Helix termination and chain reversal: Crystal and molecular structure of the alpha,beta-dehydrooctapeptide Boc-Val Delta Phe-Phe-Ala-Leu-Ala-Delta Phe-Leu-OH

The crystal structure of the dehydro octapeptide Boc-Val-Delta Phe-Phe-Ala-Leu-Ala-Delta Phe-Leu-OH has been determined to atomic resolution by X-ray crystallographic methods. The crystals grown by slow evaporation of peptide solution in methanol/water are orthorhombic, space group P2(1)2(1)2(1). The unit cell parameters are a = 8.404(3), b = 25.598(2) and c = 27.946(3) Angstrom, Z = 4. The agreement factor is R = 7.58% for 3636 reflections having (\F-o\) greater than or equal to 3 sigma (\F-o\). The peptide molecule is characterised by a 3(10)-helix at the N-terminus and a pi-turn at the C-terminus. This conformation is exactly similar to the helix termination features observed in proteins. The pi-turn conformation observed in the octapeptide is in good agreement with the conformational features of pi-turns seen in some proteins. The alpha(L)-position in the pi-turn of the octapeptide is occupied by Delta Phe(7), which shows that even bulky residues can be accommodated in this position of the pi-turns. In proteins, it is generally seen that alpha(L)-position is occupied by glycine residue. No intermolecular head-to-tail hydrogen bonds are observed in solid state structure of the octapeptide. A water molecule located in the unit cell of the peptide molecule is mainly used to hold the peptide molecule together in the crystal. The conformation observed for the octapeptide might be useful to understand the helix termination and chain reversal in proteins and to construct helix terminators for denovo protein design.

Rapid Synthesis of Ultrahigh Adsorption Capacity Zirconia by a Solution Combustion Technique

Tetragonal ZrO2 was synthesized by the solution combustion technique using glycine as the fuel. The compound was characterized by X-ray diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy, infrared spectroscopy, and BET surface area analysis. The ability of this compound to adsorb dyes was investigated, and the compound had a higher adsorption capacity than commercially activated carbon. Infrared spectroscopic observations were used to determine the various interactions and the groups responsible for the adsorption activity of the compound. The effects of the initial concentration of the dye, temperature, adsorbent concentration, and pH of the solution were studied. The kinetics of adsorption was described as a first-order process, and the relative magnitudes of internal and external mass transfer processes were determined. The equilibrium adsorption was also determined and modeled by a composite Langmuir-Freundlich isotherm.

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.

Peroxo-bridged divanadate as selective bromide oxidant in bromoperoxidation

Diperoxovanadate is effective only in presence of free vanadate in vanadium-dependent bromoperoxidation at physiological pH. Peroxide in the form of bridged divanadate complex (VOOV-type), but not the bidentate form as in diperoxovanadate, is proposed to be the oxidant of bromide. In order to obtain direct evidence, peroxo-divanadate complexes with glycyl-glycine, glycyl-alanine and glycyl-asparagine as heteroligands were synthesized. By elemental analysis and spectral studies they were characterized to be triperoxo-divanadates, [V2O2(O-2)(3)(peptide)(3)]. H2O, with the two vanadium atoms bridged by a peroxide and a heteroligand. The dipeptide seems to stabilize the peroxo-bridge by inter-ligand interaction, possibly hydrogen bonding. This is indicated by rapid degradation of these compounds on dissolving in water with partial loss of peroxide accompanied by release of bubbles of oxygen. The V-51-NMR spectra of such solutions showed diperoxovanadate and decavanadate (oligomerized from vanadate) as the products. Additional oxygen was released on treating these solutions with catalase as expected of residual diperoxovanadate. The solid compounds when added to the reaction mixtures showed transient, rapid bromoperoxidation reaction, but not oxidation of NADH or inactivation of glucose oxidase, the other two activities shown by a mixture of diperoxovanadate and vanadyl. This demonstration of peroxide-bridged divanadate as powerful, selective oxidant of bromide, active at physiological pH, should make it a possible candidate of mimic in the action of vanadium in bromoperoxidase proteins.

