3, which are highly metastable, given the large defect concentration. This defect oxide rapidly reverts back to the original hydroxide on soaking in a Na2CO3 solution. Interlayer NO3- anions, on the other hand, decompose generating a highly oxidizing atmosphere, whereby the Co-Al-NO3- LDH decomposes to form the spinel phase even in a N-2 atmosphere. The oxide with the defect rock salt structure formed by the thermal decomposition of the Co-Fe-CO32- LDH under N2, on soaking in a Na2CO3 solution, follows a different kinetic pathway and undergoes a solution transformation into the inverse spinel Co(Co, Fe)(2)O-4. Fe3+ has a low octahedral crystal field stabilization energy and therefore prefers the tetrahedral coordination offered by the structure of the inverse spinel rather than the octahedral coordination of the parent LDH. Similar considerations do not hold in the case of Ga- and In-containing LDHs, given the considerable barriers to the diffusion of M3+ (M=Ga, In) from octahedral to tetrahedral sites owing to their large size. Consequently, the In-containing oxide residue reverts back to the parent hydroxide, whereas this reconstruction is partial in the case of the Ga-containing oxide. These studies show that the reversible thermal behavior offers a competing kinetic pathway to spinel formation. Suppression of the latter induces the reversible behavior in an LDH that otherwise decomposes irreversibly to the spinel.

Photocytotoxic Lanthanum(III) and Gadolinium(III) Complexes of Phenanthroline Bases Showing Light-Induced DNA Cleavage Activity

Lanthanide complexes of formulation [La(B)(2)(NO3)(3)] (1-3) and [Gd(B)(2)(NO3)(3)] (4-6), where B is a N,N-donor phenanthroline base, namely, 1,10-phenanthroline (phen in 1, 4),dipyrido[3,2-d2',3'-f]quinoxaline (dpq in 2,5) and dipyrido[3,2-a2',3'-c]phenazine (dppz in 3, 6), have been prepared, characterized from physicochemical data, and their photoinduced DNA and protein cleavage activity studied The photocytotoxicity of the dppz complexes 3 and 6 has been studied using HeLa cancer cells. The complexes exhibitligand centered bands in the UV region The dppz complexes show thelowest energy band at 380 nm in N,N-dimethylformamide (DMF) The La(III)complexes are diamagnetic. The Gd(III) complexes (4-6) have magneticmoments that correspond to seven unpaired electrons The complexes are1(.)1 electrolytic in aqueous DMF The dpq and dppz complexes in DMFshow ligand-based reductions. The complexes display moderate binding propensity to calf thymus DNA giving binding constant values in the range of 5.7 x 10(4)-5.8 x 10(5) M-1 with a relative order. 3, 6 (dppz)> 2, 5 (dpq) > 1, 4 (phen) The binding data suggest DNA surface and/or groove binding nature of the complexes. The complexes do not show any hydrolytic cleavage of plasmid supercoiled pUC19 DNA. The dpq and dppz complexes efficiently cleave SC DNA to its nicked circular form onexposure to UV-A light of 365 nm at nanomolar complex concentration. Mechanistic studies reveal the involvement of singlet oxygen (O-1(2)) and hydroxyl radical (HO center dot) as the cleavage active species.The complexes show binding propensity to bovine serum albumin (BSA)protein giving K-BSA values of similar to 10(5) M-1. The dppz complexes 3 and 6 show BSA protein cleavage activity in UV-A light of 365 nm The dppz complexes 3 and 6 exhibit significant photocytotoxicity in HeLa cells giving respective IC50 values of 341 nM and 573 nM in UV-A light of 365 nm for an exposure time of 15 min (IC50 > 100 mu M in dark for both the complexes) Control experiments show significant dark and phototoxicity of the dppz base alone (IC50 = 413 nM in light with 4 h incubation in dark and 116 mu M in dark with 24 h incubation). A significant decrease in the dark toxicity of the dppz base is observedon binding to the lanthanide ions while retaining similar phototoxicity.

Active vibration suppression of beams with discrete actuators using optimal dynamic inversion

Most of the structural elements like beams, cables etc. are flexible and should be modeled as distributed parameter systems (DPS) to represent the reality better. For large structures, the usual approach of 'modal representation' is not an accurate representation. Moreover, for excessive vibrations (possibly due to strong wind, earthquake etc.), external power source (controller) is needed to suppress it, as the natural damping of these structures is usually small. In this paper, we propose to use a recently developed optinial dynamic inversion technique to design a set of discrete controllers for this purpose. We assume that the control force to the structure is applied through finite number of actuators, which are located at predefined locations in the spatial domain. The method used in this paper determines control forces directly from the partial differential equation (PDE) model of the system. The formulation has better practical significance, both because it leads to a closed form solution of the controller (hence avoids computational issues) as well as because a set of discrete actuators along the spatial domain can be implemented with relative ease (as compared to a continuous actuator).

