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.

Detection of a periodic structure embedded in surface roughness, for various correlation functions

This paper deals with surface profilometry, where we try to detect a periodic structure, hidden in randomness using the matched filter method of analysing the intensity of light, scattered from the surface. From the direct problem of light scattering from a composite rough surface of the above type, we find that the detectability of the periodic structure can be hindered by the randomness, being dependent on the correlation function of the random part. In our earlier works, we had concentrated mainly on the Cauchy-type correlation function for the rough part. In the present work, we show that this technique can determine the periodic structure of different kinds of correlation functions of the roughness, including Cauchy, Gaussian etc. We study the detection by the matched filter method as the nature of the correlation function is varied.

Tuning the Efficiency of Dendritic Nanocarriers using Conformational Constraints

A series of deoxycholic and cholic acid-derived oligomers were synthesized and their ability to extract hydrophilic dye molecules of different structure, size, and functional groups into nonpolar media was studied. The structure of the dye and dendritic effect in the extraction process was examined using absorption spectroscopy and dynamic light scattering (DLS). The efficiency of structurally preorganized oligomers in the aggregation process was evaluated by 1-anilinonaphthalene-8-sulfonic acid (ANS) fluorescence studies. The possible formation of globular structures for higher-generation molecules was investigated by molecular modeling studies and the results were correlated with the anomaly observed in the extraction process with this molecule. The ability of these molecules for selective extraction of specific dyes from blended colors is also reported.

Smart polymer mediated purification and recovery of active proteins from inclusion bodies

Obtaining correctly folded proteins from inclusion bodies of recombinant proteins expressed in bacterial hosts requires solubilization with denaturants and a refolding step. Aggregation competes with the second step. Refolding of eight different proteins was carried out by precipitation with smart polymers. These proteins have different molecular weights, different number of disulfide bridges and some of these are known to be highly prone to aggregation. A high throughput refolding screen based upon fluorescence emission maximum around 340 nm (for correctly folded proteins) was developed to identify the suitable smart polymer. The proteins could be dissociated and recovered after the refolding step. The refolding could be scaled up and high refolding yields in the range of 8 mg L-1 (for CD4D12, the first two domains of human CD4) to 58 mg L-1 (for malETrx, thioredoxin fused with signal peptide of maltose binding protein) were obtained. Dynamic light scattering (DLS) showed that polymer if chosen correctly acted as a pseuclochaperonin and bound to the proteins. It also showed that the time for maximum binding was about 50 min which coincided with the time required for incubation (with the polymer) before precipitation for maximum recovery of folded proteins. The refolded proteins were characterized by fluorescence emission spectra, circular dichroism (CD) spectroscopy, melting temperature (T-m), and surface hydrophobicity measurement by ANS (8-anilinol-naphthalene sulfonic acid) fluorescence. Biological activity assay for thioredoxin and fluorescence based assay in case of maltose binding protein (MBP) were also carried out to confirm correct refolding. (C) 2012 Elsevier B.V. All rights reserved.

Coupled phonons, magnetic excitations, and ferroelectricity in AlFeO3: Raman and first-principles studies

We determine the nature of coupled phonons and magnetic excitations in AlFeO3 using inelastic light scattering from 5 to 315 K covering a spectral range from 100 to 2200 cm(-1) and complementary first-principles density functional theory-based calculations. A strong spin-phonon coupling and magnetic ordering-induced phonon renormalization are evident in (1) anomalous temperature dependence of many modes with frequencies below 850 cm(-1), particularly near the magnetic transition temperature T-c approximate to 250 K, and (2) distinct changes in band positions of high-frequency Raman bands between 1100 and 1800 cm(-1); in particular, a broad mode near 1250 cm(-1) appears only below T-c, attributed to the two-magnon Raman scattering. We also observe weak anomalies in the mode frequencies similar to 100 K due to a magnetically driven ferroelectric phase transition. Understanding of these experimental observations has been possible on the basis of first-principles calculations of the phonons' spectrum and their coupling with spins.

Synthesis of Cholic Acid Oligomer-Taurine Conjugates: A Study of Their Aggregation and Cholesterol Solubilization

Taurine conjugates of two cholic acid derived oligomers with different spacers between the cholic acid units were synthesized. These molecules self-assemble in aqueous media. The critical micelle concentration (CMC) values were measured by using fluorescence spectroscopic analysis and the aggregates were characterized by dynamic light scattering and electron microscopy. The cooperativity of the cholic acid units in these tetramers to solubilize cholesterol was investigated. The ability of these molecules to act as nanocarriers for liphophilic dyes was also studied.

