Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold

The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1 ''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3

The nuclear magnetic resonance (NMR) structure of a globular domain of residues 1071 to 1178 within the previously annotated nucleic acid-binding region (NAB) of severe acute respiratory syndrome coronavirus nonstructural protein 3 (nsp3) has been determined, and N- and C-terminally adjoining polypeptide segments of 37 and 25 residues, respectively, have been shown to form flexibly extended linkers to the preceding globular domain and to the following, as yet uncharacterized domain. This extension of the structural coverage of nsp3 was obtained from NMR studies with an nsp3 construct comprising residues 1066 to 1181 [ nsp3(1066-1181)] and the constructs nsp3(1066-1203) and nsp3(1035-1181). A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands. Two antiparallel two-strand beta-sheets and two 3(10)-helices are anchored against the surface of this barrel-like molecular core. Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold.

Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus

This paper describes the structure determination of nsp3a, the N-terminal domain of the severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural protein 3. nsp3a exhibits a ubiquitin-like globular fold of residues 1 to 112 and a flexibly extended glutamic acid-rich domain of residues 113 to 183. In addition to the four beta-strands and two alpha-helices that are common to ubiquitin-like folds, the globular domain of nsp3a contains two short helices representing a feature that has not previously been observed in these proteins. Nuclear magnetic resonance chemical shift perturbations showed that these unique structural elements are involved in interactions with single-stranded RNA. Structural similarities with proteins involved in various cell-signaling pathways indicate possible roles of nsp3a in viral infection and persistence.

A hydrogen-1 nuclear magnetic resonance, mass spectral and extended Hückel study of some olefin complexes of rhodium(I) and iridium(I) and the crystal and molecular structure of η4-2,4-dimethylpenta-1,4-diene(η5-formylcyclopentadienyl)rhodium(I)

A 1H NMR study of monosubstituted η-cyclopentadienyl-rhodium(I) complexes of type LLRh(C5H4X) and -iridium(I) complexes of type L2Ir(C5H4X) (L = ethene, LL = 1,3- or 1,5-diolefin; X = C(C6H5)3, CHO, or COOCH3) has been carried out. For complexes of both metals in which the neutral ligand is ethene or a non-conjugated diolefin the NMR spectra of the cyclopentadienyl protons are unusual in that H(2), H(5) resonate to high field either at room temperature or below. The corresponding NMR spectra for the cyclopentadienyl ring protons of complexes where the neutral ligand is a conjugated diene are, with one exception, normal. A single crystal X-ray structural analysis of (η4-2,4-dimethylpenta-1,4-diene)(η5-formylcyclopentadienyl)rhodium(I) (which exhibits an abnormal 1H NMR spectrum) reveals substantial localisation of electron density in the C(3)C(4) Cp ring bond (1.283(33) Å) which may be consistent with a contribution from an ‘allyl-ene’ rotamer to the ring—metal bonding scheme. An extended Hückel calculation with self consistent charge iteration was performed on this complex. The results predict a greater Mulliken overlap population for the C(3)C(4) bond in the cyclopentadienyl ring and show that the localisation is dependent on both the Cp ring substituent and the nature of the diolefin. The mass spectral fragmentation patterns of some representative diene complexes of iridium(I) and rhodium(I) are presented.

Nuclear Magnetic Resonance Study of Hydrated Bentonite

Impedance spectroscopy and nuclear magnetic resonance (NMR) were used to investigate the mobility of water molecules located in the interlayer space of H(+) - exchanged bentonite clay. The conductivity obtained by ac measurements was 1.25 x 10(-4) S/cm at 298 K. Proton ((1)H) lineshapes and spin-lattice relaxation times were measured as a function of temperature over the temperature range 130-320 K. The NMR experiments exhibit the qualitative features associated with the proton motion, namely the presence of a (1)H NMR line narrowing and a well-defined spin-lattice relaxation rate maximum. The temperature dependence of the proton spin-lattice relaxation rates was analyzed with the spectral density function appropriate for proton dynamics in a two-dimensional system. The self-diffusion coefficient estimated from our NMR data, D similar to 2 x 10(-7) cm(2)/s at 300 K, is consistent with those reported for exchanged montmorillonite clay hydrates studied by NMR and quasi-elastic neutron scattering (QNS).

