Acid Phosphate Groups Research Articles

Grape seeds waste activated carbon as an adsorber of paracetamol drug residue: Experimental and theoretical approaches

Activated carbon (AC) derived from grape seeds wastes and chemically activated with phosphoric acid was employed to remove paracetamol (PCT); from an aqueous solution; as a pharmaceutical compound model. The AC was characterized using several techniques, and a series of batch adsorption experiments were conducted. Additionally, a theoretical study investigated the interactions of PCT with various functional groups present on the AC surface. The results demonstrated that the developed AC possessed a well-developed pore structure and a high specific surface area (SBET = 543 m2/g). The AC also exhibited an acidic surface and a low pHpzc (2.5). Adsorption experiments revealed that the pseudo-second-order (PSO) and Freundlich models provided the best fits for experimental kinetic and equilibrium data, respectively. The maximum adsorption capacity of AC for PCT was found to be 17.3 mg/g. Thermodynamic analysis suggested endothermic, favorable, and spontaneous adsorption; with low enthalpy values (ΔH° = 8.099 kJ/mol), supporting physisorption. The DLPNO-CCDT(T)/6-311G(d,p) calculation method yielded the most reliable adsorption energy (Eads) and Gibbs free energy (ΔGads) values between PCT and functional groups on the carbon surface, indicating strong interactions between the acid phosphate group of AC and the acetamide fragment of PCT (ΔGads = −7.60 kcal/mol), and strong interactions between the ketone groups and lactone cycles with the hydroxyl (ΔGads = −3.40 kcal/mol), and acetamide (ΔGads = −1.91 kcal/mol) groups of PCT, respectively. The obtained results indicated, first, that the use of activated carbon from waste is an effective alternative adsorbent for the treatment of wastewater containing pharmaceutical compounds. Second, the application of theoretical computational methods in quantum chemistry provides a thorough understanding of the mechanism of the absorption of PCT at the carbon surface.

Zirconium Phosphate Assisted Phosphoric Acid Co-Catalyzed Hydrolysis of Lignocellulose for Enhanced Extraction of Nanocellulose.

The high mechanical strength, large specific surface area, favorable biocompatibility, and degradability of nanocellulose (CNC) enable it to be a potential alternative to petroleum-based materials. However, the traditional preparation of CNCs requires a large amount of strong acid, which poses a serious challenge to equipment maintenance, waste liquid recycling, and economics. In this study, a solid and easily recoverable zirconium phosphate (ZrP) was used to assist in the phosphoric acid co-catalyzed hydrolysis of lignocellulose for extracting CNCs. Due to the presence of acidic phosphate groups, ZrP has a strong active center with a high catalytic activity. With the assistance of ZrP, the amount of phosphoric acid used in the reaction is significantly reduced, improving the equipment's durability and economic efficiency. The effects of the process conditions investigated were the phosphate acid concentration, reaction temperature, and reaction time on the yield of CNCs. The Box-Behnken design (BBD) method from the response surface methodology (RSM) was applied to investigate and optimize the preparation conditions. The optimized pre-treatment conditions were 49.27% phosphoric acid concentration, 65.38 °C reaction temperature, and 5 h reaction time with a maximal cellulose yield (48.33%). The obtained CNCs show a granular shape with a length of 40~50 nm and a diameter of 20~30 nm, while its high zeta potential (-24.5 mV) make CNCs present a stable dispersion in aqueous media. Moreover, CNCs have a high crystallinity of 78.70% within the crystal type of cellulose Ⅰ. As such, this study may pioneer the horizon for developing a green method for the efficient preparation of CNC, and it is of great significance for CNCs practical production process.

