Sequence and conformational preferences at termini of alpha-helices in membrane proteins: Role of the helix environment

-helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These -helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze -helices in a high-resolution dataset of integral -helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. Proteins 2014; 82:3420-3436. (c) 2014 Wiley Periodicals, Inc.

Mixture of Fuels Approach for the Synthesis of SrFeO3-delta Nanocatalyst and Its Impact on the Catalytic Reduction of Nitrobenzene

A modified solution combustion approach was applied in the synthesis of nanosize SrFeO3-delta (SFO) using single as well as mixture of citric acid, oxalic acid, and glycine as fuels with corresponding metal nitrates as precursors. The synthesized and calcined powders were characterized by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), thermogravimetric analysis and derivative thermogravimetric analysis (TG-DTG), scanning electron microscopy, transmission electron microscopy, N-2 physisorption methods, and acidic strength by n-butyl amine titration methods. The FT-IR spectra show the lower-frequency band at 599 cm(-1) corresponds to metal-oxygen bond (possible Fe-O stretching frequencies) vibrations for the perovskite-structure compound. TG-DTG confirms the formation temperature of SFO ranging between 850-900 degrees C. XRD results reveal that the use of mixture of fuels in the preparation has effect on the crystallite size of the resultant compound. The average particle size of the samples prepared from single fuels as determined from XRD was similar to 50-35 nm, whereas for samples obtained from mixture of fuels, particles with a size of 30-25 nm were obtained. Specifically, the combination of mixture of fuels for the synthesis of SFO catalysts prevents agglomeration of the particles, which in turn leads to decrease in crystallite size and increase in the surface area of the catalysts. It was also observed that the present approach also impacted the catalytic activity of the SFO in the catalytic reduction of nitrobenzene to azoxybenzene.

Catalytic asymmetric desymmetrization approaches to enantioenriched cyclopentanes

Catalytic asymmetric desymmetrization represents an excellent strategy for accessing highly functionalized chiral building blocks. However, the application of desymmetrization for the synthesis of enantio-enriched cyclopentane derivatives remained limited, when compared to chiral cyclohexanes. We have recently developed a desymmetrization protocol for prochiral 2,2-disubstituted cyclopentene-1,3-diones by direct catalytic asymmetric vinylogous nucleophilic addition of deconjugated butenolides. In this perspective, we give an overview of asymmetric desymmetrization reactions leading to enantioenriched cyclopentanes and their derivatives. The focus is kept confined to the diverse nature of reactions used for this purpose. A brief discussion on the potential future directions is also provided.

Mycobacterium tuberculosis Cell Division Protein, FtsE, is an ATPase in Dimeric Form

FtsE is one of the earliest cell division proteins that assembles along with FtsX at the mid-cell site during cell division in Escherichia coli. Both these proteins are highly conserved across diverse bacterial genera and are predicted to constitute an ABC transporter type complex, in which FtsE is predicted to bind ATP and hydrolyse it, and FtsX is predicted to be an integral membrane protein. We had earlier reported that the MtFtsE of the human pathogen, Mycobacterium tuberculosis, binds ATP and interacts with MtFtsX on the cell membrane of M. tuberculosis and E. coli. In this study, we demonstrate that MtFtsE is an ATPase, the active form of which is a dimer, wherein the participating monomers are held together by non-covalent interactions, with the Cys84 of each monomer present at the dimer interface. Under oxidising environment, the dimer gets stabilised by the formation of Cys84-Cys84 disulphide bond. While the recombinant MtFtsE forms a dimer on the membrane of E. coli, the native MtFtsE seems to be in a different conformation in the M. tuberculosis membrane. Although disulphide bridges were not observed on the cytoplasmic side (reducing environment) of the membrane, the two participating monomers could be isolated as dimers held together by non-covalent interactions. Taken together, these findings show that MtFtsE is an ATPase in the non-covalent dimer form, with the Cys84 of each monomer present in the reduced form at the dimer interface, without participating in the dimerisation or the catalytic activity of the protein.

