The Structural Characterization of Folded Peptides Containing the Conformationally Constrained beta-Amino Acid Residue beta(2,2)Ac(6)c

Backbone alkylation has been shown to result in a dramatic reduction in the conformational space that is sterically accessible to a-amino acid residues in peptides. By extension, the presence of geminal dialkyl substituents at backbone atoms also restricts available conformational space for beta and ? residues. Five peptides containing the achiral beta 2,2-disubstituted beta-amino acid residue, 1-(aminomethyl)cyclohexanecarboxylic acid (beta 2,2Ac6c), have been structurally characterized in crystals by X-ray diffraction. The tripeptide Boc-Aib-beta 2,2Ac6c-Aib-OMe (1) adopts a novel fold stabilized by two intramolecular H-bonds (C11 and C9) of opposite directionality. The tetrapeptide Boc-Aib-beta 2,2Ac6c]2-OMe (2) and pentapeptide Boc-Aib-beta 2,2Ac6c]2-Aib-OMe (3) form short stretches of a hybrid a beta C11 helix stabilized by two and three intramolecular H-bonds, respectively. The structure of the dipeptide Boc-Aib-beta 2,2Ac6c-OMe (5) does not reveal any intramolecular H-bond. The aggregation pattern in the crystal provides an example of an extended conformation of the beta 2,2Ac6c residue, forming a polar sheet like H-bond. The protected derivative Ac-beta 2,2Ac6c-NHMe (4) adopts a locally folded gauche conformation about the C beta?Ca bonds (?=-55.7 degrees). Of the seven examples of beta 2,2Ac6c residues reported here, six adopt gauche conformations, a feature which promotes local folding when incorporated into peptides. A comparison between the conformational properties of beta 2,2Ac6c and beta 3,3Ac6c residues, in peptides, is presented. Backbone torsional parameters of H-bonded a beta/beta a turns are derived from the structures presented in this study and earlier reports.

Influence of Side-Chain on Structural Order and Photophysical Properties in Thiophene Based Diketopyrrolopyrroles: A Systematic Study

In this work, we have synthesized a series of TDPP derivatives with different alkyl groups such as n-hexyl (-C6H13) 3a, 2-ethylhexyl (-(2-C2H5)C6H12) 3b, triethylene glycol mono methyl ether (-(CH2CH2O)(3c)H-3, TEG) 3c, and octadodecyl (-(8-C8H17)C12H22) 3d. N,N dialkylation of Othiophene-diketopyrrolopyrrole (TDPP, 1) strongly influences its solubility, solid state packing, and structural order. These materials allow us to explicitly study the influence of alkyl chain on solid state packing and photophysical properties. TDPP moiety containing two different alkyl groups 3e (TEG and 2-ethylhexyl) and 3f (TEG and n-hexyl) were synthesized for the first time. The absorption spectra of all derivatives exhibited a red shift in solid state when compared to their solution spectra. The type of alkyl chains leads to change in the optical band gaps in solid state. The fluorescence study reveals that TDPP derivatives have strong pi-pi interaction in the solid state and the extent of bathochromic shift is due to combination of intramolecular interaction and formation of aggregates in solid state. This behavior strongly depends on the nature of alkyl chain. The presence of strong C-H center dot center dot center dot O inter chain interactions and CH-pi interactions in solid state exhibits strong influence on the photophysical properties of TDPP chromophore.

Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1 alpha and PKR

Background: Interaction of non-structural protein 5A (NS5A) of Hepatitis C virus (HCV) with human kinases namely, casein kinase 1 alpha (ck1 alpha) and protein kinase R (PKR) have different functional implications such as regulation of viral replication and evasion of interferon induced immune response respectively. Understanding the structural and molecular basis of interactions of the viral protein with two different human kinases can be useful in developing strategies for treatment against HCV. Results: Serine 232 of NS5A is known to be phosphorylated by human ck1 alpha. A structural model of NS5A peptide containing phosphoacceptor residue Serine 232 bound to ck1 alpha has been generated using the known 3-D structures of kinase-peptide complexes. The substrate interacting residues in ck1 alpha has been identified from the model and these are found to be conserved well in the ck1 family. ck1 alpha - substrate peptide complex has also been used to understand the structural basis of association between ck1 alpha and its other viral stress induced substrate, tumour suppressor p53 transactivation domain which has a crystal structure available. Interaction of NS5A with another human kinase PKR is primarily genotype specific. NS5A from genotype 1b has been shown to interact and inhibit PKR whereas NS5A from genotype 2a/3a are unable to bind and inhibit PKR efficiently. This is one of the main reasons for the varied response to interferon therapy in HCV patients across different genotypes. Using PKR crystal structure, sequence alignment and evolutionary trace analysis some of the critical residues responsible for the interaction of NS5A 1b with PKR have been identified. Conclusions: The substrate interacting residues in ck1 alpha have been identified using the structural model of kinase substrate peptide. The PKR interacting NS5A 1b residues have also been predicted using PKR crystal structure, NS5A sequence analysis along with known experimental results. Functional significance and nature of interaction of interferon sensitivity determining region and variable region 3 of NS5A in different genotypes with PKR which was experimentally shown are also supported by the findings of evolutionary trace analysis. Designing inhibitors to prevent this interaction could enable the HCV genotype 1 infected patients respond well to interferon therapy.

Investigations on structural and optical properties of co-doped (Ag, Co) ZnO nanoparticles

Undoped and co-doped (Ag, Co) ZnO powders were synthesized by chemical co-precipitation method without using any capping agent. The X-ray diffraction results indicate that the undoped and co-doped ZnO powders have pure hexagonal structure and are consisting of nanosized single-crystalline particles. The size of the nanoparticles increases with increasing Ag concentration from 1 to 5 mol% as compared to that of undoped ZnO. The presence of substitution dopants of Ag and Co in the ZnO host material was confirmed by the Energy dispersive analysis of X-rays (EDAX). Optical absorption measurements indicate blue shift and red-shift in the absorption band edge upon doping concentration of Ag and blue emission was observed by photoluminescence (PL) studies.

Synthesis, structural analysis and solvatochromic behaviour of 4,6-bis (4-butoxyphenyl)-2-methoxynicotinonitrile mesogen

In this communication, we report the synthesis and characterisation of a new luminescent liquid crystalline material, 4,6-bis (4-butoxyphenyl)-2-methoxynicotinonitrile (3). We have confirmed its structure by Fourier transform infrared and 1H nuclear magnetic resonance spectroscopy, elemental analysis and X-ray single crystal diffraction studies. The newly synthesised compound crystallises in a monoclinic system with the space group C2/c and its cell parameters are found to be a?=?25.181(4) angstrom, b?=?15.651(4)angstrom, c?=?12.703(19) angstrom, V?=?4880.4 (16) angstrom, Z?=?8. The results indicate that the presence of weak CH center dot center dot center dot O and CH center dot center dot center dot N hydrogen bonding as short-range intermolecular interactions are responsible for the formation of its crystal assembly. The measured torsion angle shows the existence of a distorted structure for the molecule wherein 4-butoxyphenylene ring substituent at the fourth position of the central pyridine ring forms a torsion angle chiC(4), C(3), C(10), C(19)] of 40.55 degrees. Its liquid crystalline behaviour was investigated with the aid of polarised optical microscopy and differential scanning calorimetry. The study reveals that the compound displays a broad nematic phase in the range of 78112 degrees C. Further, solution phase optical studies indicate that it is a blue light emitter in different non-polar and polar organic solvents at a concentration of 10-5M.

Synthesis and structural characterization of two-dimensional hierarchical covellite nano-structures

We report a simple, template free and low-temperature hydrothermal reaction pathway using Cu(II) - thiourea complex (prepared in situ from copper (II) chloride and thiourea as precursors) and citric acid as complexing agent to synthesize two-dimensional hierarchical nano-structures of covellite (CuS). The product was characterized with the help of X-ray powder diffraction (XRD), scanning electron microscopy (SEM), energy dispersive analysis of X-ray spectroscopy (EDAX) and X-ray photoelectron spectroscopy (XPS). The concentration of citric acid in the hydrothermal precursor solution was seen to have a profound effect on the nanostructure of the product generated. Based on the outcoming product nano-architecture at different concentration of the ionic surfactant in the hydrothermal precursor solution a possible mechanism suited for reaction and further nucleation is also discussed. (C) 2012 Elsevier B.V. All rights reserved.