Transformation of Bacillus thuringiensis plasmid DNA by a new polyethylenimine polymeric nanoparticles method

Although electroporation technique has been mostly used to transform Bacillus thuringiensis (Bt), this method is not readily applicable to strains other than the one for which it was optimized. Polyethylenimine (PEI) is a golden standard non-viral vector that interacts with plasmids to form compact polymeric nanoparticles (PNPs) via electrostatic interactions. This PNPs system is very attractive because they are easily prepared, able to carry large nucleic acid constructs, and show low toxicity. In this study, PEI/pBTdsSBV-VP1 PNPs were successfully prepared at various N/P ratios which is positively-chargeable polymer amine (N = nitrogen) groups to negatively-charged nucleic acid phosphate (P) groups, and the internalization of the complexes into Bt 4Q7 was confirmed by confocal laser scanning microscopy. The PEI-mediated transformation showed similar efficiency comparable to that of electroporation method, suggesting that the method of PNPs will be an effective alternative for transformation of Bt strains.

Nucleic Acid Hybridization Enhanced Luminescence for Rapid and Sensitive RNA and DNA Based Diagnostics.

Long-lived emissive nucleic acid probes are widely used in biochemical analysis due to their programmable structures, high signal-to-background ratio, and high sensitivity. Homogeneous detection based on long-lived emissive nucleic acid probes is often achieved through Förster resonance energy transfer (FRET), which suffers from the limitation of a narrow effective distance range. Herein, a new strategy of accessing nucleic acid hybridization-responsive luminescent probes is presented. The photoluminescence (PL) of a Lumi4-Tb complex internally modified with DNA is switched on by nucleic acid hybridization, after which the PL is increased up to 20 times. PL lifetime analysis revealed a possible mechanism of luminescence enhancement. Due to the flexibility of single-stranded nucleic acid chains, the bases and phosphate groups can coordinate with the Tb(III), which reduces the stability of the Tb complex and results in weak PL. After hybridization, the rigid double helix structure suppresses the coordination between Tb(III) and the bases or phosphate groups, causing luminescence enhancement. As the DNA sequence can be freely designed, an array of probes for different DNA or RNA targets can be created with the same Tb complex. Moreover, the novel probe design can afford pM detection limits of DNA or RNA without any nucleic acid amplification and exhibits great potential for nucleic acid detection in clinical diagnosis.

Synthesis and Characterisation of Activated Carbon Obtained from Marula (Sclerocarya birrea) Nutshell

Globally, a ninth of people use polluted water sources because an estimated 300–400 Mt of waste and 90% of sewage are discharged into water bodies from industries and developing countries, respectively. The utilisation of indigenous fruit pits in producing novel adsorbents will greatly benefit in wastewater treatment. In most underdeveloped countries, activated carbon (AC) is imported at a high cost. The study was aimed at synthesising and characterisation of AC obtained from Marula nutshell. Carbonization of organic matter from Marula nutshell was carried out at 200°C, 400°C, 500°C, and 600°C. Sulphuric (H2SO4) and phosphoric (H3PO4) acids were used as activating agents at concentrations of 20–60% ( v / v ). Physicochemical characteristics of the AC, such as bulk density, moisture, ash, pH, and iodine number, were analyzed using standard methods. Functional groups and total carbon content were determined using the FTIR spectroscopy and Nitrogen Carbon Sulphur (NCS) analyzer, respectively. The values of carbon yield and total carbon in activated samples with H2SO4 and H3PO4 were 32.2–93.2%, 26.9–95.8%, and 46–79%, 20.8–69.8%, respectively. The pH, ash, moisture, and bulk density of activated high carbon samples with H2SO4 ranged from 2.4–6.1, 0.65–3.49%, 1.3–8.4%, and 0.42–0.62 gcm−3, respectively. Activated high carbon samples with H3PO4 had 2.7–3.2, 11.3–29.8%, 4.7–14.6%, and 0.39–0.54 gcm−3 pH, ash, moisture, and bulk density, respectively. The synthesised AC samples with 40% H3PO4 at 500°C had the highest iodine value of 1075.7 mg/g. FTIR results showed the presence of aliphatic carboxylic acid salt, inorganic nitrate (NO3−), and phosphate groups in the synthesised AC and were not significantly different ( p < 0.05 ) from commercial AC. The untreated Marula nutshell had some aliphatic hydrocarbon (alkanes), inorganic phosphate ( PO 4 3 − ), aliphatic ester (–COO), and aliphatic carboxylic acid salt (–C(=O)O–) groups. A novel adsorbent, AC was produced from Marula nutshell with the potential to be used in water treatment.