Nuclear magnetic resonance characterization of metabolite disorder in orange trees caused by citrus sudden death disease

Citrus sudden death (CSD) is a new disease of sweet orange and mandarin trees grafted on Rangpur lime and Citrus volkameriana rootstocks. It was first seen in Brazil in 1999, and has since been detected in more than four million trees. The CSD causal agent is unknown and the current hypothesis involves a virus similar to Citrus tristeza virus or a new virus named Citrus sudden death-associated virus. CSD symptoms include generalized foliar discoloration, defoliation and root death, and, in most cases, it can cause tree death. One of the unique characteristics of CSD disease is the presence of a yellow stain in the rootstock bark near the bud union. This region also undergoes profound anatomical changes. In this study, we analyse the metabolic disorder caused by CSD in the bark of sweet orange grafted on Rangpur lime by nuclear magnetic resonance (NMR) spectroscopy and imaging. The imaging results show the presence of a large amount of non-functional phloem in the rootstock bark of affected plants. The spectroscopic analysis shows a high content of triacylglyceride and sucrose, which may be related to phloem blockage close to the bud union. We also propose that, without knowing the causal CSD agent, the determination of oil content in rootstock bark by low-resolution NMR can be used as a complementary method for CSD diagnosis, screening about 300 samples per hour.

Nuclear magnetic resonance water relaxation time changes in bananas during ripening: a new mechanism

BACKGROUND: Nuclear magnetic resonance studies of banana fragments during ripening show an increase on the water transverse relaxation time (T(2)) and a decrease in water self-diffusion coefficient (D). As T(2) and D are normally directly correlated, we studied these two properties in intact bananas during ripening, in an attempt to rule out the effect of injury on the apparent discrepancies in the behavior of T(2) and D. RESULTS: The results show that injury in bananas causes a decrease in T(2) of the water in vacuoles (T(2vac)). They also show that T(2vac) increased and D decreased during ripening, ruling out the injury effect. To explain the apparent discrepancies, we propose a new hypothesis for the increase in T(2) values, based on the reduction of Fe(3+) ions to Fe(2+) by galacturonic acid, produced by the hydrolysis of pectin and a decrease in internal oxygen concentration during ripening. CONCLUSION: As injury alters T(2) values it is necessary to use intact bananas to study relaxation times during ripening. The novel interpretation for the increase in T(2vac) based on reduction of Fe(+3) and O(2) concentration is an alternative mechanism to that based on the hydrolysis of starch in amyloplasts. (C) 2010 Society of Chemical Industry

Fast and Simple Nuclear Magnetic Resonance Method To Measure Conjugated Linoleic Acid in Beef

Conjugated linoleic acids (CLAs) are a group of linoleic acid isomers that are naturally found in food products originating from ruminants (meat and dairy). These acids have received special attention in recent years due to their potential human health benefits. Research efforts have been proposed to increase the CLA content in beef to improve public health. However, because there are more than 30 million beef cattle used each year by the American food industry, it will be necessary to ensure their content in a large number of samples. Therefore, it is important to have an inexpensive and rapid analytical method to measure CLA content in food products. Because gas chromatography (GC), a current popular method for measuring CLAs, is slow, this paper describes a nuclear magnetic resonance spectroscopy ((1)H NMR) method that is potentially >10 times faster than the GC method. Analyses show a correlation coefficient of 0.97, indicating the capacity of NMR to quantify the CLA content in beef samples. Furthermore, the method proposed herein is simple and does not require sophisticated sample preparation.

Carbon Nuclear Magnetic Resonance Spectroscopic Profiles coupled to Partial Least-Squares Multivariate Regression for Prediction of Several Physicochemical Parameters of Brazilian Commercial Gasoline

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Carbon nuclear magnetic resonance spectroscopic fingerprinting of commercial gasoline: Pattern-recognition analyses for screening quality control purposes

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Screening Brazilian commercial gasoline quality by hydrogen nuclear magnetic resonance spectroscopic fingerprintings and pattern-recognition multivariate chemometric analysis

The identification of gasoline adulteration by organic solvents is not an easy task, because compounds that constitute the solvents are already in gasoline composition. In this work, the combination of Hydrogen Nuclear Magnetic Resonance ((1)H NMR) spectroscopic fingerprintings with pattern-recognition multivariate Soft Independent Modeling of Class Analogy (SIMCA) chemometric analysis provides an original and alternative approach to screening Brazilian commercial gasoline quality in a Monitoring Program for Quality Control of Automotive Fuels. SIMCA was performed on spectroscopic fingerprints to classify the quality of representative commercial gasoline samples selected by Hierarchical Cluster Analysis (HCA) and collected over a 6-month period from different gas stations in the São Paulo state, Brazil. Following optimized the (1)H NMR-SIMCA algorithm, it was possible to correctly classify 92.0% of commercial gasoline samples, which is considered acceptable. The chemometric method is recommended for routine applications in Quality-Control Monitoring Programs, since its measurements are fast and can be easily automated. Also, police laboratories could employ this method for rapid screening analysis to discourage adulteration practices. (C) 2010 Elsevier B.V. All rights reserved.

