Molecular bases of multimodal regulation of a fungal transient receptor potential (TRP) channel

Multimodal activation by various stimuli is a fundamental characteristic of TRP channels. We identified a fungal TRP channel, TRPGz, exhibiting activation by hyperosmolarity, temperature increase, cytosolic Ca(2+) elevation, membrane potential, and H2O2 application, and thus it is expected to represent a prototypic multimodal TRP channel. TRPGz possesses a cytosolic C-terminal domain (CTD), primarily composed of intrinsically disordered regions with some regulatory modules, a putative coiled-coil region and a basic residue cluster. The CTD oligomerization mediated by the coiled-coil region is required for the hyperosmotic and temperature increase activations but not for the tetrameric channel formation or other activation modalities. In contrast, the basic cluster is responsible for general channel inhibition, by binding to phosphatidylinositol phosphates. The crystal structure of the presumed coiled-coil region revealed a tetrameric assembly in an offset spiral rather than a canonical coiled-coil. This structure underlies the observed moderate oligomerization affinity enabling the dynamic assembly and disassembly of the CTD during channel functions, which are compatible with the multimodal regulation mediated by each functional module.

Mycobacterium tuberculosis RNA polymerase-binding protein A (RbpA) and its interactions with sigma factors

RNA polymerase-binding protein A (RbpA), encoded by Rv2050, is specific to the actinomycetes, where it is highly conserved. In the pathogen Mycobacterium tuberculosis, RbpA is essential for growth and survival. RbpA binds to the β subunit of the RNA polymerase where it activates transcription by unknown mechanisms, and it may also influence the response of M. tuberculosis to the current frontline anti-tuberculosis drug rifampicin. Here we report the solution structure of RbpA and identify the principle sigma factor σ(A) and the stress-induced σ(B) as interaction partners. The protein has a central ordered domain with a conserved hydrophobic surface that may be a potential protein interaction site. The N and C termini are highly dynamic and are involved in the interaction with the sigma factors. RbpA forms a tight complex with the N-terminal domain of σ(B) via its N- and C-terminal regions. The interaction with sigma factors may explain how RbpA stabilizes sigma subunit binding to the core RNA polymerase and thereby promotes initiation complex formation. RbpA could therefore influence the competition between principal and alternative sigma factors and hence the transcription profile of the cell.

Identification of a new interaction mode between the Src homology 2 domain of C-terminal Src kinase (Csk) and Csk-binding protein/phosphoprotein associated with glycosphingolipid microdomains

Proteins with Src homology 2 (SH2) domains play major roles in tyrosine kinase signaling. Structures of many SH2 domains have been studied, and the regions involved in their interactions with ligands have been elucidated. However, these analyses have been performed using short peptides consisting of phosphotyrosine followed by a few amino acids, which are described as the canonical recognition sites. Here, we report the solution structure of the SH2 domain of C-terminal Src kinase (Csk) in complex with a longer phosphopeptide from the Csk-binding protein (Cbp). This structure, together with biochemical experiments, revealed the existence of a novel binding region in addition to the canonical phosphotyrosine 314-binding site of Cbp. Mutational analysis of this second region in cells showed that both canonical and novel binding sites are required for tumor suppression through the Cbp-Csk interaction. Furthermore, the data indicate an allosteric connection between Cbp binding and Csk activation that arises from residues in the βB/βC loop of the SH2 domain.

RNA-methyltransferase TrmA is a dual-specific enzyme responsible for C5-methylation of uridine in both tmRNA and tRNA

In bacteria, trans-translation rescues stalled ribosomes by the combined action of tmRNA (transfer-mRNA) and its associated protein SmpB. The tmRNA 5' and 3' ends fold into a tRNA-like domain (TLD), which shares structural and functional similarities with tRNAs. As in tRNAs, the UUC sequence of the T-arm of the TLD is post-transcriptionally modified to m (5)UψC. In tRNAs of gram-negative bacteria, formation of m (5)U is catalyzed by the SAM-dependent methyltransferase TrmA, while formation of m (5)U at two different positions in rRNA is catalyzed by distinct site-specific methyltransferases RlmC and RlmD. Here, we show that m (5)U formation in tmRNAs is exclusively due to TrmA and should be considered as a dual-specific enzyme. The evidence comes from the lack of m (5)U in purified tmRNA or TLD variants recovered from an Escherichia coli mutant strain deleted of the trmA gene. Detection of m (5)U in RNA was performed by NMR analysis.

Oil accumulation in intact olive fruits measured by near infrared spectroscopy-acousto-optically tunable filter

BACKGROUND

A field experiment was conducted to test the reliability of the near infrared spectroscopy (NIR)-acousto-optically tunable filter (AOTF) method to measure mesocarp oil content in vivo against nuclear magnetic resonance (NMR) determinations using three different olive cultivars at different stages of ripening.

RESULTS

In the partial least squares model carried out for the cultivar 'Arbequina', the coefficient of determination in calibration (R(2)c) was 0.991, while the coefficient of determination in cross-validation (R(2)cv) was 0.979. For the cultivar 'Frantoio' the indexes were 0.982 and 0.971, respectively; while for the cultivar 'Leccino' R(2)c was 0.977 and R(2)cv was 0.965. Finally, for the combined model (sum of the three varieties) these indexes were 0.921 and 0.903, respectively. The residual predictive deviation (RPD) ratio was insufficient for the predictive model of cultivar 'Leccino' only (1.98), whereas in the other cases the RPD ratios were completely sufficient, within the estimation range over 2.5-3 (2.61 in the global model, and 4.23 in the cultivar 'Frantoio'), or in describing a large capacity with values greater than 5, as in the cultivar 'Arbequina' (9.58).

CONCLUSION

NIR-AOTF spectroscopy proved to be a novel, rapid and reliable method to monitor the oil accumulation process in intact olive fruits in the field. The innovative approach of coupling NIR and NMR technologies opens up new scenarios for determining the optimal time for harvesting olive trees to obtain maximum oil production.

Distinct binding properties of TIAR RRMs and linker region

The RNA-binding protein TIAR is an mRNA-binding protein that acts as a translational repressor, particularly important under conditions of cellular stress. It binds to target mRNA and DNA via its RNA recognition motif (RRM) domains and is involved in both splicing regulation and translational repression via the formation of "stress granules." TIAR has also been shown to bind ssDNA and play a role in the regulation of transcription. Here we show, using surface plasmon resonance and nuclear magnetic resonance spectroscopy, specific roles of individual TIAR domains for high-affinity binding to RNA and DNA targets. We confirm that RRM2 of TIAR is the major RNA- and DNA-binding domain. However, the strong nanomolar affinity binding to U-rich RNA and T-rich DNA depends on the presence of the six amino acid residues found in the linker region C-terminal to RRM2. On its own, RRM1 shows preferred binding to DNA over RNA. We further characterize the interaction between RRM2 with the C-terminal extension and an AU-rich target RNA sequence using NMR spectroscopy to identify the amino acid residues involved in binding. We demonstrate that TIAR RRM2, together with its C-terminal extension, is the major contributor for the high-affinity (nM) interactions of TIAR with target RNA sequences.