Lipopolysaccharide Preparation Derived From Porphyromonas gingivalis Induces a Weaker Immuno-Inflammatory Response in BV-2 Microglial Cells Than Escherichia coli by Differentially Activating TLR2/4-Mediated NF-κB/STAT3 Signaling Pathways.

Alzheimer’s disease (AD) is a degenerative disease of the central nervous system with unclear etiology and pathogenesis. In recent years, as the infectious theory and endotoxin hypothesis of AD has gained substantial attention, several studies have proposed that Porphyromonas gingivalis (P. gingivalis), one of the main pathogenic bacteria of chronic periodontitis, and the lipopolysaccharide (LPS) of P. gingivalis may lead to AD-like pathological changes and cognition impairment. However, research on the relationship between P. gingivalis-LPS and neuroinflammation is still lacking. Our study aimed to investigate the effects of P. gingivalis-LPS preparation on immuno-inflammation in microglial cells and further compared the differential inflammatory response induced by P. gingivalis-LPS and Escherichia coli (E. coli) LPS preparations. The results showed that P. gingivalis-LPS could upregulate the gene expression and release of pro-inflammatory factors in BV-2 microglial cells, including IL-1β, IL-6, TNF-α, IL-17, and IL-23. We also observed an increase in the level of Toll-like receptor 2/4 (TLR2/4) and NF-κB/STAT3 signaling. Moreover, the changes mentioned above were more significant in the E. coli-LPS group and the effects of both kinds of LPS could be differentially reversed by the administration of the TLR2 inhibitor C29 and TLR4 inhibitor TAK-242. The molecular simulation showed that the binding affinity of P. gingivalis-lipid A to TLR4-MD-2 was weaker than E. coli-lipid A, which was probably due to the presence of fewer acyl chains and phosphate groups of P. gingivalis-lipid A than E. coli-lipid A. We conclude that P. gingivalis-LPS could activate TLR2/4-mediated NF-κB/STAT3 signaling pathways, which ultimately resulted in an immune-inflammatory response in BV-2 microglia. In contrast to E. coli-LPS, P. gingivalis-LPS is a weaker TLR2/4 agonist and NF-κB/STAT3 signaling activator. Furthermore, the different fatty acid chains and phosphate groups between P. gingivalis-lipid A and E. coli-lipid A may be the reason for the weaker activating properties of P. gingivalis-LPS.

Towards personalised saliva spectral fingerprints: Comparison of mid infrared spectra of dried and whole saliva samples

The aims of this study were to compare two sample presentations (dry and whole) as well as the effects of both gender and age on the mid infrared (MIR) fingerprint spectra of human saliva. Unstimulated saliva was collected from 52 Female (31 subjects, aged 40.9 ± 14.6 year) and Male (21 subjects, aged 34 ± 11.8 year) participants, stored frozen, and subsequently thawed and analysed by MIR spectroscopy as whole and dried saliva, respectively. Data were analysed by means of principal components analysis (PCA) and partial least squares (PLS) to interpret and compare the effects of presentation (dry vs whole), age and gender on the MIR spectra of saliva. Interpretation of the MIR spectra of both whole and dried samples revealed specific characteristic and different spectral signals when gender and age were compared in the amide I and amide II of proteins (e.g. albumin) and DNA. While whole saliva analysis might be more convenient for rapid test, dried saliva spectra were more consistent across replicates, demonstrating greater ability to distinguish individual differences. The interpretation of the PCA and PLS loadings of both whole and dried saliva samples allowed identification of specific MIR regions associated with age and gender of participants between 1000 cm−1 and 1800 cm−1. In particular, the MIR regions associated with the absorption of polysaccharides, glycosylated proteins, and nucleic acid phosphate groups present in saliva were the most dominant. This paper demonstrates that MIR spectroscopy can be used to measure saliva samples and to interpret individual differences in participants due to age in either dry or whole samples. No clear trends were observed in the MIR spectra of the samples associated with gender when all samples were analysed together. However, PLS regression models were able to predict gender in a subset of samples having similar age. The approach described in this study shows promise for potentially using saliva as a tool in food studies (e.g. saliva interactions between food and consumers).

