Role of histidine residues in EcoP15I DNA methyltransferase activity as probed by chemical modification and site-directed mutagenesis

Towards understanding the catalytic mechanism of M.EcoP15I [EcoP15I MTase (DNA methyltransferase); an adenine methyltransferase], we investigated the role of histidine residues in catalysis. M.EcoP15I, when incubated with DEPC (diethyl pyrocarbonate), a histidine-specific reagent, shows a time- and concentration-dependent inactivation of methylation of DNA containing its recognition sequence of 5'-CAGCAG-3'. The loss of enzyme activity was accompanied by an increase in absorbance at 240 nm. A difference spectrum of modified versus native enzyme shows the formation of N-carbethoxyhistidine that is diminished by hydroxylamine. This, along with other experiments, strongly suggests that the inactivation of the enzyme by DEPC was specific for histidine residues. Substrate protection experiments show that pre-incubating the methylase with DNA was able to protect the enzyme from DEPC inactivation. Site-directed mutagenesis experiments in which the 15 histidine residues in the enzyme were replaced individually with alanine corroborated the chemical modification studies and established the importance of His-335 in the methylase activity. No gross structural differences were detected between the native and H335A mutant MTases, as evident from CD spectra, native PAGE pattern or on gel filtration chromatography. Replacement of histidine with alanine residue at position 335 results in a mutant enzyme that is catalytically inactive and binds to DNA more tightly than the wild-type enzyme. Thus we have shown in the present study, through a combination of chemical modification and site-directed mutagenesis experiments, that His-335 plays an essential role in DNA methylation catalysed by M.EcoP15I.

The core and shapley value analysis for cooperative formation of procurement networks

Formation of high value procurement networks involves a bottom-up assembly of complex production, assembly, and exchange relationships through supplier selection and contracting decisions, where suppliers are intelligent and rational agents who act strategically. In this paper we address the problem of forming procurement networks for items with value adding stages that are linearly arranged We model the problem of Procurement Network Formation (PNF) for multiple units of a single item as a cooperative game where agents cooperate to form a surplus maximizing procurement network and then share the surplus in a stable and fair manner We first investigate the stability of such networks by examining the conditions under which the core of the game is non-empty. We then present a protocol, based on the extensive form game realization of the core, for forming such networks so that the resulting network is stable. We also mention a key result when the Shapley value is applied as a solution concept.

Unusual Hydrogenation of Fumarate Anion Followed by Metal−Carbon Bond Formation: Synthesis and Characterization of Two Metallochelates

The treatment of [M(dppf)(H2O)2](OTf)2 (dppf =1,1′-bis(diphenylphosphino)ferrocene; M = Pd, Pt) with 1 equiv of disodium fumarate in methanol medium showed an unusual hydrogenation of the ethylenic bond followed by the formation of metallochelates linking M through one of the carboxylates and the β-carbon with respect to COO−. Despite the possibility of formation of a [2 + 2] or [4 + 4] self-assembled macrocycle, the reduction of fumarate to succinate, and in particular the linking through the β-carbon, is unique since a similar treatment using disodium succinate instead of disodium fumarate yielded an expected metallochelate where both the carboxylates were coordinated to the square-planar metal.

Thermotropic and hydration studies of membranes formed from gemini pseudoglyceryl lipids possessing polymethylene spacers

Membrane formation from gemini pseudoglyceryl lipids bearing n-C14H29 and n-C16H33 chains has been reported. These lipid aggregates have been characterized using transmission electron microscopy (TEM), dynamic light scattering (DLS), high sensitivity differential scanning calorimetry (DSC), and Paldan fluorescence studies. The length of the spacer between the cationic ammonium headgroups has been varied from -(CH2)(3)- (propandiyl) to -(CH2)(12)- (dodecandiyl) in these lipids. All gemini lipids were found to generate stable suspensions in aqueous media. Electron microscopic studies revealed the smaller size of the gemini lipid aggregates as compared to their monomeric lipid counterparts. DLS measurements showed that the gemini lipid suspensions with a -(CH2)(8)- spacer length were bigger in size than that of other analogues. DSC studies suggest the unusual behavior of the gemini lipids bearing -(CH2)3- propanediyl spacer based lipids. These observations were consistent irrespective of the hydrocarbon chain lengths of the lipids. Paldan fluorescence based hydration studies showed that the hexadecyl chain based gemini lipid aggregates bearing a -(CH2)(12)- spacer were the most hydrated in their gel states among all the gemini lipid series investigated herein.