Regulatory interactions between a bacterial tyrosine kinase and its cognate phosphatase

The cyclic process of autophosphorylation of the C-terminal tyrosine cluster (YC) of a bacterial tyrosine kinase and its subsequent dephosphorylation following interactions with a counteracting tyrosine phosphatase regulates diverse physiological processes, including the biosynthesis and export of polysaccharides responsible for the formation of biofilms or virulence-determining capsules. We provide here the first detailed insight into this hitherto uncharacterized regulatory interaction at residue-specific resolution using Escherichia coli Wzc, a canonical bacterial tyrosine kinase, and its opposing tyrosine phosphatase, Wzb. The phosphatase Wzb utilizes a surface distal to the catalytic elements of the kinase, Wzc, to dock onto its catalytic domain (WzcCD). WzcCD binds in a largely YC-independent fashion near the Wzb catalytic site, inducing allosteric changes therein. YC dephosphorylation is proximity-mediated and reliant on the elevated concentration of phosphorylated YC near the Wzb active site resulting from WzcCD docking. Wzb principally recognizes the phosphate of its phosphotyrosine substrate and further stabilizes the tyrosine moiety through ring stacking interactions with a conserved active site tyrosine.

NMR analysis of a novel enzymatically active unlinked dengue NS2B-NS3 protease complex

The dengue virus (DENV) is a mosquito-borne pathogen responsible for an estimated 100 million human infections annually. The viral genome encodes a two-component trypsin-like protease that contains the cofactor region from the nonstructural protein NS2B and the protease domain from NS3 (NS3pro). The NS2B-NS3pro complex plays a crucial role in viral maturation and has been identified as a potential drug target. Using a DENV protease construct containing NS2B covalently linked to NS3pro via a Gly4-Ser-Gly4 linker ("linked protease"), previous x-ray crystal structures show that the C-terminal fragment of NS2B is remote from NS3pro and exists in an open state in the absence of an inhibitor; however, in the presence of an inhibitor, NS2B complexes with NS3pro to form a closed state. This linked enzyme produced NMR spectra with severe signal overlap and line broadening. To obtain a protease construct with a resolved NMR spectrum, we expressed and purified an unlinked protease complex containing a 50-residue segment of the NS2B cofactor region and NS3pro without the glycine linker using a coexpression system. This unlinked protease complex was catalytically active at neutral pH in the absence of glycerol and produced dispersed cross-peaks in a (1)H-(15)N heteronuclear single quantum correlation spectrum that enabled us to conduct backbone assignments using conventional techniques. In addition, titration with an active-site peptide aldehyde inhibitor and paramagnetic relaxation enhancement studies demonstrated that the unlinked DENV protease exists predominantly in a closed conformation in solution. This protease complex can serve as a useful tool for drug discovery against DENV.

Identification and characterization of process-related impurities of trans-resveratrol

This article deals with the identification and characterization of process-related impurities of trans-resveratrol (3,5,4′-trihydroxystilbene), which exhibits several health benefits, including cancer prevention. During the synthesis of the bulk drug resveratrol, three new impurities were observed. The impurities were detected using the high-performance liquid chromatographic (HPLC) method, whose area percentages ranged from 0.05 to 0.3%. A systematic study was carried out to characterize them. These impurities were isolated by preparative HPLC and characterized by spectral data, subjected to co-injection in HPLC, and were found to be matching with the impurities present in the sample. LC-MS was performed to identify the mass of these impurities. Based on their spectral data (IR, NMR, and Mass), these impurities were characterized as 2-benzyl-5-[(E)-2-(4-hydroxyphenyl)ethenyl]benzene-1,3-diol [Impurity-B], 3-(benzyloxy)-5-[(E)-2-(4-hydroxyphenyl)ethenyl]phenol [Impurity-C], 5-{(E)-2-[4-(benzyloxy)phenyl]ethenyl}benzene-1,3-diol [Impurity-D). These compounds are not reported earlier as process-related impurities.

NMR-based metabolomics of urine in a mouse model of Alzheimer's disease: identification of oxidative stress biomarkers

Alzheimer's disease (AD) is the most common cause of neurodegenerative dementia among elderly patients. A biomarker for the disease could make diagnosis easier and more accurate, and accelerate drug discovery. In this study, NMR-based metabolomics analysis in conjunction with multivariate statistics was applied to examine changes in urinary metabolites in transgenic AD mice expressing mutant tau and β-amyloid precursor protein. These mice showed significant changes in urinary metabolites throughout the progress of the disease. Levels of 3-hydroxykynurenine, homogentisate and allantoin were significantly higher compared to control mice in 4 months (prior to onset of AD symptoms) and reverted to control values by 10 months of age (early/middle stage of AD), which highlights the relevance of oxidative stress to this neurodegenerative disorder even prior the onset of dementia. The level of these changed metabolites at very early period may provide an indication of disease risk at asymptomatic stage.

Observation of Optical Chemical Shift by Precision Nuclear Spin Optical Rotation Measurements and Calculations

Nuclear spin optical rotation (NSOR) is a recently developed technique for detection of nuclear magnetic resonance via rotation of light polarization, instead of the usual long-range magnetic fields. NSOR signals depend on hyperfine interactions with virtual optical excitations, giving new information about the nuclear chemical environment. We use a multipass optical cell to perform the first precision measurements of NSOR signals for a range of organic liquids and find clear distinction between proton signals for different compounds, in agreement with our earlier theoretical predictions. Detailed first-principles quantum mechanical NSOR calculations are found to be in agreement with the measurements.

The Absolute Shielding Constants of Heavy Nuclei: Resolving the Enigma of the (119)Sn Absolute Shielding

We demonstrate that the apparent disagreement between experimental determinations and four-component relativistic calculations of the absolute shielding constants of heavy nuclei is due to the breakdown of the commonly assumed relation between the electronic contribution to the nuclear spin-rotation constants and the paramagnetic contribution to the NMR shielding constants. We demonstrate that this breakdown has significant consequences for the absolute shielding constant of (119)Sn, leading to errors of about 1000 ppm. As a consequence, we expect that many absolute shielding constants of heavy nuclei will be in need of revision.

pH-Sensitive MR Responses Induced by Dendron-Functionalized SPIONs

We report a series of investigations of the pH-sensitive magnetic resonance (MR) responses of various surface-functionalized SPIONs (superparamagnetic iron oxide nanoparticles). First, functionalization of ~12 nm highly monocrystalline SPION cores with three different generations of melamine-dendrons was optimized to give agents with high molar relaxivities (e.g. R2m ~300 mM-1·s-1 at 7 T and R1m ~20-30 mM-1·s-1 at 0.5 T) and excellent aqueous stabilities. Molar relaxivities were found to exhibit great sensitivity to pH at physiologically-relevant ionic strengths, with sharp inflections observed at pH values near the pKa of the melamine monomer. The strength of the effect was observed to grow with increasing dendron generation (with concomitant shift in the position of the main pH inflection). Opposing behavior in R2m and R2m * trends may be exploited to provide a ratiometric MR response to pH. Combined with TEM and corresponding MR measurements from solutions of varying ionic strengths, these results are consistent with the pH-sensitive behavior originating from transient, reversible SPION clustering modulated by an interplay between SPION surface charge density and solution ionic strength. Studies of SPION cellular uptake and MR response in HeLa cell cultures are also presented. Finally, comparisons with the MR responses of SPIONs with alternative functionalities-derivatives of nitrilotriacetic acid or poly(1-vinylimidazole)-indicate that these types of pH-sensitive MR responses can be highly dependent upon the chemical composition of the surface species (and thus amenable to modulation through rational design).