Protein Side-Chain-DNA Contacts Probed by Fast Magic-Angle Spinning NMR.

Protein–nucleic acid interactions are essential in a variety of biological events ranging from the replication of genomic DNA to the synthesis of proteins. Noncovalent interactions guide such molecular recognition events, and protons are often at the center of them, particularly due to their capability of forming hydrogen bonds to the nucleic acid phosphate groups. Fast magic-angle spinning experiments (100 kHz) reduce the proton NMR line width in solid-state NMR of fully protonated protein–DNA complexes to such an extent that resolved proton signals from side-chains coordinating the DNA can be detected. We describe a set of NMR experiments focusing on the detection of protein side-chains from lysine, arginine, and aromatic amino acids and discuss the conclusions that can be obtained on their role in DNA coordination. We studied the 39 kDa enzyme of the archaeal pRN1 primase complexed with DNA and characterize protein–DNA contacts in the presence and absence of bound ATP molecules.

Hydrophilic/hydrophobic modifications of a PnBA-b-PDMAEA copolymer and complexation behaviour with short DNA

We present studies on the quaternization of poly[(n-butyl acrylate)-block-(2-dimethylamino)ethyl acrylate], PnBA40-b-PDMAEA60 diblock (where subscripts denote %wt composition of the components), synthesized by reversible addition fragmentation chain transfer (RAFT) polymerization, the self-assembly of the quaternized copolymers, as well as their capability in binding with a short nucleic acid. Methyl iodide (CH3I) and 1-iodohexane (C6H13I) are used for the quaternization of tertiary amines of the PDMAEA block. The quaternized PnBA21-b-Q1PDMAEA79 and PnBA33-b-Q6PDMAEA30 (where Q1 and Q6 prefixes denote the CH3I and C6H13I modifications) block polyelectrolytes are studied by fluorescence spectroscopy (FS) and their self-assembling behavior is investigated by dynamic and electrophoretic light scattering techniques (DLS and ELS). The PnBA21-b-Q1PDMAEA79 polyelectrolytes seem to self-assemble into small spherical micelles with a PnBA core in aqueous media, whereas a less well defined aggregation behavior is observed for the PnBA33-b-Q6PDMAEA30 copolymer, probably due to the presence of the six methylene hydrophobic side chains (C6H13) in the hydrophilic part of the copolymer, forming the micellar corona. The DNA binding capability of PnBA21-b-Q1PDMAEA79 and PnBA33-b-Q6PDMAEA30 chemically modified cationic block polyelectrolytes is studied and compared to the DNA complexation behaviour of the corresponding PnBA40-b-PDMAEA60 amino precursor. The formation and structure of polyplexes is studied by DLS, ELS, FS and UV–Vis techniques at various N/P ratios of positively-chargeable polymer amine (N = nitrogen) groups to negatively-charged nucleic acid phosphate (P) groups. The mass, size and surface potential of the polyplexes present a strong dependence on the N/P ratio. The stability of the polyplexes is determined by changes in their hydrodynamic parameters in the presence of salt. The PnBA33-b-Q6PDMAEA30 quaternized copolymer exhibits a more effective binding with DNA, presumably due to the existence of both electrostatic interactions and reinforced hydrophobic interactions between Q6PDMAEA chains and DNA base pairs.