Unique Utilization of a Phosphoprotein Phosphatase Fold by a Mammalian Phosphodiesterase Associated with WAGR Syndrome

Metallophosphoesterase-domain-containing protein 2 (MPPED2) is a highly evolutionarily conserved protein with orthologs found from worms to humans. The human MPPED2 gene is found in a region of chromosome 11 that is deleted in patients with WAGR (Wilms tumor, aniridia, genitourinary anomalies, and mental retardation) syndrome, and MPPED2 may function as a tumor suppressor. However, the precise cellular roles of MPPED2 are unknown, and its low phosphodiesterase activity suggests that substrate hydrolysis may not be its prime function. We present here the structures of MPPED2 and two mutants, which show that the poor activity of MPPED2 is not only a consequence of the substitution of an active-site histidine residue by glycine but also due to binding of AMP or GMP to the active site. This feature, enhanced by structural elements of the protein, allows MPPED2 to utilize the conserved phosphoprotein-phosphatase-like fold in a unique manner, ensuring that its enzymatic activity can be combined with a possible role as a scaffolding or adaptor protein. (C) 2011 Elsevier Ltd. All rights reserved.

CO oxidation by CeO(2)-Al(2)O(3)-CeAlO(3) hybrid oxides

A modified solution combustion technique was successfully used to synthesize sub-10 nm crystallites of hybrid CeO(2)-Al(2)O(3)-CeAlO(3). The fuel in the solution combustion was tuned to obtain mixed oxides and solid solutions of the compound. The compounds were characterized by X-ray diffraction, transmission electron microscopy and X-ray photoelectron spectroscopy. XRD and TEM analysis showed the substitution of Al(3+) ions in the CeO(2) matrix when a combination of glycine, urea, hexamine and oxalyl dihydrazide was used as fuel for the synthesis. The compounds showed high activity for CO oxidation and the activity of the compounds was dependent upon the composition of the oxide.

Subdiffusion as a model of transport through the nuclear pore complex

Cargo transport through the nuclear pore complex continues to be a subject of considerable interest to experimentalists and theorists alike. Several recent studies have revealed details of the process that have still to be fully understood, among them the apparent nonlinearity between cargo size and the pore crossing time, the skewed, asymmetric nature of the distribution of such crossing times, and the non-exponentiality in the decay profile of the dynamic autocorrelation function of cargo positions. In this paper, we show that a model of pore transport based on subdiffusive particle motion is in qualitative agreement with many of these observations. The model corresponds to a process of stochastic binding and release of the particle as it moves through the channel. It suggests that the phenylalanine-glycine repeat units that form an entangled polymer mesh across the channel may be involved in translocation, since these units have the potential to intermittently bind to hydrophobic receptor sites on the transporter protein. (C) 2011 American Institute of Physics. [doi:10.1063/1.3651100]

The beta-Glucoside (bgl) Operon of Escherichia coli Is Involved in the Regulation of oppA, Encoding an Oligopeptide Transporter

We report that the bgl operon of Escherichia coli, encoding the functions necessary for the uptake and metabolism of aryl-beta-glucosides, is involved in the regulation of oligopeptide transport during stationary phase. Global analysis of intracellular proteins from Bgl-positive (Bgl(+)) and Bgl-negative (Bgl(-)) strains revealed that the operon exerts regulation on at least 12 downstream target genes. Of these, oppA, which encodes an oligopeptide transporter, was confirmed to be upregulated in the Bgl(+) strain. Loss of oppA function results in a partial loss of the growth advantage in stationary-phase (GASP) phenotype of Bgl(+) cells. The regulatory effect of the bgl operon on oppA expression is indirect and is mediated via gcvA, the activator of the glycine cleavage system, and gcvB, which regulates oppA at the posttranscriptional level. We show that BglG destabilizes the gcvA mRNA in vivo, leading to reduced expression of gcvA in the stationary phase. Deletion of gcvA results in the downregulation of gcvB and upregulation of oppA and can partially rescue the loss of the GASP phenotype seen in Delta bglG strains. A possible mechanism by which oppA confers a competitive advantage to Bgl(+) cells relative to Bgl(-) cells is discussed.