The lipidome and proteome of oil bodies from Helianthus annuus (common sunflower)

In this paper we report the molecular profiling, lipidome and proteome, of the plant organelle known as an oil body (OB). The OB is remarkable in that it is able to perform its biological role (storage of triglycerides) whilst resisting the physical stresses caused by changes during desiccation (dehydration) and germination (rehydration). The molecular profile that confers such extraordinary physical stability on OBs was determined using a combination of ³¹P/¹H nuclear magnetic resonance (NMR), high-resolution mass spectrometry and nominal mass-tandem mass spectrometry for the lipidome, and gel-electrophoresis-chromatography-tandem mass spectrometry for the proteome. The integrity of the procedure for isolating OBs was supported by physical evidence from small-angle neutron-scattering experiments. Suppression of lipase activity was crucial in determining the lipidome. There is conclusive evidence that the latter is dominated by phosphatidylcholine (∼60 %) and phosphatidylinositol (∼20 %), with a variety of other head groups (∼20 %). The fatty acid profile of the surface monolayer comprised palmitic, linoleic and oleic acids (2:1:0.25, ¹H NMR) with only traces of other fatty acids (C24:0, C22:0, C18:0, C18:3, C16:2; by MS). The proteome is rich in oleosins (78 %) with the remainder being made up of caleosins and steroleosins. These data are sufficiently detailed to inform an update of the understood model of this organelle and can be used to inform the use of such components in a range of molecular biological, biotechnological and food industry applications. The techniques used in this study for profiling the lipidome throw a new light on the lipid profile of plant cellular compartments.

Investigation of Behavior of Forced Degradation of Lidocaine HCl by NMR Spectroscopy and GC-FID Methods: Validation of GC-FID Method for Determination of Related Substance in Pharmaceutical Formulations

The forced degradation study of lidocaine HCl was carried out according to the ICH guideline Q1A (R2). The degradation conditions were assessed to be hydrolysis, oxidation, photolysis and dry heat during 24 h, 48 h and 72 h and then the samples were investigated by GC-FID method and nuclear magnetic resonance (NMR) spectroscopy. According to these results, the degradation products were not observed in all reaction conditions during the 72 h period. Only spectral changes in the 1H and 13C-NMR spectrum were observed in hydrogen peroxide and acid degradation. As a result of this degradation, n-oxide was formed. After acid-induced degradation with HCl, the secondary amine salt was formed. Furthermore, trifluoroacetic acid (TFA) was used as the acidic media, and the decomposition products were observed. A simple and reliable gas chromatography method with flame ionization detection (GC-FID) was developed and validated for the determination of lidocaine HCl in pharmaceutical formulations in the form of a cream and injections. The GC-FID method can be used for a routine analysis of lidocaine HCl in pharmaceutical formulations and the proposed method, together with NMR spectroscopy, can be applied in stability studies.

NMR Metabolomics Analysis of Parkinson's Disease

Parkinson's disease (PD) is a neurodegenerative disease, which is characterized by progressive death of dopaminergic neurons in the substantia nigra pars compacta. Although mitochondrial dysfunction and oxidative stress are linked to PD pathogenesis, its etiology and pathology remain to be elucidated. Metabolomics investigates metabolite changes in biofluids, cell lysates, tissues and tumors in order to correlate these metabolomic changes to a disease state. Thus, the application of metabolomics to investigate PD provides a systematic approach to understand the pathology of PD, to identify disease biomarkers, and to complement genomics, transcriptomics and proteomics studies. This review will examine current research into PD mechanisms with a focus on mitochondrial dysfunction and oxidative stress. Neurotoxin-based PD animal models and the rationale for metabolomics studies in PD will also be discussed. The review will also explore the potential of NMR metabolomics to address important issues related to PD treatment and diagnosis.

Saturation transfer difference NMR for fragment screening

Fragment screening by saturation transfer difference nuclear magnetic resonance (STD-NMR) is a robust method for identifying small molecule binders and is well suited to a broad set of biological targets. STD-NMR is exquisitely sensitive for detecting weakly binding compounds (a common characteristic of fragments), which is a crucial step in finding promising compounds for a fragment-based drug discovery campaign. This protocol describes the development of a library suitable for STD-NMR fragment screening, as well as preparation of protein samples, optimization of experimental conditions, and procedures for data collection and analysis.

Tracing Metabolite Footsteps of Escherichia coli Along the Time Course of Recombinant Protein Expression by Two-Dimensional NMR Spectroscopy

The recombinant expression of proteins has been the method of choice to meet the demands from proteomics and structural genomics studies. Despite its successful production of many heterologous proteins, Escherichia coli failed to produce many other proteins in their native forms. This may be related to the fact that the stresses resulting from the overproduction interfere with cellular processes. To better understand the physiological change during the overproduction phase, we profiled the metabolites along the time course of the recombinant protein expression. We identified 32 metabolites collected from different time points in the protein production phase. The stress induced by protein production can be characterized by (A) the increased usage of aspartic acid, choline, glycerol, and N-acetyllysine; and (B) the accumulation of adenosine, alanine, oxidized glutathione, glycine, N-acetylputrescine, and uracil. We envision that this work can be used to create a strategy for the production of usable proteins in large quantities.

Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation

Solid-state NMR can provide atomic-resolution information about protein motions occurring on a vast range of time scales under similar conditions to those of X-ray diffraction studies and therefore offers a highly complementary approach to characterizing the dynamic fluctuations occurring in the crystal. We compare experimentally determined dynamic parameters, spin relaxation, chemical shifts, and dipolar couplings, to values calculated from a 200 ns MD simulation of protein GB1 in its crystalline form, providing insight into the nature of structural dynamics occurring within the crystalline lattice. This simulation allows us to test the accuracy of commonly applied procedures for the interpretation of experimental solid-state relaxation data in terms of dynamic modes and time scales. We discover that the potential complexity of relaxation-active motion can lead to significant under- or overestimation of dynamic amplitudes if different components are not taken into consideration.