Selective colorimetric detection of nanomolar Cr (VI) in aqueous solutions using unmodified silver nanoparticles

In this study we present a colorimetric detection method for Cr (VI) in aqueous solution based on as synthesized silver nanoparticles (Ag NPs) without surface functionalization. The method principle involves reduction of Cr (VI) to Cr (III) by excess reductant present in as synthesized Ag NP dispersion, and subsequent aggregation of Ag NPs by Cr (III) leading to red-shift of the surface plasmon resonance (SPR) peak. The UV-vis absorption spectra. Zeta potentials, dynamic light scattering measurements, and scanning electron microscopy (SEM) confirmed the aggregation of the Ag NPs. Under the optimized conditions, a good linear relationship (correlation coefficient r=0.981) was obtained between the ratio of the absorbance at 550 nm to that at 390 nm (A(550/390)) and the concentration of Cr (VI) over the range of 10(-3)-10(-9) M 50 mg/L to 50 ng/L]. The reported probe has a limit of detection down to 1 nM, which, to the best of our knowledge, is the lowest ever reported for the colorimetric detection of Cr (VI). Furthermore, a remarkable feature of this method is that it involves a simple technique exhibiting high selectivity to Cr (VI) over other tested heavy metal ions. (C) 2012 Elsevier BM. All rights reserved.

Synthesis and characterization of high molecular weight polyaniline for organic electronic applications

High molecular weight polyaniline (PANI) was synthesized by a combined procedure incorporating various synthesis methods. Temperature and open circuit potential of the reaction mixture were collected to monitor the reaction progress. The polymer is characterized by various techniques including gel permeation chromatography, dynamic light scattering, infrared spectroscopy, solid-state nuclear magnetic resonance, and differential scanning calorimetry for elucidating the molecular architecture obtained by this method. As-synthesized PANI was found to possess high molecular weight, reduced branching, reduced cross-linking, and to predominantly consist of linear polymer chains. This polymer was also found to be more stable in solution form. JV characteristics of as-synthesized PANI films indicate a high current density which is due to increased free pathways and less traps for the charge transport to occur in PANI films. POLYM. ENG. SCI., 2012. (C) 2012 Society of Plastics Engineers

Synthesis and characterization of nickel/barium hexa-aluminate composite coatings

Electrodeposition of nickel/barium hexa-aluminate (Ni/BHA) composite coatings has been carried out from a Watt's bath on mild steel substrate. BHA powders with plate habit were synthesized by solution combustion synthesis followed by heat treatment to ensure complete conversion to the hexa-aluminate phase. Heat treated material was characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM) combined with X-ray analysis. The dispersion behaviour and stability of BHA suspensions with cationic and anionic surfactants at room temperature were studied by dynamic light scattering under different pH. The influence of BHA concentration in the electrolytic bath, deposition temperature, pH, current density and duty cycle on particle incorporation in the coatings were studied and conditions for maximum particle incorporation were established. Coatings with a roughness of about 0 center dot 4 mu m were produced by using this technique. Effect of BHA content on microhardness was also investigated. A reasonably good thickness of the coatings was achieved in a given set of conditions.

Anomalous optical phonons in Cs-0.9(NH4)(0.1)H2AsO4: a temperature-dependent Raman study

We determine the nature of coupled phonons in mixed crystal of Cs-0.9(NH4)(0.1)H2AsO4 using inelastic light scattering studies in the temperature range of 5 K to 300 K covering a spectral range of 60-1100 cm(-1). The phase transition in this system are marked by the splitting of phonon modes, appearance of new modes and anomalies in the frequency as well as linewidth of the phonon modes near transition temperature. In particular, we observed the splitting of symmetric (v(1)) and antisymmetric (v(3)) stretching vibrations associated with AsO4 tetrahedra below transition temperature (T-c(*) similar to 110 K) attributed to the lowering of site symmetry of AsO4 in orthorhombic phase below transition temperature. In addition, the step-up (hardening) and step-down (softening) of the AsO4 bending vibrations (v(4) (S9, S11) and v(2) (S6)) below transition temperature signals the rapid development of long range ferroelectric order and proton ordering. The lowest frequency phonon (S1) mode observed at similar to 92 cm(-1) shows anomalous blue shift (similar to 12 %) from 300 K to 5 K with no sharp transition near T-c(*) unlike other observed phonon modes signaling its potential coupling with the proton tunneling mode. (C) 2013 Author(s).

Gene Transfection in High Serum Levels: Case Studies with New Cholesterol Based Cationic Gemini Lipids