Rapid reduction of GO by hydrogen spill-over mechanism by in situ generated nanoparticles at room temperature and their catalytic performance towards 4-nitrophenol reduction and ethanol oxidation

Here, we report the clean and facile synthesis of Pt and Pd nanoparticles decorated on reduced graphene oxide (rGO) by the simultaneous reduction of graphene oxide (GO) and the metal ions in Mg/acid medium. As-generated Pt and Pd nanoparticles serve as a heterogeneous catalyst for the further reduction of the rGO by the hydrogen spill-over process. The C/O ratio is much higher as compared to the rGO obtained by the reduction of GO by only Mg/acid. Overall, the process is rapid, facile and green that does not require any toxic chemical agent or any rigorous chemical reactions. We perform the catalytic reduction of 4-nitophenol (4-NP) to 4-aminophenol (4-AP) at room temperature by Pd@rGO and Pt@rGO. The reduction is complete within 35 s for Pd@rGO and 60 s for Pt@rGO when 50 mu g of hybrid catalyst is used for 0.5 ml of 1 mM of 4-NP. In case of ethanol oxidation, the current density for Pd@rGO is comparable to commercial Pt/C but is doubled for Pt@rGO. Overall, both structures show highly stable catalytic activity compared to commercial Pt/C. (C) 2014 Elsevier B.V. All rights reserved.

Membrane-based deformable mirror: intrinsic aberrations and alignment issues

A deformable mirror (DM) is an important component of an adaptive optics system. It is known that an on-axis spherical/parabolic optical component, placed at an angle to the incident beam introduces defocus as well as astigmatism in the image plane. Although the former can be compensated by changing the focal plane position, the latter cannot be removed by mere optical realignment. Since the DM is to be used to compensate a turbulence-induced curvature term in addition to other aberrations, it is necessary to determine the aberrations induced by such (curved DM surface) an optical element when placed at an angle (other than 0 deg) of incidence in the optical path. To this effect, we estimate to a first order the aberrations introduced by a DM as a function of the incidence angle and deformation of the DM surface. We record images using a simple setup in which the incident beam is reflected by a 37 channel micro-machined membrane deformable mirror for various angles of incidence. It is observed that astigmatism is a dominant aberration, which was determined by measuring the difference between the tangential and sagittal focal planes. We justify our results on the basis of theoretical simulations and discuss the feasibility of using such a system for adaptive optics considering a trade-off between wavefront correction and astigmatism due to deformation. (C) 2015 Optical Society of America

Modification of crosslinked chitosan membrane using NaY zeolite for pervaporation separation of water-isopropanol mixtures

The blocked diisocyanate crosslinked chitosan membrane was modified by incorporating different mass% of NaY zeolite. The physico-chemical properties of resulting composite membranes were studied using Fourier transform infrared spectroscopy (FTIR), wide-angle X-ray diffraction (WAXD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and scanning electron microscopy (SEM). The mechanical properties of the membranes were studied using universal testing machine (UTM). After measuring the equilibrium swelling, membranes were subjected to pervaporation for separation of water-isopropanol mixtures. Both flux and selectivity were increased with increasing NaY zeolite content in the membranes. The membrane containing 40 mass% of NaY zeolite exhibited the highest separation selectivity of 11,241 with a flux of 11.37 x 10(-2) kg/m(2) h for 10 mass% of water in the feed. The total flux and flux of water are almost overlapping each other, suggesting that these membranes could be effectively used to break the azeotropic point of water-isopropanol mixture. From the temperature dependent diffusion and permeation values, the Arrhenius activation parameters were estimated. All the composite membranes exhibited lower activation energy compared to crosslinked membrane, indicating that the permeants require less energy during the process because of molecular sieving action attributed to the presence of sodalite and super cages in the framework of Nay zeolite. The Henry's mode of sorption dominates the process, giving an endothermic contribution. (C) 2014 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.

Ni Nano-particle Encapsulated in Hollow Carbon Sphere Electrocatalyst in Polymer Electrolyte Membrane Water Electrolyzer

The present study evaluates the synthesis by solvo-thermal method and electrocatalytic activity of nickel nano-particles encapsulated in hollow carbon sphere, in hydrogen and oxygen evolution reaction in PEM water electrolyzer. The XRD patterns have ascertained the formation of nickel metal with different planes in face centered cubic (fcc) and hexagonal closed pack (hcp) form. SEM and TEM images have confirmed the nickel nano-particles with diameter of 10-50 nm inside the 0.2 mu m sized hollow carbon spheres. The BET surface area values gradually decreased with greater encapsulation of nickel; although the electrochemical active surface area (ECSA) values have been calculated as quite higher. It confirms the well dispersion of nickel in the materials and induces their electrocatalytic performance through the active surface sites. The cyclic voltammetric studies have evaluated hydrogen desorption peaks as five times more intense in nickel encapsulated materials, in comparison to the pure hollow carbon spheres. The anodic peak current density value has reached the highest level of 1.9 A cm(-2) for HCSNi10, which gradually decreases with lesser amount of nickel in the electrocatalysts. These electrocatalysts have been proved electrochemically stable during their usage for 48 h long duration under potentiostatic condition. (C) 2015 Elsevier Ltd. All rights reserved.