Glycosaminoglycan analogs as a novel anti-inflammatory strategy

Heparin, a glycosaminoglycan (GAG), has both anti-inflammatory and anti-coagulant properties. The clinical use of heparin against inflammation, however, has been limited by concerns about increased bleeding. While the anti-coagulant activity of heparin is well understood, its anti-inflammatory properties are less so. Heparin is known to bind to certain cytokines, including chemokines, small proteins which mediate inflammation through their control of leukocyte migration and activation. Molecules which can interrupt the chemokine-GAG interaction without inhibiting coagulation could therefore, represent a new class of anti-inflammatory agents. In the present study, two approaches were undertaken, both focusing on the heparin-chemokine relationship. In the first, a structure based strategy was used: after an initial screening of potential small molecule binders using protein NMR on a target chemokine, binding molecules were optimized through structure-based design. In the second approach, commercially available short oligosaccharides were polysulfated. In vitro, these molecules prevented chemokine-GAG binding and chemokine receptor activation without disrupting coagulation. However, in vivo, these compounds caused variable results in a murine peritoneal recruitment assay, with a general increase of cell recruitment. In more disease specific models, such as antigen-induced arthritis and delayed-type hypersensitivity, an overall decrease in inflammation was noted, suggesting that the primary anti-inflammatory effect may also involve factors beyond the chemokine system.

Kinetic profile of amyloid formation in the presence of an aromatic inhibitor by nuclear magnetic resonance

The self-assembly of amyloid proteins into β-sheet rich assemblies is associated with human amyloidoses including Alzheimer's disease, Parkinson's disease, and type 2 diabetes. An attractive therapeutic strategy therefore is to develop small molecules that would inhibit protein self-assembly. Natural polyphenols are potential inhibitors of β-sheet formation. How these compounds affect the kinetics of self-assembly studied by thioflavin T (ThT) fluorescence is not understood primarily because their presence interferes with ThT fluorescence. Here, we show that by plotting peak intensities from nuclear magnetic resonance (NMR) against incubation time, kinetic profiles in the presence of the polyphenol can be obtained from which kinetic parameters of self-assembly can be easily determined. In applying this technique to the self-assembly of the islet amyloid polypeptide in the presence of curcumin, a biphenolic compound found in turmeric, we show that the kinetic profile is atypical in that it shows a prenucleation period during which there is no observable decrease in NMR peak intensities.

Recent trends in the impurity profile of pharmaceuticals

Various regulatory authorities such as the International Conference on Harmonization (ICH), the United States Food and Drug administration (FDA), and the Canadian Drug and Health Agency (CDHA) are emphasizing on the purity requirements and the identification of impurities in Active Pharmaceutical Ingredients (APIs). The various sources of impurity in pharmaceutical products are — reagents, heavy metals, ligands, catalysts, other materials like filter aids, charcoal, and the like, degraded end products obtained during \ after manufacturing of bulk drugs from hydrolysis, photolytic cleavage, oxidative degradation, decarboxylation, enantiomeric impurity, and so on. The different pharmacopoeias such as the British Pharmacopoeia, United State Pharmacopoeia, and Indian Pharmacopoeia are slowly incorporating limits to allowable levels of impurities present in APIs or formulations. Various methods are used to isolate and characterize impurities in pharmaceuticals, such as, capillary electrophoresis, electron paramagnetic resonance, gas–liquid chromatography, gravimetric analysis, high performance liquid chromatography, solid-phase extraction methods, liquid–liquid extraction method, Ultraviolet Spectrometry, infrared spectroscopy, supercritical fluid extraction column chromatography, mass spectrometry, Nuclear magnetic resonance (NMR) spectroscopy, and RAMAN spectroscopy. Among all hyphenated techniques, the most exploited techniques for impurity profiling of drugs are Liquid Chromatography (LC)-Mass Spectroscopy (MS), LC-NMR, LC-NMR-MS, GC-MS, and LC-MS. This reveals the need and scope of impurity profiling of drugs in pharmaceutical research.

A new flavonol glycoside from the Abelmoschus esculentus Linn

Background:

Abelmoschus esculentus L. belonging to the family Malvaceae is a kind of one year herbage plant, which is one of the most important vegetables widely grown in Nigeria for its tender fruits and young leaves. It's easy to be cultivated and grows well in both tropical and temperate zones, that is, it is widely planted from Africa to Asia, South European to America. A new flavonol glycoside characterized as 5,7,3′,4′-tetrahydroxy-4′′-O-methyl flavonol -3-O-β-D- glucopyranoside (1) has been isolated from the fruit of A. esculentus together with one known compound 5,7,3′,4′-tetrahydroxy flavonol -3-O-[β-D-glucopyranosyl-(1→6)]-β-D-glucopyranoside (2). The structure of the new compound was elucidated on the basis of its spectral data, including 2-D NMR and mass (MS) spectra. The antioxidant activities of the isolated compounds 1 and 2 were evaluated by 2 assays, the 1,1-diphenyl-2-picryl-hydrazyl (DPPH) and ferric reducing antioxidant power (FRAP). The present work deals with the isolation, identification and antioxidant activity of the two compounds.

Materials and Methods:

The compounds were isolated by Diaion HP-20, Sephedex LH-20 column chromatography methods, their structures were identified by physicochemical properties and spectroscopic analysis. The antioxidant activities of the isolated compounds 1 and 2 were evaluated by two assays, e.g., DPPH and FRAP.

Results:

Two flavonol glycosides have been isolated from the fruit of Abelmoschus esculentus L. for the first time, and the compound 1 was a new compound, the compound 2 was isolated from the plant for the first time.

Conclusion:

The results show that the two flavonol glycosides have strong ability for scavenging DPPH and FRAP free radical by the experiment of antioxidant activities, so A. esculentus may be a natural antioxidants resource.

Magnetic excitations in iron chalcogenide superconductors

Nuclear magnetic resonance and neutron scattering experiments in iron chalcogenide superconductors are reviewed to make a survey of the magnetic excitations in FeSe, FeSe1-x Te x and alkali-metal-doped Ax Fe2-y Se2 (A = K, Rb, Cs, etc). In FeSe, the intimate relationship between the spin fluctuations and superconductivity can be seen universally for the variations in the off-stoichiometry, the Co-substitution and applied pressure. The isovalent compound FeTe has a magnetic ordering with different wave vector from that of other Fe-based magnetic materials. The transition temperature Tc of FeSe increases with Te substitution in FeSe1-x Te x with small x, and decreases in the vicinity of the end member FeTe. The spin fluctuations are drastically modified by the Te substitution. In the vicinity of the end member FeTe, the low-energy part of the spin fluctuation is dominated by the wave vector of the ordered phase of FeTe; however, the reduction of Tc shows that it does not support superconductivity. The presence of same wave vector as that of other Fe-based superconductors in FeSe1-x Te x and the observation of the resonance mode demonstrate that FeSe1-x Te x belongs to the same group as most of other Fe-based superconductors in the entire range of x, where superconductivity is mediated by the spin fluctuations whose wave vector is the same as the nesting vector between the hole pockets and the electron pockets. On the other hand, the spin fluctuations differ for alkali-metal-doped Ax Fe2-y Se2 and FeSe or other Fe-based superconductors in their wave vector and strength in the low-energy part, most likely because of the different Fermi surfaces. The resonance mode with different wave vector suggests that Ax Fe2-y Se2 has an exceptional superconducting symmetry among Fe-based superconductors.