Background: Six new cationic gemini lipids based on cholesterol possessing different positional combinations of hydroxyethyl (-CH2CH2OH) and oligo-oxyethylene -(CH2CH2O)(n)- moieties were synthesized. For comparison the corresponding monomeric lipid was also prepared. Each new cationic lipid was found to form stable, clear suspensions in aqueous media. Methodology/Principal Findings: To understand the nature of the individual lipid aggregates, we have studied the aggregation properties using transmission electron microscopy (TEM), dynamic light scattering (DLS), zeta potential measurements and X-ray diffraction (XRD). We studied the lipid/DNA complex (lipoplex) formation and the release of the DNA from such lipoplexes using ethidium bromide. These gemini lipids in presence of a helper lipid, 1, 2-dioleoyl phophatidyl ethanol amine (DOPE) showed significant enhancements in the gene transfection compared to several commercially available transfection agents. Cholesterol based gemini having -CH2-CH2-OH groups at the head and one oxyethylene spacer was found to be the most effective lipid, which showed transfection activity even in presence of high serum levels (50%) greater than Effectene, one of the potent commercially available transfecting agents. Most of these geminis protected plasmid DNA remarkably against DNase I in serum, although the degree of stability was found to vary with their structural features. Conclusions/Significance: -OH groups present on the cationic headgroups in combination with oxyethylene linkers on cholesterol based geminis, gave an optimized combination of new genera of gemini lipids possessing high transfection efficiency even in presence of very high percentage of serum. This property makes them preferential transfection reagents for possible in vivo studies.

On the Mechanism of Phase Transfer Catalysis in Brust-Schiffrin Synthesis of Metal Nanoparticles

The two-phase Brust-Schiffrin method (BSM) is used to synthesize highly stable nanoparticles of noble metals. A phase transfer catalyst (PTC) is used to bring in aqueous phase soluble precursors into the organic phase to enable particle synthesis there. Two different mechanisms for phase transfer are advanced in the literature. The first mechanism considers PTC to bring in an aqueous phase soluble precursor by complexing with it. The second mechanism considers the ionic species to be contained in inverse micelles of PTC, with a water core inside. A comprehensive experimental study involving measurement of interfacial tension, viscosity, water content by Karl-Fischer titration, static light scattering, H-1 NMR, and small-angle X-ray scattering is reported in this work to establish that the phase transfer catalyst tetraoctylammonium bromide transfers ions by complexing with them, instead of encapsulating them in inverse micelles. The findings have implications for particle synthesis in two-phase methods such as BSM and their modification to produce more monodispersed particles.

A promising ketone containing alternating copolymer for organic photovoltaics

An alternating copolymer containing dithienylcyclopentadienone, thiophene and benzothiadiazole was synthesized by palladium (0) catalyzed Stille coupling reaction. Structural characterization of the synthesized alternating copolymer was carried out by NMR and FTIR spectroscopy. This solution processable copolymer shows an excellent thermal stability and has a broad absorption range from 300-800 nm. High LUMO energy level and low band gap of the synthesized copolymers suggest that, this copolymer will be a better donor material for application in organic photovoltaics. Particle size analysis and molecular weight determination of the synthesized copolymer through dynamic light scattering experiment indicates that, high molecular weight copolymer was obtained by this polymerization route. Photovoltaic devices were fabricated from the blend of copolymer and phenyl-C61- butyric acid methyl ester as the active material. Fabricated photovoltaic device results show that this alternating copolymer is a promising candidate for use in organic photovoltaics.

Efficacious Anticancer Drug Delivery Mediated by a pH-Sensitive Self-Assembly of a Conserved Tripeptide Derived from Tyrosine Kinase NGF Receptor

We present herein a short tripeptide sequence (Lys-Phe-Gly or KFG) that is situated in the juxtamembrane region of the tyrosine kinase nerve growth factor (Trk NGF) receptors. KFG self-assembles in water and shows a reversible and concentration-dependent switching of nanostructures from nanospheres (vesicles) to nanotubes, as evidenced by dynamic light scattering, transmission electron microscopy, and atomic force microscopy. The morphology change was associated with a transition in the secondary structure. The tripeptide vesicles have inner aqueous compartments and are stable at pH7.4 but rupture rapidly at pH approximate to 6. The pH-sensitive response of the vesicles was exploited for the delivery of a chemotherapeutic anticancer drug, doxorubicin, which resulted in enhanced cytotoxicity for both drug-sensitive and drug-resistant cells. Efficient intracellular release of the drug was confirmed by fluorescence-activated cell sorting analysis, fluorescence microscopy, and confocal microscopy.

Metal nanoparticles as better protein-aggregation prevention agents than chaperones

Prevention or suppression of protein aggregation is of great importance in the context of protein storage, transportation and delivery. Traditionally chaperones or other chemically active agents are used to stop or diffuse native protein aggregation. We have used gold nanoparticles to prevent thermal aggregation of alcohol dehydrogenase (ADH), a protein that maintains the alcohol level in the liver and stomach. A light-scattering assay has been used to investigate the effect of gold nanoparticles on thermal aggregation of ADH and the result of our study has been summarized in Fig. 1. The scattered light intensity from the solution containing ADH decreases when 45 nm gold nanoparticles are added prior to heating (thermal denaturation) the solution, which indicates prevention of aggregation. The aggregation of the protein is suppressed to the extent of 96% with picomolar concentration of 45 nm gold nanoparticles while micromolar amounts of other proteins and biological substances are necessary to achieve the same effect. The extent varies with the size and the concentration of the gold NPs for the same protein concentration.