Enzymatic degumming of corn oil using phospholipase C from a selected strain of Pichia pastoris

Degumming is a necessary refining step for all crude vegetable oils. Purifine® PLC is a new enzyme used for industrial oil degumming. In the present study, enzymatic degumming trials were performed on crude corn oil using a commercial phospholipase C enzyme Purifine® PLC with the aim of determining its optimum process conditions. Enzymatic degumming applying 200 mg/kg of Purifine® PLC during 120 min at 60 °C, and a pH of 5.7 using chemical conditioning, resulted in a residual phosphorus content of 27 mg/kg and an absolute diacylglycerol increase of 0.54 wt%. Compared to water degumming, enzymatic degumming with Purifine® PLC provided a better degumming (67 mg/kg versus 27 mg/kg) and an increase in the diacylglycerol content. The pH adjustment of crude corn oil performed by means of a caustic pretreatment was not able to keep the pH at an optimal stable value due to the continuous release of acidic phosphate groups. Analysis of the composition of remaining phospholipids in the gums fraction showed that Purifine® PLC could effectively convert phosphatidylcholine and phosphatidylethanolamine into diacylglycerols, whereas it could not convert phosphatidylinositol and phosphatidic acid. These results confirm that Purifine® PLC degumming is a commercially feasible alternative to traditional degumming processes.

Starch Phosphate Microgels for Controlled Release of Biomacromolecules

Gel-forming starch phosphates with a content of acidic phosphate groups ranging from 2.1 to 3.8 mmol/g were obtained in a phosphoric acid-urea system. The rates of starch phosphate degradation in buffer solution in the absence of amylase and in the presence of this enzyme were investigated in vitro. Starch phosphate gels were shown to be prone to enzymatic degradation. However, the rate of biodegradation decreased gradually as the content of phosphate groups increased. The use of microgels with average particle sizes in the range of 7.8–60.1 μm for the production of controlled-release preparations of interferon-alpha 2b has been demonstrated to be possible in principle.

"In Silico" Characterization of 3-Phytase A and 3-Phytase B from Aspergillus niger.

Phytases are used for feeding monogastric animals, because they hydrolyze phytic acid generating inorganic phosphate. Aspergillus niger 3-phytase A (PDB: 3K4Q) and 3-phytase B (PDB: 1QFX) were characterized using bioinformatic tools. Results showed that both enzymes have highly conserved catalytic pockets, supporting their classification as histidine acid phosphatases. 2D structures consist of 43% alpha-helix, 12% beta-sheet, and 45% others and 38% alpha-helix, 12% beta-sheet, and 50% others, respectively, and pI 4.94 and 4.60, aliphatic index 72.25 and 70.26 and average hydrophobicity of −0,304 and −0.330, respectively, suggesting aqueous media interaction. Glycosylation and glycation sites allowed detecting zones that can affect folding and biological activity, suggesting fragmentation. Docking showed that H59 and H63 act as nucleophiles and that D339 and D319 are proton donor residues. MW of 3K4Q (48.84 kDa) and 1QFX (50.78 kDa) is similar; 1QFX forms homodimers which will originate homotetramers with several catalytic center accessible to the ligand. 3K4Q is less stable (instability index 45.41) than 1QFX (instability index 33.66), but the estimated lifespan for 3K4Q is superior. Van der Waals interactions generate hydrogen bonds between the active center and O2 or H of the phytic acid phosphate groups, providing greater stability to these temporal molecular interactions.

High-Confidence Sequencing of Phosphopeptides by Electron Transfer Dissociation Mass Spectrometry Using Dinuclear Zinc(II) Complex.

Phosphorylation is the most abundant protein modification, and tandem mass spectrometry (MS2) with electron transfer dissociation (ETD) has proven to be a promising method for phosphoproteomic applications owing to its ability to determine phosphorylation sites on proteins. However, low precursor charge states hinder the ability to obtain useful information through peptide sequencing by ETD, and the presence of acidic phosphate groups contributes to a low charge state of peptide ions. In the present report, we used a dinuclear zinc complex, (Zn2L)3+ (L = alkoxide form of 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-ol) for electrospray ionization (ESI), followed by ETD-MS2 analysis. Since (Zn2L)3+ selectively bound to phosphopeptide with addition of a positive charge per phosphate group, the use of (Zn2L)3+ for ESI improved the ionization yield of phosphopeptides in phosphoprotein digest. Additionally, an increase in the charge state of phosphopeptides were observed by addition of (Zn2L)3+, facilitating phosphopeptide sequencing by ETD-MS2. Since the binding between (Zn2L)3+ and the phosphate group was retained during the ETD process, a comparison between the ETD mass spectra obtained using two dinuclear zinc complex derivatives containing different zinc isotopes, namely (64Zn2L)3+ and (68Zn2L)3+, provided information about the number of phosphate groups in each fragment ion, allowing the phosphorylation site to be unambiguously determined. The details of the fragmentation processes of the (Zn2L)3+-phosphopeptide complex were investigated using a density functional theory calculation. As in the case of protonated peptides, ETD induced peptide backbone dissociation in the (Zn2L)3+-phosphopeptide complex proceeded through an aminoketyl radical intermediate.

