Structure and nucleotide specificity of Staphylococcus aureus dihydrodipicolinate reductase (DapB)

Lysine biosynthesis proceeds by the nucleotide-dependent reduction of dihydrodipicolinate (DHDP) to tetrahydrodipicolinate (THDP) by dihydrodipicolinate reductase (DHDPR). The S. aureus DHDPR structure reveals different conformational states of this enzyme even in the absence of a substrate or nucleotide-cofactor. Despite lacking a conserved basic residue essential for NADPH interaction, S. aureus DHDPR differs from other homologues as NADPH is a more preferred co-factor than NADH. The structure provides a rationale-Lys35 compensates for the co-factor site mutation. These observations are significant for bi-ligand inhibitor design that relies on ligand-induced conformational changes as well as co-factor specificity for this important drug target. Structured summary of protein interactions: DHDPR binds to DHDPR by molecular sieving (View interaction). DHDPR binds to DHDPR by dynamic light scattering (View interaction). DHDPR binds to DHDPR by X-ray crystallography (View interaction). (C) 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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.

Synthesis of new (Bi, La)(3)MSb(2)O(11) phases (M = Cr, Mn, Fe) with KSbO(3)-type structure and their magnetic and photocatalytic properties

Synthesis and structure of new (Bi, La)(3)MSb(2)O(11) phases (M = Cr, Mn, Fe) are reported in conjunction with their magnetic and photocatalytic properties. XRD refinements reflect that Bi(3)CrSb(2)O(11), Bi(2)LaCrSb(2)O(11), Bi(2)LaMnSb(2)O(11) and Bi(2)LaFeSb(2)O(11) adopt KSbO(3)-type structure (space group, Pn (3) over bar). The structure can be described through three interpenetrating networks where the first is the (M/Sb)O(6) octahedral network and other two are the identical networks having Bi(6)O(4) composition. The magnetic measurements on Bi(2)LaCrSb(2)O(11) and Bi(2)LaMnSb(2)O(11) show paramagnetic behaviour with magnetic moments close to the expected spin only magnetic moments of Cr(+3) and Mn(+3). The UV-Visible diffuse reflectance spectra are broad and indicate that these materials possess a bandgap of similar to 2 eV. The photocatalytic activity of these materials has been investigated by degrading Malachite Green (MG) under exposure to UV light.

Coupled electro-mechanical response of an electroactive polymer cantilever structure and its application in energy harvesting

Ionic polymer-metal composites (IPMC), piezoelectric polymer composites and nematic elastomer composites are materials, which exhibit characteristics of both sensors and actuators. Large deformation and curvature are observed in these systems when electric potential is applied. Effects of geometric non-linearity due to the chargeinduced motion in these materials are poorly understood. In this paper, a coupled model for understanding the behavior of an ionic polymer beam undergoing large deformation and large curvature is presented. Maxwell's equations and charge transport equations are considered which couple the distribution of the ion concentration and the pressure gradient along length of a cantilever beam with interdigital electrodes. A nonlinear constitutive model is derived accounting for the visco-elasto-plastic behavior of these polymers and based on the hypothesis that the presence of electrical charge stretches/contracts bonds, which give rise to electrical field dependent softening/hardening. Polymer chain orientation in statistical sense plays a role on such softening or hardening. Elementary beam kinematics with large curvature is considered. A model for understanding the deformation due to electrostatic repulsion between asymmetrical charge distributions across the cross-sections is presented. Experimental evidence that Silver(Ag) nanoparticle coated IPMCs can be used for energy harvesting is reported. An IPMC strip is vibrated in different environments and the electric power against a resistive load is measured. The electrical power generated was observed to vary with the environment with maximum power being generated when the strip is in wet state. IPMC based energy harvesting systems have potential applications in tidal wave energy harvesting, residual environmental energy harvesting to power MEMS and NEMS devices.

Structure and Bonding in Stannadiphospholes and their Dianions SnC(2)P(2)R(2)(m) (R=H, tBu m=0,-2): A Comparative Study with C(5)H(5)(+) and C(5)H(5)(-) Analogues