Solution NMR structure of hypothetical protein CV_2116 encoded by a viral prophage element in Chromobacterium violaceum

CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e⁻⁰⁷) corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the function of CV_2116. The CV_2116 gene was cloned into the p15TvLic expression plasmid, transformed into E. coli, and ¹³C- and ¹⁵N-labeled NMR samples of CV_2116 were overexpressed in E. coli and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β-sheets in the N-terminal two-thirds of the protein and one α-helix in the C-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of CV_2116 encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, C. violaceum exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages) due to bacteriophage infection. Indeed, C. violaceum has been shown to contain four prophage elements and CV_2116 resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in C. violaceum.

The monoclonal antibody HCM31 specifically recognises the Sd(a) tetrasaccharide in goblet cell mucin

Rat small intestinal goblet cell mucins reacting with monoclonal antibody HCM31 increase significantly during regeneration from experimental mucosal damage and at the period of expulsion of parasitic nematode, Nippostrongylus brasiliensis (N.b). The reduction in reactivity of HCM31 with mucin upon neuraminidase treatment, suggested that HCM31 recognizes sialylated oligosaccharide on mucin. HCM31-reactive sialomucins are therefore considered to play an important role in the physiological and pathological changes in the gastrointestinal mucosa. To determine the epitope for HCM31, oligosaccharide-alditols reacted with HCM31 were obtained from the small intestinal mucins of N.b-infected rats and purified by ion-exchange chromatography followed by normal-phase HPLC. Two HCM31-reactive oligosaccharide-alditols were obtained. Analyses using tandem mass spectrometry and NMR spectroscopy showed that these oligosaccharides were core 4 mucin-type oligosaccharides having a common tetrasaccharide sequence, NeuAcα2-3(GalNAcβ1-4)Galβ1-4GlcNAcβ- (Sd(a) blood group antigen). These structures were not found in the small intestinal mucin oligosaccharides from uninfected rats. This epitope specificity of HCM31 was also confirmed using previously established anti-GM2 and anti-Sd(a) antibodies. Taken together, these results strongly suggest that HCM31 specifically recognizes mucin-type oligosaccharides with the Sd(a) tetrasaccharide sequence. Immunohistochemical examination of human gastrointestinal tracts showed that HCM31 site-specifically stained the goblet cells in normal sigmoid colon and normal rectum, but the goblet cells stained with HCM31 were reduced in the corresponding cancer tissues. HCM31 seems to be useful for diagnosis of colonic cancer and for examining the function of secretory-type mucin with Sd(a) antigen.

Creating Long-Lived Spin States at Variable Magnetic Field by Means of Photochemically Induced Dynamic Nuclear Polarization

We have shown that long-lived spin states (LLS) can be selectively populated by photogenerated chemically induced dynamic nuclear polarization (CIDNP) over a wide range of magnetic fields. Relaxation times of LLS of the β-CH2 protons in N-acetyl histidine and partially deuterated histidine have been measured. Our experiments demonstrate that CIDNP enables creating LLS in the amino acid in a field range of up to a few Tesla and that their lifetimes can be 45 times longer than T1. The advantage of the method is thus two-fold: it allows one to accumulate high levels of spin hyperpolarization and to preserve them for periods of time far exceeding T1. Therefore, photo-CIDNP is a technique suitable for creating long-lived spin order in biologically relevant molecules.

Functional expression in Escherichia coli of the disulfide-rich sea anemone peptide APETx2, a potent blocker of acid-sensing ion channel 3

Acid-sensing ion channels (ASICs) are proton-gated sodium channels present in the central and peripheral nervous system of chordates. ASIC3 is highly expressed in sensory neurons and plays an important role in inflammatory and ischemic pain. Thus, specific inhibitors of ASIC3 have the potential to be developed as novel analgesics. APETx2, isolated from the sea anemone Anthopleura elegantissima, is the most potent and selective inhibitor of ASIC3-containing channels. However, the mechanism of action of APETx2 and the molecular basis for its interaction with ASIC3 is not known. In order to assist in characterizing the ASIC3-APETx2 interaction, we developed an efficient and cost-effective Escherichia coli periplasmic expression system for the production of APETx2. NMR studies on uniformly (13)C/(15)N-labelled APETx2 produced in E. coli showed that the recombinant peptide adopts the native conformation. Recombinant APETx2 is equipotent with synthetic APETx2 at inhibiting ASIC3 channels expressed in Xenopus oocytes. Using this system we mutated Phe15 to Ala, which caused a profound loss of APETx2's activity on ASIC3. These findings suggest that this expression system can be used to produce mutant versions of APETx2 in order to facilitate structure-activity relationship studies.

Structural analysis of hypothetical proteins from Helicobacter pylori: an approach to estimate functions of unknown or hypothetical proteins

Helicobacter pylori (H. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MALT) lymphoma, gastric cancer, etc. Based on genomic research of H. pylori, over 1600 genes have been functionally identified so far. However, H. pylori possess some genes that are uncharacterized since: (i) the gene sequences are quite new; (ii) the function of genes have not been characterized in any other bacterial systems; and (iii) sometimes, the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which raises questions about the function of the protein produced in H. pylori. Thus, there are still a lot of genes to be biologically or biochemically characterized to understand the whole picture of gene functions in the bacteria. In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. Here, we show the 3D structures of some hypothetical proteins determined by NMR spectroscopy and X-ray crystallography as a part of the structural genomics of H. pylori. In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information.

Triterpenoid saponins from the roots of Acanthophyllum gypsophiloides Regel

Two new triterpenoid saponins 1 and 2 were isolated from the methanol extract of the roots of Acanthophyllum gypsophiloides Regel. These saponins have quillaic acid or gypsogenin moieties as an aglycon, and both bear similar sets of two oligosaccharide chains, which are 3-O-linked to the triterpenoid part trisaccharide α-L-Arap-(1→3)-[α-D-Galp-(1→2)]-β-D-GlcpA and pentasaccharide β-D-Xylp-(1→3)-β-D-Xylp-(1→3)-α-L-Rhap-(1→2)-[β-D-Quip-(1→4)]-β-D-Fucp connected through an ester linkage to C-28. The structures of the obtained saponins were elucidated by a combination of mass spectrometry and 2D NMR spectroscopy. A study of acute toxicity, hemolytic, anti-inflammatory, immunoadjuvant and antifungal activity was carried out. Both saponins 1 and 2 were shown to exhibit immunoadjuvant properties within the vaccine composition with keyhole limpet hemocyanin-based immunogen. The availability of saponins 1 and 2 as individual pure compounds from the extract of the roots of A. gypsophiloides makes it a prospective source of immunoactive agents.

Carbon-Detected (15)N NMR Spin Relaxation of an Intrinsically Disordered Protein: FCP1 Dynamics Unbound and in Complex with RAP74

Intrinsically disordered proteins (IDPs) lack unique 3D structures under native conditions and as such exist as highly dynamic ensembles in solution. We present two (13)C-direct detection experiments for the measurement of (15)N NMR spin relaxation called the CON(T1)-IPAP and CON(T2)-IPAP that quantify backbone dynamics on a per-residue basis for IDPs in solution. These experiments have been applied to the intrinsically disordered C-terminal of FCP1, both free in solution and while bound to the RAP74 winged-helix domain. The results provide evidence that most of FCP1 remains highly dynamic in both states, while the 20 residues forming direct contact with RAP74 become more ordered in the complex. Parallel analysis of RAP74 backbone (15)N NMR spin relaxation reveals only very limited ordering of RAP74 upon FCP1 binding. Taken together, these data show that folding-upon-binding is highly local in this system, with disorder prevailing even in the complex.