Calcification of aortic human valves studied in situ by Raman microimaging: following mineralization from small grains to big deposits

AbstractA Raman microimaging‐based approach has been used in the current study to evaluate formation and progression of calcification in situ in human stenotic aortic valves obtained during surgical valve replacement. The capability of the method to visualize distribution of the calcified deposits resulted in structural characterization of deposits in the various phases of development. A high spatial resolution of the method along with the confocal depth profiling enabled to identify extremely small salt inclusions (of ca. 0.5 µm in diameter), formed probably at the very early stage of calcification. Structurally, these inclusions are built from an octacalcium phosphate‐like compound that during grains' growth transforms into tricalcium phosphate, mixed with the salt containing the acidic phosphate groups (HPO42−) and, finally, into stable B‐type hydroxyapatite that is the only salt present in large‐area calcium salt deposits. Copyright © 2013 John Wiley & Sons, Ltd.

Down-State Model of the Voltage-Sensing Domain of a Potassium Channel

Voltage-sensing domains (VSDs) of voltage-gated potassium (Kv) channels undergo a series of conformational changes upon membrane depolarization, from a down state when the channel is at rest to an up state, all of which lead to the opening of the channel pore. The crystal structures reported to date reveal the pore in an open state and the VSDs in an up state. To gain insights into the structure of the down state, we used a set of experiment-based restraints to generate a model of the down state of the KvAP VSD using molecular-dynamics simulations of the VSD in a lipid bilayer in excess water. The equilibrated VSD configuration is consistent with the biotin-avidin accessibility and internal salt-bridge data used to generate it, and with additional biotin-avidin accessibility data. In the model, both the S3b and S4 segments are displaced ∼10 Å toward the intracellular side with respect to the up-state configuration, but they do not move as a rigid body. Arginine side chains that carry the majority of the gating charge also make large excursions between the up and down states. In both states, arginines interact with water and participate in salt bridges with acidic residues and lipid phosphate groups. An important feature that emerges from the down-state model is that the N-terminal half of the S4 segment adopts a 310-helical conformation, which appears to be necessary to satisfy a complex salt-bridge network.

GROATITE, Na Ca Mn2+2 (PO4) [PO3(OH)]2, A NEW MINERAL SPECIES OF THE ALLUAUDITE GROUP FROM THE TANCO PEGMATITE, BERNIC LAKE, MANITOBA, CANADA: DESCRIPTION AND CRYSTAL STRUCTURE