Structure-function relationship in serine hydroxymethyltransferase

Serine hydroxymethyltransferase (SHMT), a pyridoxal-5V-phosphate (PLP)-dependent enzyme catalyzes thetetrahydrofolate (H4-folate)- dependent retro-aldol cleavage of serine to form 5,10-methylene H4-folate and glycine. The structure–function relationship of SHMT wasstudied in our laboratory initially by mutation of residues that are conserved in all SHMTs and later by structure-based mutagenesis of residues located in the active site. The analysis of mutants showed that K71, Y72, R80, D89, W110, S202, C203, H304, H306 and H356 residues are involved in maintenance of the oligomeric structure. The mutation of D227, a residue involved in charge relay system, led to the formation of inactive dimers, indicating that this residue has a role in maintaining the tetrameric structure and catalysis. E74, a residue appropriately positioned in the structure of the enzyme to carry out proton abstraction, was shown by characterization of E74Q and E74K mutants to be involved in conversion of the enzyme from an ‘open’ to ‘closed’ conformation rather than proton abstraction from the hydroxylgroup of serine. K256, the residue involved in the formation of Schiffs base with PLP, also plays a crucial role in the maintenance of the tetrameric structure. Mutation of R262 residue established the importance of distal interactions in facilitating catalysis and Y82 is not involved in the formaldehyde transfer via the postulated hemiacetal intermediate but plays a role in stabilizing the quinonoid intermediate.The mutational analysis of scSHMT along with the structure of recombinant Bacillus stearothermophilus SHMT and its substrate(s)complexes was used to provide evidence for a direct transfer mechanism rather than retro-aldol cleavage for the reaction catalyzed by SHMT.

Solution Combustion Synthesis of Nanosized Copper Chromite and Its Use as a Burn Rate Modifier in Solid Propellants

Nano sized copper chromite, which is used as a burn rate accelerator for solid propellants, was synthesized by the solution combustion process using citric acid and glycine as fuel. Pure spinel phase copper chromite (CuCr2O4) was synthesized, and the effect of different ratios of Cu-Cr ions in the initial reactant and various calcination temperatures on the final properties of the material were examined. The reaction time for the synthesis with glycine was lower compared to that with citric acid. The synthesized samples from both fuel cycles were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), BET surface area analysis, and scanning electron microscope (SEM). Commercial copper chromite that is currently used in solid propellant formulation was also characterized by the same techniques. XRD analysis shows that the pure spinel phase compound is formed by calcination at 700 degrees C for glycine fuel cycle and between 750 and 800 degrees C for citric acid cycle. XPS results indicate the variation of the oxidation state of copper in the final compound with a change in the Cu-Cr mole ratio. SEM images confirm the formation of nano size spherical shape particles. The variation of BET surface area with calcination temperature was studied for the solution combusted catalyst. Burn rate evaluation of synthesized catalyst was carried out and compared with the commercial catalyst. The comparison between BET surface area and the burn rate depicts that surface area difference caused the variation in burn rate between samples. The reason behind the reduction in surface area and the required modifications in the process are also described.

Effect of different fuels on structural, thermo and photoluminescent properties of Gd 2O 3 nanoparticles

Gd 2O 3 nanoparticles (27-60nm) have been synthesized by the low temperature solution combustion method using citric acid, urea, glycine and oxalyl dihydrazide (ODH) as fuels in a short time. The structural and luminescence properties have been carried out using powder X-ray diffraction (PXRD), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), Raman, UV-Vis, photoluminescence (PL) and thermoluminescence (TL) techniques. The optical band gap values were estimated for as formed and 800°C calcined samples. The band gap values in as-formed and calcined samples were found to be in the range 4.89-5.59eV. It is observed that, the band gap values are lower for as-formed products and it has been attributed to high degree of structural defects. However, in calcined samples, structure becomes more order with reduced structure defects. Upon 270nm excitation, deep blue UV-band at �390nm along with blue (420-482nm), green (532nm) and red emission (612nm) was observed. The 390nm emission peak may be attributed to recombination of delocalized electron close to the conduction band with a single charged state of surface oxygen vacancy. TL measurements were carried out on Gd 2O 3 prepared by different fuels by irradiating with γ-rays (1kGy). A well resolved glow peak at 230°C was observed for all the samples. It is observed that TL intensity is found to be higher in for urea fuel when compared to others. From TL glow curves the kinetic parameters were estimated using Chen's peak shape method and results are discussed in detail. © 2012 Elsevier B.V.

Cis-trans peptide variations in structurally similar proteins

The presence of energetically less favourable cis peptides in protein structures has been observed to be strongly associated with its structural integrity and function. Inter-conversion between the cis and trans conformations also has an important role in the folding process. In this study, we analyse the extent of conservation of cis peptides among similar folds. We look at both the amino acid preferences and local structural changes associated with such variations. Nearly 34% of the Xaa-Proline cis bonds are not conserved in structural relatives; Proline also has a high tendency to get replaced by another amino acid in the trans conformer. At both positions bounding the peptide bond, Glycine has a higher tendency to lose the cis conformation. The cis conformation of more than 30% of beta turns of type VIb and IV are not found to be conserved in similar structures. A different view using Protein Block-based description of backbone conformation, suggests that many of the local conformational changes are highly different from the general local structural variations observed among structurally similar proteins. Changes between cis and trans conformations are found to be associated with the evolution of new functions facilitated by local structural changes. This is most frequent in enzymes where new catalytic activity emerges with local changes in the active site. Cis-trans changes are also seen to facilitate inter-domain and inter-protein interactions. As in the case of folding, cis-trans conversions have been used as an important driving factor in evolution.