Novel Fe3+-Based 1H MRI β-Galactosidase Reporter Molecules**

There is increasing interest in the development of reporter agents to reveal enzyme activity in vivo using small animal imaging. We have previously demonstrated the feasibility of detecting lacZ gene activity using the commercially available 3,4-cyclohexenoesculetin-β-D-galactopyranoside (S-Gal™) as a 1H MRI reporter. Specifically, β-galactosidase (β-gal) releases the aglycone, which forms an MR contrast-inducing paramagnetic precipitate in the presence of Fe3+. Contrast was primarily T2-weighted signal loss, but T1 effects were also observed. Since T1-contrast generally provides signal enhancement as opposed to loss, it appeared attractive to explore whether analogues could be generated with enhanced characteristics. We now report the design and successful synthesis of novel analogues together with characterization of 1H MRI contrast based on both T1 and T2 response to β-gal activity in vitro for the lead agent.

Exploring Mass Transfer in Mesoporous Zeolites by NMR Diffusometry

With the advent of mesoporous zeolites, the exploration of their transport properties has become a task of primary importance for the auspicious application of such materials in separation technology and heterogeneous catalysis. After reviewing the potential of the pulsed field gradient method of NMR (PFG NMR) for this purpose in general, in a case study using a specially prepared mesoporous zeolite NaCaA as a host system and propane as a guest molecule, examples of the attainable information are provided.

Deconvolution and Estimation of Water Diffusion in Sulfonated Polyethersulfone Membranes Using Diffusion-Weighted Inversion Recovery

An NMR method was applied for the deconvolution of specific water in sulfonated polyether sulfone membranes, where sulfonated polyethersulfone is a proton-conducting polymer in polymer electrolyte membrane fuel cells. The distribution of (1)H longitudinal relaxation times obtained by the inverse Laplace method was utilized to estimate the volume fraction of proton species as a function of relative humidity (RH). The relaxation time distribution clearly revealed two distinguished peaks on the order of 10(-3) and 10(-2) s, which corresponded to water in the larger and smaller channels for proton transports, respectively. We applied a pulse sequence to understand the water species by diffusion-weighted inversion recovery, which led to individual self-diffusion coefficients for deconvoluted water by using the longitudinal relaxation time. At 30% RH, the diffusion coefficient of water in small-sized channels is greater than that in large-sized channels. On the other hand, the diffusion coefficients of protons with smaller and larger water channels are almost the same at 50, 70, and 90% RH.

Structural basis for the regulation of L-type voltage-gated calcium channels: interactions between the N-terminal cytoplasmic domain and Ca(2+)-calmodulin

It is well-known that the opening of L-type voltage-gated calcium channels can be regulated by calmodulin (CaM). One of the main regulatory mechanisms is calcium-dependent inactivation (CDI), where binding of apo-CaM to the cytoplasmic C-terminal domain of the channel can effectively sense an increase in the local calcium ion concentration. Calcium-bound CaM can bind to the IQ-motif region of the C-terminal region and block the calcium channel, thereby providing a negative feedback mechanism that prevents the rise of cellular calcium concentrations over physiological limits. Recently, an additional Ca²⁺/CaM-binding motif (NSCaTE, N-terminal spatial Ca²⁺ transforming element) was identified in the amino terminal cytoplasmic region of Ca_v1.2 and Ca_v1.3. This motif exists only in Ca_v1.2 and Ca_v1.3 channels, and a pronounced N-lobe (Ca²⁺/CaM) CDI effect was found for Ca_v1.3. To understand the molecular basis of this interaction, the complexes of Ca²⁺/CaM with the biosynthetically produced N-terminal region (residues 1–68) and NSCaTE peptide (residues 48–68) were investigated. We discovered that the NSCaTE motif in the N-terminal cytoplasmic region adopts an α-helical conformation, most likely due to its high alanine content. Additionally, the complex exhibits an unusual 1:2 protein:peptide stoichiometry when bound to Ca²⁺-CaM, and the N-lobe of CaM has a much stronger affinity for the peptide than the C-lobe. The complex structures of the isolated N- and C-lobe of Ca²⁺/CaM and the NSCaTE peptide were determined by nuclear magnetic resonance spectroscopy and data-driven protein-docking methods. Moreover, we also demonstrated that calcium binding protein 1, which competes with CaM for binding to the C-terminal cytoplasmic domain, binds only weakly to the NSCaTE region. The structures provide insights into the possible roles of this motif in the calcium regulatory network. Our study provides structural evidence for the CaM-bridge model proposed in previous studies.

Self-Diffusion of Chain Molecules in the Metal-Organic Framework IRMOF-1: Simulation and Experiment

Metal-organic frameworks (MOFs) possess characteristics, such as tunable pore size and chemical functionality, that make them attractive candidates for separations, catalysis, gas storage, and sensing applications. The rate of diffusion of guest molecules in the pores is an important property for all of these potential applications. In this work, the self-diffusion of hydrocarbons in IRMOF-1 was studied as a function of chain length with a combination of molecular dynamics simulations and pulsed field gradient NMR experiments. Excellent agreement is seen between the experiments and simulations, and the self-diffusion coefficients in IRMOF-1 are on the same order as those in the bulk liquid. Additionally, the effect of concentration on diffusivity was found to be very small for low to moderate loadings. Molecular dynamics simulations also provided insights about the preferential diffusion pathways of these guests in IRMOF-1.

An Open-Source Sandbox for Increasing the Accessibility of Functional Programming to the Bioinformatics and Scientific Communities

Scientists are continually faced with the need to express complex mathematical notions in code. The renaissance of functional languages such as LISP and Haskell is often credited to their ability to implement complex data operations and mathematical constructs in an expressive and natural idiom. The slow adoption of functional computing in the scientific community does not, however, reflect the congeniality of these fields. Unfortunately, the learning curve for adoption of functional programming techniques is steeper than that for more traditional languages in the scientific community, such as Python and Java, and this is partially due to the relative sparseness of available learning resources. To fill this gap, we demonstrate and provide applied, scientifically substantial examples of functional programming, We present a multi-language source-code repository for software integration and algorithm development, which generally focuses on the fields of machine learning, data processing, bioinformatics. We encourage scientists who are interested in learning the basics of functional programming to adopt, reuse, and learn from these examples. The source code is available at: https://github.com/CONNJUR/CONNJUR-Sandbox (see also http://www.connjur.org).