Groatite, ideally Na Ca Mn 2+ 2 (PO 4 ) [PO 3 (OH)] 2 , is a new mineral species from the Tanco pegmatite at Bernic Lake, Manitoba, Canada. It was found in a phosphate–carbonate mass in a spodumene-rich boulder. Groatite occurs sparingly as slightly divergent sprays of acicular crystals, embedded stellate sprays and as a tabular mass of densely intergrown acicular crystals. Groatite is closely associated with whitlockite, crandallite, an unidentified Na–Al phosphate and quartz; fairfieldite and manganese-rich overite are among the less closely associated phosphates; this assemblage may be secondary, following apparent dissolution of lithiophosphate and possibly of primary lithiophilite. Groatite is translucent, colorless to pale yellow and pale orange with a white streak and vitreous luster; it does not fluoresce under ultraviolet light. The Mohs hardness is 3. Groatite is brittle with an uneven fracture, and has a calculated density of 3.213 g/cm 3 . It is biaxial positive with α 1.622, β 1.634, γ 1.663 (all ±0.001), and is nonpleochroic; 2 V (obs.) = 67(1), 2 V (calc.) = 66.5°. It is monoclinic, space group C 2/ c , a 12.5435(9), b 12.4324(9), c 6.7121(4) A, β 115.332(2)°, V 946.07(19) A 3 , Z = 4. The six strongest lines in the X-ray powder-diffraction pattern [ d in A(I)( hkl )] are as follows: 3.187(100)(112), 2.726(90)(402, 240), 6.204(80)(020), 2.788(80)(330), 5.653(70)(200), and 2.580(70)(132, 420). Chemical analysis by electron microprobe gave P 2 O 5 46.66, FeO 0.49, MnO 29.31, CaO 12.51, Na 2 O 6.87, H 2 O (calc.) 3.93, sum 99.77 wt.%, where the H 2 O content was determined by crystal-structure refinement as OH = 2.0 apfu . The resulting empirical formula, on the basis of 10 O atoms and 2 (OH) groups pfu , is Na 1.02 Ca 1.02 (Mn 1.90 Fe 2+ 0.03 ) ∑ 1.93 P 3.02 O 10 (OH) 2 . The crystal structure of groatite was refined to an R index of 2.7% based on 831 unique reflections collected on a four-circle diffractometer with Mo K α X-radiation and a 4K CCD detector. There are two tetrahedrally coordinated T -sites occupied by P. There are two octahedra, M (1) and M (2), and an eight-coordinated A (2) site which are occupied by Ca, Mn and Na, respectively. The observed site-scattering, mean bond-lengths and bond-valence sums at these sites are in agreement with complete chemical order of Ca at M (1), Mn 2+ at M (2) and Na at A (2). A (PO 4 ) group is centered at the T (1) site and a PO 3 (OH) group at T (2). The H atom is located near the O(4) anion and provides a strong hydrogen bond to the O(2) anion. Groatite is isostructural with the acid arsenate mineral o’danielite and is a member of the alluaudite group; it is the first alluaudite-group mineral with an acid phosphate group. The new mineral is named in honor of Lee A. Groat, Professor of Mineralogy at the University of British Columbia in Vancouver. The species and the name groatite were approved by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association (IMA 2008–054).

Self-emulsifiable soybean oil phosphate ester polyols for low-VOC corrosion resistant coatings

A series of soybean oil phosphate ester polyols (SOPEP) was prepared by reaction of fully epoxidized soybean oil with phosphoric acid and simultanoeous hydrolysis in the presence of a polar solvent. The polyols were characterized by determination of acid value, oxirane number, hydroxyl value, molecular weight (GPC), and FTIR spectra. These polyols with varying amounts of acid phosphate groups could be self-emulsified to form aqueous dispersions after neutralization with organic base. These aqueous dispersion showed varying degrees of stability and their appearance ranged from opaque dispersions to translucent to clear solutions. Waterborne coating compositions were prepared using these aqueous dispersions as principal components and their thermally cured film properties were studied. it was found that by careful selection and formulation, SOPEPs can be successfully used for low-VOC waterborne coating formulations. SOPEPs with 3.5% phosphate ester content showed visibly superior corrosion resistance properties.

The Crystal Structure of Human Geranylgeranyl Pyrophosphate Synthase Reveals a Novel Hexameric Arrangement and Inhibitory Product Binding