Temperature dependent structural and dielectric investigations of PbZr0.5Ti0.5O3 solid solution at the morphotropic phase boundary

PbZr1-xTixO3 ceramics synthesised by low temperature calcination followed by sintering at 1280 degrees C show a Morphotropic Phase Boundary (MPB) for compositions of x=0.44-0.51. The morphotropic phase boundary is wider for samples with smaller grain sizes due to the synthesis route. A Rietveld analysis is performed on a composition of x=0.5 composition to quantify the phase fractions of the tetragonal and monoclinic phases present in the PZT system. Temperature dependent X-ray diffraction and dielectric studies of PbZr0.5Ti0.5O3 composition demonstrated a phase transformation from monoclinic to tetragonal at 270 degrees C followed by a ferroelectric tetragonal to a paraelectric cubic transition at 370 degrees C. Thus, the poling of these ceramics should be performed below 270 degrees C to benefit from the presence of a monoclinic phase. (C) 2012 Elsevier Ltd and Techna Group S.r.l. All rights reserved.

Structural and mechanical properties of room temperature sputter deposited CrN coatings

Chromium nitride (CrN) thin films were deposited at room temperature on silicon and glass substrates using DC reactive magnetron sputtering in Ar + N-2 plasma. Structure and mechanical properties of these films were examined by using XRD, FESEM and nanoindentation techniques. XRD studies revealed that films are of mixed phase at lower nitrogen partial pressure (P-N2) and single phase at higher (P-N2). Microscopy results show that the films were composed of non-equiaxed columns with nanocrystallite morphology. The hardness and elastic modulus of the films increase with increasing nitrogen partial pressure (P-N2). A maximum hardness of similar to 29 GPa and elastic modulus of 341 GPa were obtained, which make these films useful for several potential applications. (C) 2012 Elsevier Ltd. All rights reserved.

Effect of Calcination Temperature on Structural, Photoluminescence, and Thermo luminescence Properties of Y2O3:Eu3+ Nanophosphor

Red light emitting cubic Y1.95Eu0.05O3 nanophosphors have been synthesized by a low temperature solution combustion method using ethylene diamine tetra acetic acid (EDTA) as fuel. The systematic studies on the effect of calcination temperature on its structural, photoluminescence (PL), and thermoluminescence (TL) properties were reported. The crystallinity of the samples increases, and the strain is reduced with increasing calcination temperature. SEM micrographs reveal that samples lose their porous nature with an increase in calcination temperature. PL spectra show that the intensity of the red emission (611 nm) is highly dependent on the calcination temperature and is found to be 10 times higher when compared to as-formed samples. The optical band gap (E-g) was found to reduce with an increase of calcination temperature due to reduction of surface defects. The thermoluminescence (TL) intensity was found to be much enhanced in the 1000 degrees C calcined sample. The increase of PL and TL intensity with calcination temperature is attributed to the decrease of the nonradiative recombination probability, which occurs through the elimination of quenching defects. The trap parameters (E, b, s) were estimated from Chen's glow peak shape method and are discussed in detail for their possible usage in dosimetry.

A sequential dual method for structural SVMs

In many real world prediction problems the output is a structured object like a sequence or a tree or a graph. Such problems range from natural language processing to compu- tational biology or computer vision and have been tackled using algorithms, referred to as structured output learning algorithms. We consider the problem of structured classifi- cation. In the last few years, large margin classifiers like sup-port vector machines (SVMs) have shown much promise for structured output learning. The related optimization prob -lem is a convex quadratic program (QP) with a large num-ber of constraints, which makes the problem intractable for large data sets. This paper proposes a fast sequential dual method (SDM) for structural SVMs. The method makes re-peated passes over the training set and optimizes the dual variables associated with one example at a time. The use of additional heuristics makes the proposed method more efficient. We present an extensive empirical evaluation of the proposed method on several sequence learning problems.Our experiments on large data sets demonstrate that the proposed method is an order of magnitude faster than state of the art methods like cutting-plane method and stochastic gradient descent method (SGD). Further, SDM reaches steady state generalization performance faster than the SGD method. The proposed SDM is thus a useful alternative for large scale structured output learning.