Dispersed ZrO2 nanoparticles in MCM-48 with high adsorption activity

A new two-step synthesis of ZrO2-MCM nanocomposites using the gel combustion technique was accomplished; the resulting material had a high-surface area and showed very high adsorption activity. The deposition of 25 nm ZrO2 particles over MCM was achieved using gel combustion technique with glycine as a fuel, and the formation of nanocomposites was confirmed using transmission electron microscopy. The composites were also characterized by XRD, SEM, FTIR and N2 adsorption-desorption analysis. The nanocomposites were tested for the adsorption of cationic dyes. High rates of adsorption and large dye uptake were observed over the nanocomposites. The rate of adsorption over the nanocomposites was higher than that observed for physical ZrO2-MCM mixtures and commercial activated carbon. The nanocomposite with 10 wt % ZrO2 showed the highest rate of adsorption owing to the synergistic effects of ZrO2 surface groups, smaller particle size, fine dispersion and high-surface area of the composite. (c) 2012 American Institute of Chemical Engineers AIChE J, 58: 29872996, 2012

Synthesis and characterization of nano CoFe2O4 by low‐temperature combustion synthesis using different fuels

The combustion synthesis has been utilized to prepare nanophased powders of cobalt spinel ferrite using ODH and glycine fuels. The product was characterized by X‐ray diffraction; Fourier transformed spectroscopy, scanning electron microscopy, UV‐Vis absorption etc. The XRD patterns reveal spinal cubic structure. SEM profiles show the product is porous, agglomeration, irregular in shape. The crystallite size was estimated using Scherer’s formula and W‐H plots and show nano in size (13 nm: ODH & 36 nm: Glycine). The UV‐Vis absorption shows at ∼430 nm in both the samples.

Platinum Ion-Doped TiO2: High Catalytic Activity of Pt2+ with Oxide Ion Vacancy in Ti1-x4+Ptx2+O2-x Compared to Pt4+ without Oxide Ion Vacancy in Ti1-x4+Ptx4+O2

Ti0.97Pt0.032+O1.97 and Ti0.97Pt0.034+O2 have been synthesized by a solution combustion method using alanine and glycine as the fuels, respectively. Both crystallize in anatase TiO2 structure with 15 nm average crystallite size. X-ray photoelectron spectroscopy (XPS) confirmed Pt ions are in the 2+ state in Ti0.97Pt0.03O1.97 (alanine) and 4+ state in Ti0.97Pt0.03O2 (glycine). The rate of CO oxidation occurring over Ti0.97Pt0.032+O1.97 (0.76 mu mol.g(-1).s(-1)) is similar to 10, times more than that over Ti0.97Pt0.034+O2 at 60 degrees C (0.08 mu mol.g(-1).s(-1)). A large shift in 100% hydrocarbons conversion to lower temperature was observed for Pt2+ ion-substituted TiO2 relative 10 that for Pt4+ ion-substituted TiO2. After reoxidation of the reduced compound by H-2 as well as CO, Pt ions are stabilized in mixed valences, 2+ and 4+ states. The role of oxide ion vacancy has been demonstrated by CO oxidation and H-2 + O-2 recombination reactions in the presence and absence of O-2. We analyze the activated lattice oxygens upon substitution of Pt2+ and Pt4+ ions in TiO2, using first-principles density functional theory (DFT) calculations with supercells of Ti31Pt1O63, Ti30Pt2O62, and Ti29Pt3O61 for Pt2+ ion substitution and Ti31Pt1O64, Ti30Pt2O62, and Ti29Pt3O61 for Pt4+ ion substitution in TiO2. We find that the local structure of Pt2+ ion has a distorted square planar geometry and that of Pt4+ ion has an octahedral geometry similar to that of Ti4+ ion in pure TiO2. The change in coordination of Pt2+ ion gives rise to weakly bonded oxygens, and these oxygens are involved in high rates of catalytic reaction. Thus, the high catalytic activity results from synergistic roles of Pt2+ ion and oxide ion vacancy and weakly bonded lattice oxygen.