Structural basis for the catalytic mechanism of homoserine dehydrogenase

Homoserine dehydrogenase (HSD) is an oxidoreductase in the aspartic acid pathway. This enzyme coordinates a critical branch point of the metabolic pathway that leads to the synthesis of bacterial cell-wall components such as L-lysine and m-DAP in addition to other amino acids such as L-threonine, L-methionine and L-isoleucine. Here, a structural rationale for the hydride-transfer step in the reaction mechanism of HSD is reported. The structure of Staphylococcus aureus HSD was determined at different pH conditions to understand the basis for the enhanced enzymatic activity at basic pH. An analysis of the crystal structure revealed that Lys105, which is located at the interface of the catalytic and cofactor-binding sites, could mediate the hydride-transfer step of the reaction mechanism. The role of Lys105 was subsequently confirmed by mutational analysis. Put together, these studies reveal the role of conserved water molecules and a lysine residue in hydride transfer between the substrate and the cofactor.

Effect of the nature of a transition metal dopant in BaTiO3 perovskite on the catalytic reduction of nitrobenzene

In the present study, we have synthesized Fe, Co and Ni doped BaTiO3 catalyst by a wet chemical synthesis method using oxalic acid as a chelating agent. The concentration of the metal dopant varies from 0 to 5 mol% in the catalysts. The physical and chemical properties of doped BaTiO3 catalysts were studied using various analytical methods such as X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), BET surface area and Transmission electron microscopy (TEM). The acidic strength of the catalysts was measured using a n-butylamine potentiometric titration method. The bulk BaTiO3 catalyst exhibits a tetragonal phase with the P4mm space group. A structural transition from tetrahedral to cubic phase was observed for Fe, Co and Ni doped BaTiO3 catalysts with an increase in doped metal concentration from 1 to 5 mol%. The particle sizes of the catalysts were calculated from TEM images and are in the range of 30-80 nm. All the catalysts were tested for the catalytic reduction of nitrobenzene to azoxybenzene. The BaTiO3 catalyst was found to be highly active and less selective compared to the doped catalysts which are active and highly selective towards azoxybenzene. The increase in selectivity towards azoxybenzene is due to an increase in acidic strength and reduction ability of the doped metal. It was also observed that the nature of the metal dopant and their content at the B-site has an impact on the catalytic reduction of nitrobenzene. The Co doped BaTiO3 catalyst showed better activity with only 0.5 mol% doping than Fe and Ni doped BaTiO3 catalysts with maximum nitrobenzene conversion of 91% with 78% selectivity to azoxybenzene. An optimum Fe loading of 2.5 mol% in BaTiO3 is required to achieve 100% conversion with 93% selectivity whereas Ni with 5 mol% showed a conversion of 93% and a azoxybenzene selectivity of 84%.

Identification of key amino acid residues in the catalytic mechanism of diaminopropionate ammonialyase from Salmonella typhimurium

Diaminopropionate ammonialyase (DAPAL), a fold-typeII pyridoxal 5-phosphate-dependent enzyme, catalyzes the ,-elimination of diaminopropionate (DAP) to pyruvate and ammonia. DAPAL was able to utilize both d- and l-DAP as substrates with almost equal efficiency. Mutational analysis of functionally important residues such as Thr385, Asp125 and Asp194 was carried out to understand the mechanism by which the isomers are hydrolyzed. Further, the putative residues involved in the formation of disulfide bond Cys271 and Cys299 were also mutated. T385S, T385D sDAPAL were as active with dl-DAP as substrate as sDAPAL, whereas the later exhibited a threefold increase in catalytic efficiency with d-Ser as substrate. Further analysis of these mutants suggested that DAPAL might follow an anti-E-2 mechanism of catalysis that does not involve the formation of a quinonoid intermediate. Of the two mutants of Asp125, D125E showed complete loss of activity with d-DAP as substrate, whereas the reaction with l-DAP was not affected significantly, demonstrating that Asp125 was essential for abstraction of protons from the d-isomer. By contrast, mutational analysis of Asp194 showed that the residue may not be directly involved in proton abstraction from l-DAP. sDAPAL does not form a disulfide bond in solution, although the position of Cys299 and Cys271 in the modeled structure of sDAPAL favored the formation of a disulfide bond. Further, unlike eDAPAL, sDAPAL could be activated by monovalent cations. Mutation of the cysteine residues showed that Cys271 may be involved in coordinating the monovalent cation, as observed in the case of other fold-typeII enzymes.