Dramatic Structural Changes Resulting from the Loss of a Crucial Hydrogen Bond in the Hinge Region Involved in C-Terminal Helix Swapping in SurE: A Survival Protein from Salmonella typhimurium

Domain swapping is an interesting feature of some oligomeric proteins in which each protomer of the oligomer provides an identical surface for exclusive interaction with a segment or domain belonging to another protomer. Here we report results of mutagenesis experiments on the structure of C-terminal helix swapped dimer of a stationary phase survival protein from Salmonella typhimurium (StSurE). Wild type StSurE is a dimer in which a large helical segment at the C-terminus and a tetramerization loop comprising two beta strands are swapped between the protomers. Key residues in StSurE that might promote C-terminal helix swapping were identified by sequence and structural comparisons. Three mutants in which the helix swapping is likely to be avoided were constructed and expressed in E. coli. Three-dimensional X-ray crystal structures of the mutants H234A and D230A/H234A could be determined at 2.1 angstrom and 2.35 angstrom resolutions, respectively. Contrary to expectations, helix swapping was mostly retained in both the mutants. The loss of the crucial D230 OD2- H234 NE2 hydrogen bond (2.89 angstrom in the wild type structure) in the hinge region was compensated by new inter and intra-chain interactions. However, the two fold molecular symmetry was lost and there were large conformational changes throughout the polypeptide. In spite of these changes, the dimeric structure and an approximate tetrameric organization were retained, probably due to the interactions involving the tetramerization loop. Mutants were mostly functionally inactive, highlighting the importance of precise inter-subunit interactions for the symmetry and function of StSurE.

Optical and structural properties of nanostructured oxide thin films by sol‐gel technique

TiO2 and Al2O3 are commonly used materials in optical thin films in the visible and near‐infrared wavelength region due to their high transparency and good stability. In this work, TiO2 and Al2O3 single, and nano composite thin films with different compositions were deposited on glass and silicon substrates at room temperature using a sol‐gel spin coater. The optical properties like reflectance, transmittance and refractive index have been studied using Spectrophotometer, and structural properties using X‐Ray Diffraction (XRD) and Scanning Electron Microscopy (SEM).

Structural, EPR, optical and magnetic properties of alpha-Fe2O3 nanoparticles

alpha-Fe2O3 nanoparticles were synthesized by a low temperature solution combustion method. The structural, magnetic and luminescence properties were studied. Powder X-ray diffraction (PXRD) pattern of alpha-Fe2O3 exhibits pure rhombohedral structure. SEM micrographs reveal the dumbbell shaped particles. The EPR spectrum shows an intense resonance signal at g approximate to 5.61 corresponding to isolated Fe3+ ions situated in axially distorted sites, whereas the g approximate to 2.30 is due to Fe3+ ions coupled by exchange interaction. Raman studies show A(1g) (225 cm(-1)) and E-g (293 and 409 cm(-1)) phonon modes. The absorption at 300 nm results from the ligand to metal charge transfer transitions whereas the 540 nm peak is mainly due to the (6)A(1) + (6)A(1) —> T-4(1)(4G) + T-4(1)(4G) excitation of an Fe3+-Fe3+ pair. A prominent TL glow peak was observed at 140 C at heating rate of 5 degrees C s(-1). The trapping parameters namely activation energy (E), frequency factor (s) and order of kinetics (b) were evaluated and discussed. (C) 2012 Elsevier B.V. All rights reserved.

Structural and relaxor characteristics of Ca0.18Sr0.226Ba0.594Nb2O6

Polycrystalline Ca0.18Sr0.226Ba0.594Nb2O6 (CSBN18) was synthesized via the solid-state reaction route. X-ray structural studies confirmed it belonged to the tetragonal tungsten bronze family. Rietveld refinement of the X-ray data has been carried out for CSBN18 where the atomic positions and site occupancy factors for A-sites have been determined. The dielectric properties of CSBN18 ceramic were studied as a function of temperature in the 100 Hz - 1 MHz frequency range. The dielectric relaxation followed the Vogel-Fulcher relation wherein E-a = 37.4 meV; T-f = 131.5 degrees C and omega(0) = 4.31 x 10(9) rad s(-1). A high pyroelectric coefficient of similar to 250 mu C m(-2).K was obtained around the transition temperature (similar to 150 degrees C). This is significantly higher than that reported for polycrystalline SrxBa1-xNb2O6 (SBN). However, the piezoelectric coefficient (d(33)) of the title composition was as low as 6 pC N-1.