Dynamics and activation in response regulators: the β4-α4 loop

Two-component signal transduction systems of microbes are a primary means to respond to signals emanating from environmental and metabolic fluctuations as well as to signals coordinating the cell cycle with macromolecular syntheses, among a large variety of other essential roles. Signals are recognized by a sensor domain of a histidine kinase which serves to convert signal binding to an active transmissible phosphoryl group through a signal-induced ATP-dependent autophosphorylation reaction directed to histidine residue. The sensor kinase is specifically mated to a response regulator, to which it transfers the phosphoryl group that activates the response regulator's function, most commonly gene repression or activation but also interaction with other regulatory proteins. Two-component systems have been genetically amplified to control a wide variety of cellular processes; for example, both Escherichia coli and Pseudomonas aeruginosa have 60 plus confirmed and putative two-component systems. Bacillus subtilis has 30 plus and Nostoc punctiformis over 100. As genetic amplification does not result in changes in the basic structural folds of the catalytic domains of the sensor kinase or response regulators, each sensor kinase must recognize its partner through subtle changes in residues at the interaction surface between the two proteins. Additionally, the response regulator must prepare itself for efficient activation by the phosphorylation event. In this short review, we discuss the contributions of the critical β4-α4 recognition loop in response regulators to their function. In particular, we focus on this region's microsecond-millisecond timescale dynamics propensities and discuss how these motions play a major role in response regulator recognition and activation.

Metabolic Profiling Comparison of Human Pancreatic Ductal Epithelial Cells and Three Pancreatic Cancer Cell Lines using NMR Based Metabonomics

Metabolic profiles of hydrophilic and lipophilic cell extracts from three cancer cell lines, Miapaca-2, Panc-1 and AsPC-1, and a non-cancerous pancreatic ductal epithelial cell line, H6C7, were examined by proton nuclear magnetic resonance spectroscopy. Over twenty five hydrophilic metabolites were identified by principal component and statistical significance analyses as distinguishing the four cell types. Fifteen metabolites were identified with significantly altered concentrations in all cancer cells, e.g. absence of phosphatidylgrycerol and phosphatidylcholine, and increased phosphatidylethanolamine and cholesterols. Altered concentrations of metabolites involved in glycerophospholipid metabolism, lipopolysaccharide and fatty acid biosynthesis indicated differences in cellular membrane composition between non-cancerous and cancer cells. In addition to cancer specific metabolites, several metabolite changes were unique to each cancer cell line. Increased N-acetyl groups in AsPC-1, octanoic acids in Panc-1, and UDP species in Miapaca-2 indicated differences in cellular membrane composition between the cancer cell lines. Induced glutamine metabolism and protein synthesis in cancer cells were indicated by absence of glutamine other metabolites such as acetate, lactate, serine, branched amino acids, and succinate. Knowledge of the specifically altered metabolic pathways identified in these pancreatic cancer cell lines may be useful for identifying new therapeutic targets and studying the effects of potential new therapeutic drugs.

Role of the HIV-1 Matrix Protein in Gag Intracellular Trafficking and Targeting to the Plasma Membrane for Virus Assembly

Human immunodeficiency virus type-1 (HIV-1) encodes a polypeptide called Gag that is able to form virus-like particles in vitro in the absence of any cellular or viral constituents. During the late phase of the HIV-1 infection, Gag polyproteins are transported to the plasma membrane (PM) for assembly. In the past two decades, in vivo, in vitro, and structural studies have shown that Gag trafficking and targeting to the PM are orchestrated events that are dependent on multiple factors including cellular proteins and specific membrane lipids. The matrix (MA) domain of Gag has been the focus of these studies as it appears to be engaged in multiple intracellular interactions that are suggested to be critical for virus assembly and replication. The interaction between Gag and the PM is perhaps the most understood. It is now established that the ultimate localization of Gag on punctate sites on the PM is mediated by specific interactions between the MA domain of Gag and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P(2)], a minor lipid localized on the inner leaflet of the PM. Structure-based studies revealed that binding of PI(4,5)P(2) to MA induces minor conformational changes, leading to exposure of the myristyl (myr) group. Exposure of the myr group is also triggered by binding of calmodulin, enhanced by factors that promote protein self-association like the capsid domain of Gag, and is modulated by pH. Despite the steady progress in defining both the viral and cellular determinants of retroviral assembly and release, Gag's intracellular interactions and trafficking to its assembly sites in the infected cell are poorly understood. In this review, we summarize the current understanding of the structural and functional role of MA in HIV replication.

Sorbate Transport in Carbon Molecular Sieve Membranes and FAU/EMT Intergrowth by Diffusion NMR

In this paper we present and discuss selected results of our recent studies of sorbate self-diffusion in microporous materials. The main focus is given to transport properties of carbon molecular sieve (CMS) membranes as well as of the intergrowth of FAU-type and EMT-type zeolites. CMS membranes show promise for applications in separations of mixtures of small gas molecules, while FAU/EMT intergrowth can be used as an active and selective cracking catalyst. For both types of applications diffusion of guest molecules in the micropore networks of these materials is expected to play an important role. Diffusion studies were performed by a pulsed field gradient (PFG) NMR technique that combines advantages of high field (17.6 T) NMR and high magnetic field gradients (up to 30 T/m). This technique has been recently introduced at the University of Florida in collaboration with the National Magnet Lab. In addition to a more conventional proton PFG NMR, also carbon-13 PFG NMR was used.

Molecular structure and target recognition of neuronal calcium sensor proteins

Neuronal calcium sensor (NCS) proteins, a sub-branch of the EF-hand superfamily, are expressed in the brain and retina where they transduce calcium signals and are genetically linked to degenerative diseases. The amino acid sequences of NCS proteins are highly conserved but their physiological functions are quite distinct. Retinal recoverin and guanylate cyclase activating proteins (GCAPs) both serve as calcium sensors in retinal rod cells, neuronal frequenin (NCS1) modulates synaptic activity and neuronal secretion, K⁺ channel interacting proteins (KChIPs) regulate ion channels to control neuronal excitability, and DREAM (KChIP3) is a transcriptional repressor that regulates neuronal gene expression. Here we review the molecular structures of myristoylated forms of NCS1, recoverin, and GCAP1 that all look very different, suggesting that the sequestered myristoyl group helps to refold these highly homologous proteins into very different structures. The molecular structure of NCS target complexes have been solved for recoverin bound to rhodopsin kinase (RK), NCS-1 bound to phosphatidylinositol 4-kinase, and KChIP1 bound to A-type K⁺ channels. We propose that N-terminal myristoylation is critical for shaping each NCS family member into a different structure, which upon Ca²⁺-induced extrusion of the myristoyl group exposes a unique set of previously masked residues that interact with a particular physiological target.

Surface-Selective Solution NMR Studies of Functionalized Zeolite Nanoparticles

The surface chemistry of zeolite nanoparticles functionalized with the organosilane aminopropyldimethylmethoxysilane (APDMMS) was selectively probed using solution (1)H NMR spectroscopy. The use of solution NMR spectroscopy results in high-resolution NMR spectra, and the technique is selective for protons on the surface organic functional groups due to their motional averaging in solution. In this study, (1)H solution NMR spectroscopy was used to investigate the interface of the organic functional groups of APDMMS-functionalized silicalite nanoparticles (∼35 nm) in D2O. The pKa for the amine group of APDMMS-functionalized silicalite nanoparticles in D2O was determined using an NMR-pH titration method based on the variation in the proton chemical shift for the alkyl group protons closest to the amine group with pH. The resulting NMR spectra demonstrate the sensitivity of solution NMR spectroscopy to the electronic environment and structure of the surface functional groups.