The potential energy surfaces of both neutral and dianionic SnC(2)P(2)R(2) (R=H, tBu) ring systems have been explored at the B3PW91/LANL2DZ (Sn) and 6-311 + G* (other atoms) level. In the neutral isomers the global minimum is a nido structure in which a 1,2-diphosphocyclobutadiene ring (1,2-DPCB) is capped by the Sn. Interestingly, the structure established by Xray diffraction analysis, for R=tBu, is a 1,3-DPCB ring capped by Sn and it is 2.4 kcal mol(-1) higher in energy than the 1,2-DPCB ring isomer. This is possibly related to the kinetic stability of the 1,3-DPCB ring, which might originate from the synthetic precursor ZrCp(2)tBu(2)C(2)P(2). In the case of the dianionic isomers we observe only a 6 pi-electron aromatic structure as the global minimum, similarly to the cases of our previously reported results with other types of heterodiphospholes.([1,4,19]) The existence of large numbers of cluster-type isomers in neutral and 6 pi-planar structures in the dianions SnC(2)P(2)R(2)(2-) (R=H, tBu) is due to 3D aromaticity in neutral clusters and to 2D pi aromaticity of the dianionic rings. Relative energies of positional isomers mainly depend on: 1) the valency and coordination number of the Sn centre, 2) individual bond strengths, and 3) the steric effect of tBu groups. A comparison of neutral stannadiphospholes with other structurally related C(5)H(5)(+) analogues indicates that Sn might be a better isolobal analogue to P(+) than to BH or CH(+). The variation in global minima in these C(5)H(5)(+) analogues is due to characteristic features such as 1) the different valencies of C, B, P and Sn, 2) the electron deficiency of B, 3) weaker p pi-p pi bonding by P and Sn atoms, and 4) the tendency of electropositive elements to donate electrons to nido clusters. Unlike the C5H5+ systems, all C(5)H(5)(-) analogues have 6 pi-planar aromatic structures as global minima. The differences in the relative ordering of the positional isomers and ligating properties are significant and depend on 1) the nature of the pi orbitals involved, and 2) effective overlap of orbitals.

Relationship Between Physical Structure and Tribology of Single Soot Particles Generated by Burning Ethylene

Ethylene gas is burnt and the soot generated is sampled thermophoretically at different heights along the flame axis starting from a region close to the root of the flame. The morphology and crystallinity of the particle are recorded using high resolution transmission electron microscopes. The hardness of a single particle is measured using a nanoindenter. The frictional resistance and material removal of a particle are measured using an atomic force microscope. The particles present in the mid-flame region are found to have a crystalline shell. The ones at the flame root are found to be highly disordered and the ones at the flame tip and above have randomly distributed pockets of short range order. The physical state of a particle is found to relate, but not very strongly, with the mechanical and tribological properties of the particles.

Correlations between structure and thermodynamic properties of spinels and their applications in technology

Measurements a/the Gibbs' energy enthalpy and entrupy vffarmation oj chromites, vanadites and alumlnat.:s 0/ F", Ni. Co'. Mn, Zn Mg and Cd, using solid oxide galvanic cells over a ternperature range extending approximately lOOO°C, have shown that the '~'Ilir"!,,, J'JrIl/iJ~ tion 0/ cubic 2-3 oxide spinel phases (MX!O,), from component oxide (MO) with rock-salt and X.Os whir c(1f'l/!ldwn st!'llt'lw,·. call b,' represented by a semi-empirical correlalion, ~S~ = --LiS + L'i,SM +~S~:"d(±O.3) cal.deg-1 mol-1 where /',.SM Is the entropy 0/calian mixing oillhe tetrahedral alld octahedral sites o/the spinel and Sr:~ is tlie enfropy associaf,'d Wifh Ih,' randomization a/the lahn-Telier distortions. A review a/the methods/or evaluating the cation distriblltion lfl spille!s suggeJ{j' l/r,l! Ihe most promising scheme is based Oil octahedral site preference energies from the crystal field theory for the Iral1silioll IIIl'f"! IlIIL';. For I/""-Irallsifioll melal cal ions site preference energies are derived relative /0 thol'lt fLI, [ransilion metal ions from measured high tClllP('ftJi ure Cal iUlI disll iiJuriol1 in spine! phases thar contail! one IransilioJl metal and another non-transition metal carion. For 2-3 srinds compulatiorrs b,IS"J Oil i.!c[J;' Temkin mixing on each catioll subialtice predici JistributionJ that are In fair agreement with X-ray and 1I1'IIIrOll ditTraction, /IIdg""!ic dll.! electrical propcrries, and spectroscopic measurements. In 2-4 spineis mixing vI ions do not foliow strictly ideal slllIistli:al Jaws, Th,' OIl/up) associated with the randomizalion 0/the Jllhn-Teller dislOriioll" appear to be significant, only ill spinels witll 3d'. 3d', 3d' (ifld~UI' iOtls in tetrahedral and 3d' and 3d9 ions in octahedral positions. Application 0/this structural model for predicting the thermodynamic proputies ofspinel solid .,olutiofl5 or,' illustrated. F,lr complex systems additional contributions arising from strain fields, redox equilibria and off-center ions have to be qllalllififti. The entropy correlation for spinels provides a method for evaluating structure tran:.jormafiofl entropies in silllple o.\id.-s, ["founlllion on the relative stabilities ofoxides in different crystallCtructures is USe/III for computer ea/culaliof! a/phase dfugrullls ofIlIrer,',,1 III (N.lll1ie5 by method, similar to thost: used by Kaufman and Bernstein for refractory alloy systems. Examples oftechnoiogical appliCation tnclude the predictioll ofdeoxidation equilibria in Fe-Mn-AI-O s),slelll at 1600°C duj ,'Ulllpltfalion 0/phase relutions in Fe-Ni-Cr-S system,