Catalytic pathway, substrate binding and stability in SAICAR synthetase: A structure and molecular dynamics study

The de novo purine biosynthesis is one of the highly conserved pathways among all organisms and is essential for the cell viability. A clear understanding of the enzymes in this pathway would pave way for the development of antimicrobial and anticancer drugs. Phosphoribosylaminoimidazole-succinocar boxamide (SAICAR) synthetase is one of the enzymes in this pathway that catalyzes ATP dependent ligation of carboxyaminoimidazole ribotide (CAIR) with L-aspartate (ASP). Here, we describe eight crystal structures of this enzyme, in C222(1) and H3 space groups, bound to various substrates and substrate mimics from a hyperthermophilic archaea Pyrococcus horikoshii along with molecular dynamics simulations of the structures with substrates. Complexes exhibit minimal deviation from its apo structure. The CAIR binding site displays a preference for pyrimidine nucleotides. In the ADP.TMP-ASP complex, the ASP binds at a position equivalent to that found in Saccharomyces cerevisiae structure (PDB: 2CNU) and thus, clears the ambiguity regarding ASP's position. A possible mode for the inhibition of the enzyme by CTP and UTP, observed earlier in the yeast enzyme, is clearly illustrated in the structures bound to CMP and UMP. The ADP.Mg2+.PO4.CD/MP complex having a phosphate ion between the ATP and CAIR sites strengthens one of the two probable pathways (proposed in Escherichia coli study) of catalytic mechanism and suggests the possibility of a phosphorylation taking place before the ASP's attack on CAIR. Molecular dynamic simulations of this enzyme along with its substrates at 90 degrees C reveal the relative strengths of substrate binding, possible antagonism and the role of Mg2+ ions. (C) 2015 Elsevier Inc. All rights reserved.

High Catalytic Activity of Amorphous Ir-Pi for Oxygen Evolution Reaction

Large-scale production of hydrogen gas by water electrolysis is hindered by the sluggish kinetics of oxygen evolution reaction (OER) at the anode. The development of a highly active and stable catalyst for OER is a challenging task. Electrochemically prepared amorphous metal-based catalysts have gained wide attention after the recent discovery of a cnbalt-phosphate (Co-Pi) catalyst: Herein, an amorphous iridium-phosphate (Ir-Pi) is investigated as an oxygen evolution catalyst. The catalyst is prepared by the anodic polarization of carbon paper electrodes in neutral phosphate buffer solutions containing IrCl3. The Ir-Pi film deposited on the substrate has significant amounts of phosphate and It centers in an oxidation state higher than +4. Phosphate plays a significant role in the deposition of the catalyst and also in its activity toward OER. The onset potential of OER on the Ir-Pi is about 150 mV lower in comparison with the Co-Pi under identical experimental conditions. Thus, Ir-Pi is a promising catalyst for electrochemical oxidation of water.

Molecular mechanism of water permeation in a helium impermeable graphene and graphene oxide membrane

Layers of graphene oxide (GO) are found to be good for the permeation of water but not for helium (Science, 2012, 335(6067), 442-444) suggesting that the GO layers are dynamic in the formation of a permeation route depending on the environment they are in (i.e., water or helium). To probe the microscopic origin of this observation we calculate the potential of mean force (PMF) of GO sheets (with oxidized and reduced parts), with the inter-planar distance as a reaction coordinate in helium and water. Our PMF calculation shows that the equilibrium interlayer distance between the oxidized part of the GO sheets in helium is at 4.8 angstrom leaving no space for helium permeation. In contrast, the PMF of the oxidized part of the GO in water shows two minima, one at 4.8 angstrom and another at 6.8 angstrom, corresponding to no water and a water filled region, thus giving rise to a permeation path. The increased electrostatic interaction between water with the oxidized part of the sheet helps the sheet open up and pushes water inside. Based on the entropy calculations for water trapped between graphene sheets and oxidized graphene sheets at different inter-sheet spacings, we also show the thermodynamics of filling.