Suppression of charge order, disappearance of antiferromagnetism, and emergence of ferromagnetism in Nd0.5Ca0.5MnO3 nanoparticles

Nd0.5Ca0.5MnO3 nanoparticles (average diameter similar to 20 and 40 nm) are synthesized by the polymeric precursor sol-gel method and characterized by various physico-chemical techniques. Quite strikingly, in the 20 nm particles, the charge-ordered (CO) and the antiferromagnetic phases observed in the bulk below 250 K and 160 K, respectively, are completely absent. Instead, a ferromagnetic (FM) transition is observed at 95 K followed by an insulator-to-metal transition at 75 K. The 40 nm particles show a residual CO phase but a transition to the FM state also occurs, at a slightly higher temperature of 110 K.

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.

Activation barrier for the alpha.-cleavage process in thiones

The Occurrence of the Norrish type I a-cleavage process in some thio compounds has been examined by using the MIND013 method and employing the configuration interaction. Results reveal that where the radiationless process is not efficient, thio compounds can undergo photodissociation into radicals in their lowest triplet and singlet excited states. The activation barriers in all these cases arise from an avoided crossing between two states of different symmetries. The calculations of activation barriers by the CNDO-CI and MINDO-CI procedures reveal that the MINDO-CI method leads to realistic values of the activation energies.

Photocytotoxic and anaerobic DNA cleavage activity of binuclear 3,3 '-dithiodipropionic acid cobalt(II) complexes having phenanthroline bases

Dicobalt(II) complexes [{(B)Co-11)(2)(mu-dtdp)(2)] (1-3) of 3,3'-dithiodipropionic acid (dtdp) and phenanthroline bases (B), viz. 1,10-phenanthroline (phen in 1), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq in 2) and dipyrido13,2-a:2',3'-clphenazine (dppz in 3), have been prepared, characterized and their photo-induced anaerobic DNA cleavage activity studied. The elemental analysis and mass spectral data suggest binuclear formulation of the complexes. The redox inactive complexes have magnetically non-interacting dicobalt(II) core showing magnetic moment of similar to 3.9 p per cobalt(II) center. The complexes show good binding propensity to calf thymus DNA giving K-b values within 4.3 x 10(5)-4.0 x 10(6) M-1. Thermal melting and viscosity data predict DNA groove binding and/or partial intercalative nature of the complexes. The complexes show significant anaerobic DNA cleavage activity in green light under argon atmosphere possibly involving radical species generated from the disulfide moiety in a type-I pathway. The DNA cleavage reaction under aerobic medium in green light is found to involve hydroxyl radical species. The dppz complex 3 exhibits significant photocytotoxicity in HeLa cervical cancer cells with an IC50 value of 2.31 mu M in UV-A light of 365 nm, while it is essentially non-toxic in dark giving an IC50 value of >200 mu M. A significant reduction of the dark toxicity of the organic dppz base (IC50 = 8.3 mu M in dark) is observed on binding to the cobalt(II) center while essentially retaining its photocytotoxicity in UV-A light (IC50 = 0.4 mu M). (C) 2010 Elsevier Ltd. All rights reserved.

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.

Photochemical, photophysical, and theoretical studies on cyclobutanethiones..alpha.-Cleavage reactions

Photophysics and photochemistry of cyclobutanethiones 1-5 have been studied with the view to generalize the a-cleavage reactions of cyclobutanethiones. The above cyclobutanethiones possess a unit intersystem crossing efficiency from S1 to T1, a high self-quenching rate (-4 X lo9 M-' s-'), and a short triplet lifetime (<0.50 ws). Photolysis of 1-5 yields in benzene a product resulting from 1,3-transposition and in methanol two cyclic thioacetals.The origin of these products is traced to the triplet excited state. A mechanistic scheme involving a-cleavage as the primary photoprocess and diradicals and thiacarbenes as intermediates has been formulated to rationalize the formation of thioacetals and rearranged products. The proposed mechanistic scheme is supported by UHF MIND013 calculations performed on four model systems, cyclobutanethiones and 1,3-cyclobutanedithiones 18-21. These calculations indicate that formation of diradical is favored thermodynamically and kinetically for systems analogous to 19 and 21, while rearrangement to thiacarbene is likely only for those similar to 21.

Synthesis, structure and DNA cleavage studies of coumarin analogues of tetrahydroisoquinoline and protoberberine alkaloids

Novel molecular matrices have been derived from coumarin-4-acetic acids and beta-phenylethylamines using the Bischler-Napieralski protocol which has led to the synthesis of analogues of tetrahydropapaverine in which the dimethoxybenzene moiety has been replaced by substituted coumarins. One carbon homologation has led to cyclization at the C3 position of coumarin generating the protoberberine skeleton. Structures have been confirmed by diffraction studies. The results showed that compounds 6e, 6f, 7e and 7f were found to be very effective against DNA samples of Gram positive bacterium Staphylococcus aureus and fungus Aspergillus niger. (C) 2010 Elsevier Masson SAS. All rights reserved.