Stereochemical behavior of (77)Se-(1)H spin-spin coupling constants in pyrazolyl-1,3-diselenanes and 1,2-diselenolane

Conformational study of five derivatives of 2-(pyrazol-4-yl)-1,3-diselenane together with related 1,2-diselenolane in respect to the stereochemical trends of geminal and vicinal (77)Se-(1)H spin-spin coupling constants has been carried out by means of high-level theoretical calculations in combination with experiment. The marked dihedral angle dependences for both types of couplings accounted for the lone pair effect in the case of geminal coupling constants and the Karplus-type relationship for vicinal couplings have been established, which is of major importance for the stereochemical analysis of saturated selenium containing heterocycles.

DFT calculations of structures, (13)C NMR chemical shifts, and Raman RBM mode of simple models of small-diameter zigzag (4,0) carboxylated single-walled carbon nanotubes

Linearly conjugated benzene rings (acenes), belt-shaped molecules (cyclic acenes), and models of single-walled carbon nanotubes (SWCNTs) with one carboxylic group at the open end were fully optimized at the B3LYP/6-31G* level of theory. These models were selected to obtain some insight into the nuclear isotropic changes resulting from systematically increasing the basic building units of open-tip-monocarboxylated SWCNTs. In addition, the position of radial breathing mode (RBM), empirically correlated with the SWCNT diameter, was directly related with the radius of model cyclic acene rings. A regular convergence of selected structural, NMR, and Raman parameters with the molecular system size increase was observed, and a simple two-parameter mathematical formula enabled their estimation in infinity. The predicted (13) C NMR chemical shifts of carbon atoms close to the substituted rim of carboxylated models of zigzag (4,0) SWCNTs differed significantly from the pristine nanotubes.

Hartmann-Hahn 2D-map to optimize the RAMP-CPMAS NMR experiment for pharmaceutical materials

Cross polarization-magic angle spinning (CPMAS) is the most used experiment for solid-state NMR measurements in the pharmaceutical industry, with the well-known variant RAMP-CPMAS its dominant implementation. The experimental work presented in this contribution focuses on the entangled effects of the main parameters of such an experiment. The shape of the RAMP-CP pulse has been considered as well as the contact time duration, and a particular attention also has been devoted to the radio-frequency (RF) field inhomogeneity. (13)C CPMAS NMR spectra have been recorded with a systematic variation of (13)C and (1)H constant radiofrequency field pair values and represented as a Hartmann-Hahn matching two-dimensional map. Such a map yields a rational overview of the intricate optimal conditions necessary to achieve an efficient CP magnetization transfer. The map also highlights the effects of sweeping the RF by the RAMP-CP pulse on the number of Hartmann-Hahn matches crossed and how RF field inhomogeneity helps in increasing the CP efficiency by using a larger fraction of the sample. In the light of the results, strategies for optimal RAMP-CPMAS measurements are suggested, which lead to a much higher efficiency than constant amplitude CP experiment.

A Potential Biomarker for Acute Kidney Injury in Preterm Infants from Metabolic Profiling

BACKGROUND

Currently used biomarkers for acute kidney injury (AKI), namely Ngal, SCr, and BUN, are inadequate for timely detection of AKI in preterm infants.

METHODS

Nuclear magnetic resonance (NMR) spectroscopy-based metabolic profiling was conducted on urines from 20 preterm infants to determine if novel metabolic biomarkers could be identified for early detection of AKI. Urines were collected from every patient each day for the first 14 days of life. NMR spectra were measured for all urines and metabolic profiling analysis conducted.

RESULTS

One metabolite, carnitine, increased significantly in urines of three extremely low birth weight (ELBW) infants starting on day five of life. The three affected infants either received prolonged antibiotic treatment, extended treatment with indomethacin, or both. One ELBW patient who received both treatments and reached the highest urinary carnitine level died on day 10 of life due to localized gut perforation complicated by suspected AKI.

CONCLUSIONS

It was concluded that carnitine increased in the three neonates in part due to antibiotic- and/or indomethacin-induced AKI. It is hypothesized that combined antibiotic and indomethacin treatment promoted AKI resulting in reduced proximal renal tubule reabsorption of carnitine and that β-lactam antibiotics blocked renal carnitine uptake by human organic cation transporter, hOCTN2.

Density functional theory study of (13)C NMR chemical shift of chlorinated compounds

The use of the standard density functional theory (DFT) leads to an overestimation of the paramagnetic contribution and underestimation of the shielding constants, especially for chlorinated carbon nuclei. For that reason, the predictions of chlorinated compounds often yield too high chemical shift values. In this study, the WC04 functional is shown to be capable of reducing the overestimation of the chemical shift of Cl-bonded carbons in standard DFT functionals and to show a good performance in the prediction of (13)C NMR chemical shifts of chlorinated organic compounds. The capability is attributed to the minimization of the contributions that intensively increase the chemical shift in the WC04. Extensive computations and analyses were performed to search for the optimal procedure for WC04. The B3LYP and mPW1PW91 standard functionals were also used to evaluate the performance. Through detailed comparisons between the basis set effects and the solvent effects on the results, the gas-phase GIAO/WC04/6-311+G(2d,p)//B3LYP/6-31+G(d,p) was found to be specifically suitable for the prediction of (13)C NMR chemical shifts of chlorides in both chlorinated and non-chlorinated carbons. Further tests with eight molecules in the probe set sufficiently confirmed that WC04 was undoubtedly effective for accurately predicting (13) C NMR chemical shifts of chlorinated organic compounds.

Halogenated chamigrane sesquiterpenes from Laurencia okamurae

Three new halogenated chamigrane sesquiterpenes, laurokamin A (1), laurokamin B (2), and laurokamin C (3), and four known halogenated chamigrane sesquiterpenes, 10-bromo-α-chamigrene (4), 10-bromo-β-chamigrene (5), 2,10-dibromo-3-chloro-β-chamigrene (6), and obtusane (7), were isolated from the marine red alga Laurencia okamurae collected from the coast of Rongcheng, China. The structures of these compounds were unambiguously identified by one- and two-dimensional NMR and mass spectroscopic methods. The antimicrobial activity of compounds 1-3 was evaluated.

Identification of (-)(E)-N-[2(S)-Hydroxy-2-(4-hydroxyphenyl) ethyl]ferulamide, a natural product isolated from Croton pullei: theoretical and experimental analysis

Ferulic acid (FA) and its derivatives (FADs) are known for a variety of biological activities, such as photo-protective agent, antioxidant, antiatherogenic and antiplasmodial activities. During structural definition of a FAD isolated from Croton pullei, the possibility of a heterologous series made this definition difficult. In this regard, computational simulations were performed using theoretical calculations at DFT level to predict Infrared (IR) and Nuclear Magnetic Resonance (NMR) data. The IR and NMR ¹³C and ¹H data were compared with the theoretical calculations performed for three structural possibilities of a heterologous series. The theoretical results were compared with the experimental data through linear regression in order to define the most probable structure and showed satisfactory values.