Use of on-line liquid chromatography-nuclear magnetic resonance spectroscopy for the rapid investigation of flavonoids from Sorocea bomplandii

This paper reports the identification of di- and triglycosylated flavonoids from Sorocea bomplandii (Moraceae) by liquid chromatography coupled on-line to nuclear magnetic resonance (LC-NMR). These glycosylated flavonoids may be used as a taxonomic marker in future work. (C) 2002 Elsevier B.V. B.V All rights reserved.

Structural studies of NaPO3-MoO3 glasses by solid-state nuclear magnetic resonance and raman spectroscopy

Vitreous samples were prepared in the (100 - x)% NaPO3-x% MoO3 (0 <= x <= 70) glass-forming system by a modified melt method that allowed good optical quality samples to be obtained. The structural evolution of the vitreous network was monitored as a function of composition by differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR), Raman scattering, and solid-state nuclear magnetic resonance (NMR) for P-31, Na-23, and Mo-95 nuclei. Addition of MoO3 to the NaPO3 glass melt leads to a pronounced increase in the glass transition temperatures up to x = 45, suggesting a significant increase in network connectivity. For this same composition range, vibrational spectra suggest that the Mo6+ ions are bonded to some nonbridging oxygen atoms (Mo-O- or Mo=O bonded species). Mo-O-Mo bond formation occurs only at MoO3 contents exceeding x = 45. P-31 magic-angle spinning (MAS) NMR spectra, supported by two-dimensional J-resolved spectroscopy, allow a clear distinction between species having two, one, and zero P-O-P linkages. These sites are denoted as Q(2Mo)((2)), Q(1Mo)((2)), and Q(0Mo)((2)), respectively. For x < 0.45, the populations of these sites can be described along the lines of a binary model, according to which each unit of MoO3 converts two Q(nMo)((2)) sites into two Q((n+1)Mo)((2)) sites (n = 0, 1). This structural model is consistent with the presence of tetrahedral Mo(=O)(2)(O-1/2)(2) environments. Indeed, Mo-95 NMR data suggest that the majority of the molybdenum species are four-coordinated. However, the presence of additional six-coordinate molybdenum in the MAS NMR spectra indicates that the structure of these glasses may be more complicated and may additionally involve sharing of network modifier oxide between the network formers phosphorus and molybdenum. This latter hypothesis is further supported by Na-23{P-31} rotational echo double resonance (REDOR) data, which clearly reveal that the magnetic dipole-dipole interactions between P-31 and Na-23 are increasingly diminished with increasing molybdenum content. The partial transfer of modifier from the phosphate to the molybdate network former implies a partial repolymerization of the phosphate species, resulting in the formation of Q(nMo)((3)) species and accounting for the observed increase in the glass transition temperature with increasing MoO3 content that is observed in the composition range 0 <= x <= 45. Glasses with MoO3 contents beyond x = 45 show decreased thermal and crystallization stability. Their structure is characterized by isolated phosphate species [most likely of the P(OMo)(4) type] and molybdenum oxide clusters with a large extent of Mo-O-Mo connectivity.

Differential scanning calorimetry, x-ray diffraction and F-19 nuclear magnetic resonance investigations of the crystallization of InF3-based glasses

Results of differential scanning calometry (DSC), x-ray diffraction (XRD), and F-19 nuclear magnetic resonance (NMR) of InF3-based glasses, treated at different temperatures, ranging from glass transition temperature (T-g) to crystallization temperature (T-c), are reported. The main features of the experimental results are as follows. DSC analysis emphasizes several steps in the crystallization process. Heat treatment at temperatures above T-g enhances the nucleation of the first growing phases but has little influence on the following ones. XRD results show that several crystalline phases are formed, with solid state transitions when heated above 680 K, the F-19 NMR results show that the spin-lattice relaxation, for the glass samples heat treated above 638 K, is described by two time constants. For samples treated below this temperature a single time constant T-1 was observed. Measurements of the F-19 spin-lattice relaxation time (T-1), as a function of temperature,made possible the identification of the mobile fluoride ions. The activation energy, for the ionic motion, in samples treated at crystallization temperature was found to be 0.18 +/- 0.01 eV. (C) 1998 American Institute of Physics.