Modeling of formation of gold nanoparticles by citrate method

Properties of nanoparticles are size dependent, and a model to predict particle size is of importance. Gold nanoparticles are commonly synthesized by reducing tetrachloroauric acid with trisodium citrate, a method pioneered by Turkevich et al (Discuss. Faraday Soc. 1951, 11, 55). Data from several investigators that used this method show that when the ratio of initial concentrations of citrate to gold is varied from 0.4 to similar to 2, the final mean size of the particles formed varies by a factor of 7, while subsequent increases in the ratio hardly have any effect on the size. In this paper, a model is developed to explain this widely varying dependence. The steps that lead to the formation of particles are as follows: reduction of Au3+ in solution, disproportionation of Au+ to gold atoms and their nucleation, growth by disproportionation on particle surface, and coagulation. Oxidation of citrate results in the formation of dicarboxy acetone, which aids nucleation but also decomposes into side products. A detailed kinetic model is developed on the basis of these steps and is combined with population balance to predict particle-size distribution. The model shows that, unlike the usual balance between nucleation and growth that determines the particle size, it is the balance between rate of nucleation and degradation of dicarboxy acetone that determines the particle size in the citrate process. It is this feature that is able to explain the unusual dependence of the mean particle size on the ratio of citrate to gold salt concentration. It is also found that coagulation plays an important role in determining the particle size at high concentrations of citrate.

Small-angle x-ray scattering study of the aggregation of gold nanoparticles during formation at the toluene-water interface

We report the results of an in situ small-angle x-ray scattering (SAXS) study of the aggregation of gold nanoparticles formed by an interfacial reaction at the toluene-water interface. The SAXS data provide a direct evidence for aggregate formation of nanoparticles having 1.3 nm gold core and an organic shell that gives a core-core separation of about 2.5 nm. Furthermore, the nanoparticles do not occupy all the cites of 13-member cluster. This occupancy decreases with reaction time and indicate reorganization of the clusters that generates planner disklike structures. A gradual increase in fractal dimension from 1.82 to 2.05 also indicate compactification of cluster aggregation with reaction time, the final exponent being close to 2 expected for disklike aggregates.

Unraveling the packing pattern leading to gelation using SS NMR and X-ray diffraction: direct observation of the evolution of self-assembled fibers

A detailed understanding of the mode of packing patterns that leads to the gelation of low molecular mass gelators derived from bile acid esters was carried out using solid state NMR along with complementary techniques such as powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and polarizing optical microscopy (POM). Solid state C-13{H-1} cross polarization (CP) magic angle spinning (MAS) NMR of the low molecularmass gel in its native state was recorded for the first time. A close resemblance in the packing patterns of the gel, xerogel and bulk solid states was revealed upon comparing their C-13{H-1} CPMAS NMR spectral pattern. A doublet resonance pattern of C-13 signals in C-13{H-1}CPMAS NMR spectra were observed for the gelator molecules, whereas the non-gelators showed simple singlet resonance or resulted inthe formation of inclusion complexes/solvates. PXRD patterns revealed a close isomorphous nature of the gelators indicating the similarity in the mode of the packing pattern in their solid state. Direct imaging of the evolution of nanofibers (sol-gel transition) was carried out using POM, which proved the presence of self-assembled fibrillar networks (SAFINs) in the gel. Finally powder X-ray structure determination revealed the presence of two non-equivalent molecules in an asymmetric unit which is responsible for the doublet resonance pattern in the solid state NMR spectra.

A Model of Anomalous Enzyme-Catalyzed Gel Degradation Kinetics

We show that a model of target location involving n noninteracting particles moving subdiffusively along a line segment (a generalization of a model introduced by Sokolov et al. [Biophys. J. 2005, 89, 895.]) provides a basis for understanding recent experiments by Pelta et al. [Phys. Rev. Lett. 2007, 98, 228302.] on the kinetics of diffusion-limited gel degradation. These experiments find that the time t(c) taken by the enzyme thermolysin to completely hydrolyze a gel varies inversely as roughly the 3/2 power of the initial enzyme concentration [E]. In general, however, this time would be expected to vary either as [E](-1) or as [E](-2), depending on whether the Brownian diffusion of the enzyme to the site of cleavage took place along the network chains (1-d diffusion) or through the pore spaces (3-d diffusion). In our model, the unusual dependence of t(c) on [E] is explained in terms of a reaction-diffusion equation that is formulated in terms of fractional rather than ordinary time derivatives.

Ion channel formation by zervamicin-IIB. A molecular modelling study.

Zervamicin-IIB (Zrv-IIB) is a 16 residue peptaibol which forms voltage-activated, multiple conductance level channels in planar lipid bilayers. A molecular model of Zrv-IIB channels is presented. The structure of monomeric Zrv-IIB is based upon the crystal structure of Zervamicin-Leu. The helical backbone is kinked by a hydroxyproline residue at position 10. Zrv-IIB channels are modelled as helix bundles of from 4 to 8 parallel helices surrounding a central pore. The monomers are packed with their C-terminal helical segments in close contact, and the bundles are stabilized by hydrogen bonds between glutamine 11 and hydroxyproline 10 of adjacent helices. Interaction energy profiles for movement of three different probes species (K+, Cl- and water) through the central pore are analyzed. The conformations of: (a) the sidechain of glutamine 3; (b) the hydroxyl group of hydroxyproline 10; and (c) the C-terminal hydroxyl group are "optimized" in order to maximize favourable interactions between the channel and the probes, resulting in favourable interaction energy profiles for all three. This suggests that conformational flexibility of polar sidechains enables the channel lining to mimic an aqueous environment.