Modification of GTPases with isoprenoid molecules derived from geranylgeranyl pyrophosphate or farnesyl pyrophosphate is an essential requisite for cellular signaling pathways. The synthesis of these isoprenoids proceeds in mammals through the mevalonate pathway, and the final steps in the synthesis are catalyzed by the related enzymes farnesyl pyrophosphate synthase and geranylgeranyl pyrophosphate synthase. Both enzymes play crucial roles in cell survival, and inhibition of farnesyl pyrophosphate synthase by nitrogen-containing bisphosphonates is an established concept in the treatment of bone disorders such as osteoporosis or certain forms of cancer in bone. Here we report the crystal structure of human geranylgeranyl pyrophosphate synthase, the first mammalian ortholog to have its x-ray structure determined. It reveals that three dimers join together to form a propeller-bladed hexameric molecule with a mass of approximately 200 kDa. Structure-based sequence alignments predict this quaternary structure to be restricted to mammalian and insect orthologs, whereas fungal, bacterial, archaeal, and plant forms exhibit the dimeric organization also observed in farnesyl pyrophosphate synthase. Geranylgeranyl pyrophosphate derived from heterologous bacterial expression is tightly bound in a cavity distinct from the chain elongation site described for farnesyl pyrophosphate synthase. The structure most likely represents an inhibitory complex, which is further corroborated by steady-state kinetics, suggesting a possible feedback mechanism for regulating enzyme activity. Structural comparisons between members of this enzyme class give deeper insights into conserved features important for catalysis.

Indirect NMR Spin−Spin Coupling Constants 3J(P,C) and 2J(P,H) across the P−O···H−C Link Can Be Used for Structure Determination of Nucleic Acids

Calculated indirect NMR spin-spin coupling constants (3)J(P,C) and (2)J(P,H) were correlated with the local structure of the P-O...H-C linkage between the nucleic acid (NA) backbone phosphate and the H-C group(s) of a nucleic acid base. The calculations were carried out for selected nucleotides from the large ribosomal subunit (Ban et al. Science 2000, 289, 905) with the aim of identifying NMR parameters suitable for detection of certain noncanonical RNA structures. As calculations in the model system, dimethyl-phosphate-guanine, suggest, the calculated indirect spin-spin couplings across the linkage are sensitive to the mutual orientation and distance between the phosphate and nucleic acid base. A short distance between the nucleic acid base and phosphate group and the angles C...P-O and P...C-H smaller than 50 degrees are prerequisites for a measurable spin-spin interaction of either coupling (|J| > 1 Hz). A less favorable arrangement of the P-O...H-C motif, e.g., in nucleotides of the canonical A-RNA, results in an effective dumping of both spin-spin interactions and insignificant values of the NMR coupling constants. The present work indicates that quantum chemical calculations of the indirect spin-spin couplings across the P-O...H-C motif can help detect some rare but important backbone topologies, as seen for example in the reverse kink-turn. Measuring of (3)J(P,C) and (2)J(P,H) couplings can therefore provide critical constraints on the NA base and phosphate geometry and help to determine the structure of NAs.

Formation of phosphopeptide‐metal ion complexes in liquid chromatography/electrospray mass spectrometry and their influence on phosphopeptide detection

Despite major advances in mass spectrometry, the detection of phosphopeptides by liquid chromatography with electrospray mass spectrometry (LC/ES-MS) still remains very challenging in proteomics analysis. Phosphopeptides do not protonate efficiently due to the presence of one or more acidic phosphate groups, making their detection difficult. However, other mechanisms also contribute to the difficulties in phosphopeptide analysis by LC/ES-MS. We report here on one such undocumented problem: the formation of phosphopeptide-metal ion complexes during LC/ES-MS. It is demonstrated that both synthetic phosphopeptides and phosphopeptides from bovine beta-casein and alpha-casein form phosphopeptide-metal ion complexes containing iron and aluminum ions, resulting in a dramatic decrease in signal intensity of the protonated phosphopeptides. The interaction of phosphopeptides with metal ions on the surface of the C18 stationary phase is also shown to alter their chromatographic behavior on reversed-phase columns such that the phosphopeptides, especially multiply phosphorylated peptides, become strongly retained and very difficult to elute. The sources of iron and aluminum are from the solvents, stainless steel, glassware and C18 material. It was also found that, upon addition of EDTA, the formation of the phosphopeptide-metal ion complex is diminished, and the phosphopeptides that did not elute from the LC column can now be detected efficiently as protonated molecules. The sensitivity of detection was greatly increased such that a tetra-phosphorylated peptide, RELEELNVPGEIVEpSLpSpSpSEESITR from the tryptic digestion of bovine beta-casein, was detected at a limit of detection of 25 fmol, which is 400 times lower than without EDTA.