Relation between Local Structure and Glass Forming Ability of Liquid Alloys

An attempt has been made to describe the glass forming ability (GFA) of liquid alloys, using the concepts of the short range order (SRO) and middle range order (MRO) characterizing the liquid structure.A new approach to obtain good GFA of liquid alloys is based on the following four main factors: (1) formation of new SRO and competitive correlation with two or more kinds of SROs for crystallization, (2) stabilization of dense random packing by interaction between different types of SRO, (3) formation of stable cluster (SC) or middle range order (MRO) by harmonious coupling of SROs, and (4) difference between SRO characterizing the liquid structure and the near-neighbor environment in the corresponding equilibrium crystalline phases. The atomic volume mismatch estimated from the cube of the atomic radius was found to be a close relation with the minimum solute concentration for glass formation. This empirical guideline enables us to provide the optimum solute concentration for good GFA in some ternary alloys. Model structures, denoted by Bernal type and the Chemical Order type, were again tested in the novel description for the glass structure as a function of solute concentration. We illustrated the related energetics of the completion between crystal embryo and different types of SRO. Recent systematic measurements also provide that thermal diffusivity of alloys in the liquid state may be a good indicator of their GFA.

Structure and temperature dependence of conductivity of Ag2.5Se‐Se composite

Rapid solidification of Ag‐53 at. % Se alloy resulted in the formation of a composite mixture of Ag2.5Se and Se. The microstructure consists of spherical Se grains of 2–20 μm size, randomly distributed in a matrix of Ag2.5 Se. The Se grains were found to be layered hexagonal while the Ag2.5 Se had an orthorhombic crystal structure. The unit cell size of this phase, however, was twice that reported for the equilibrium orthorhombic Ag2 Se compound. The conductivity σ variation with temperature in the range 80–320 K was found to be similar to that observed in degenerate semiconductors. The σ decreased from 295 Ω−1 cm−1 at room temperature to a saturation value of 70 Ω−1 cm−1 for temperatures <80 K. The results are discussed in terms of percolation conduction in the Ag2.5 Se phase.

Structure and dynamics of protein excited states with millisecond lifetimes

An in-depth understanding of biological processes often requires detailed atomic resolution structures of the molecules involved. However in solution where most of these processes occur the conformation of biomolecules like RNA, DNA and proteins is not static but fluctuates. Routinely used structural techniques like X-ray crystallography, NMR spectroscopy and cryo-electron microscopy have almost always been used to determine the structure of the dominant conformation or obtain an average structure of the biomolecule in solution with very little detailed information regarding the dynamics of these molecules in solution. Over the last few years, NMR based methods have been developed to study the dynamics of these biomolecules in solution in a site-specific manner with the aim of generating structures of the different conformations that these molecules can adopt in solution. One powerful technique is the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiment, which can be used to detect and characterize protein excited states that are populated for as less as 0.5% of the time with ∼0.5–10 millisecond lifetimes. Due to recent advances in NMR pulse sequences and labeling methodology, it is now possible to determine the structures of these transiently populated excited states with millisecond lifetimes by obtaining accurate chemical shifts, residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) of these excited states. In these excited states the dynamics of some methyl containing residues can also be studied.

Structure and Photocatalytic Activity of Ti 1- x M x O 2±δ (M = W, V, Ce, Zr, Fe, and Cu) Synthesized by Solution Combustion Method

The W, V, Ce, Zr, Fe, and Cu metal ion substituted nanocrystalline anatase TiO2 was prepared by solution combustion method and characterized by XRD, Raman, BET, EPR, XPS, IR TGA, UV absorption, and photoluminescence measurements. The structural studies indicate that the solid solution formation was limited to a narrow range of concentrations of the dopant ions. The photocatalytic degradation of 4-nitrophenol under UV and solar exposure was investigated with Ti1-xMxO2±δ. The degradation rates of 4-nitrophenol with these catalysts were lesser than the degradation rates of 4-nitrophenol with undoped TiO2 both with UV exposure and solar radiation. However, the photocatalytic activities of most metal ion doped TiO2 are higher than the activity of the commercial TiO2, Degussa P25. The decrease in photocatalytic activity is correlated with decrease in photoluminescence due to electron states of metal ions within the band gap of TiO2.

Synthesis, structure and photocatalytic activity of nano TiO2 and nano Ti1-xMxO2-delta (M = Cu, Fe, Pt, Pd, V, W, Ce, Zr)

We have synthesized 5-7 nm size, highly crystalline TiO2 which absorbs radiation in the visible region of solar spectrum. The material shows higher photocatalytic activity both in UV and visible region of the solar radiation compared to commercial Degussa P25 TiO2. Transition metal ion substitution for Ti4+ creates mid-gap, states which act as recombination centers for electron-hole induced by photons thus reducing photocatalytic activity. However, Pt, Pd and Cu ion substituted TiO2 are excellent CO oxidation and NO reduction catalysts at temperatures less than 100 degrees C.