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.

Characterization of Alkali Induced Formation of Lanthionine, Trisulfides, and Tetrasulfides from Peptide Disulfides using Negative Ion Mass Spectrometry

Peptide disulfides are unstable under alkaline conditions, resulting in the formation of products containing lanthionine and polysulfied linkages. Electrospray ionization mass spectrometry has been used to characterize major species obtained when cyclic and acyclic peptide disulfides are exposed to alkaline media. Studies on a model cyclic peptide disulfide (Boc - Cys - Pro - Leu - Cys - NHMe) and an acyclic peptide, oxidized glutathione, bis ((gamma)Glu Cys - Gly - COOH), are described. Disulfide cleavage reactions are initiated by the abstraction of (CH)-H-alpha or (CH)-H-beta protons of Cys residues, with Subsequent elimination of H2S or H2S2. The buildup of reactive thiol species which act on intermediates containing dehydroalanine residues, rationalizes the formation of lanthionine and polysulfide products. In the case of the cyclic peptide disulfide, the formation of cyclic products is facilitated by the intramolecular nature of the Michael addition reaction of thiols to the dehydroalanine residue. Mass spectral evidence for the intermediate species is presented by using alkylation of thiol groups as a trapping method. Mass spectral fragmentation in the negative ion mode of the peptides derived from trisulfides and tetrasulfides results in elimination of S-2. (J Am Soc Mass Spectrom 2009, 20, 783-791) (C) 2009 American Society for Mass Spectrometry.

Characterization of Alkali Induced Formation of Lanthionine, Trisulfides, and Tetrasulfides from Peptide Disulfides using Negative Ion Mass Spectrometry

Peptide disulfides are unstable under alkaline conditions, resulting in the formation of products containing lanthionine and polysulfied linkages. Electrospray ionization mass spectrometry has been used to characterize major species obtained when cyclic and acyclic peptide disulfides are exposed to alkaline media. Studies on a model cyclic peptide disulfide (Boc - Cys - Pro - Leu - Cys - NHMe) and an acyclic peptide, oxidized glutathione, bis ((gamma)Glu Cys - Gly - COOH), are described. Disulfide cleavage reactions are initiated by the abstraction of (CH)-H-alpha or (CH)-H-beta protons of Cys residues, with Subsequent elimination of H2S or H2S2. The buildup of reactive thiol species which act on intermediates containing dehydroalanine residues, rationalizes the formation of lanthionine and polysulfide products. In the case of the cyclic peptide disulfide, the formation of cyclic products is facilitated by the intramolecular nature of the Michael addition reaction of thiols to the dehydroalanine residue. Mass spectral evidence for the intermediate species is presented by using alkylation of thiol groups as a trapping method. Mass spectral fragmentation in the negative ion mode of the peptides derived from trisulfides and tetrasulfides results in elimination of S-2. (J Am Soc Mass Spectrom 2009, 20, 783-791) (C) 2009 American Society for Mass Spectrometry.

Glycosphingolipids in microdomain formation and their spatial organization

Plasma membranes regulate the influx and efflux of molecules across themselves and are also responsible for primary signal transduction between cells or within the same cell. Presence of lateral heterogeneity and the ability of reorganization are essential requirements for effective functioning of biomembranes. Lipid rafts are small, heterogeneous, dynamic domains enriched in glycosphingolipids, sphingomyelin and cholesterol, and profoundly influence membrane organization. Glycosphingolipids are inclined towards formation of liquid-ordered phases in membranes, both with and without cholesterol; they are therefore prime players in domain formation. Here, we discuss the role of glycosphingolipids in microdomain formation and their spatial organization within these rafts.

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.

Formation of an oxo-radical of peroxovanadate during reduction of diperoxovanadate with vanadyl sulfate or ferrous sulfate

Formation of oxygen radicals during reduction of H2O2 or diperoxovanadate with vanadyl sulfate or ferrous sulfate was indicated by the 1:2:2:1 electron spin resonance (ESR) signals of the DMPO adduct typical of standard radical dotOH radical. Signals derived from diperoxovanadate remained unchanged in the presence of ethanol in contrast to those from H2O2. This gave the clue that they represent a different radical, possibly radical dotOV(O2)2+, formed on breaking a peroxo-bridge of diperoxovanadate complex. The above reaction mixtures evolved dioxygen or, when NADH was present, oxidized it rapidly which was accompanied by consumption of dioxygen. Operation of a cycle of peroxovanadates including this new radical is suggested to explain these redox activities both with vanadyl and ferrous sulfates. It can be triggered by ferrous ions released from cellular stores in the presence of catalytic amounts of peroxovanadates.