Complete Nuclear Magnetic Resonance Assignments Research Articles

Structural and Bioactivity Characterization of Filipin Derivatives from Engineered Streptomyces filipinensis Strains Reveals Clues for Reduced Haemolytic Action.

The rise in the number of immunocompromised patients has led to an increased incidence of fungal infections, with high rates of morbidity and mortality. Furthermore, misuse of antifungals has boosted the number of resistant strains to these agents; thus, there is urgent need for new drugs against these infections. Here, the in vitro antifungal activity of filipin III metabolic intermediates has been characterized against a battery of opportunistic pathogenic fungi—Candida albicans, Candida glabrata, Candida krusei, Cryptococcus neoformans, Trichosporon cutaneum, Trichosporon asahii, Aspergillus nidulans, Aspergillus niger, and Aspergillus fumigatus—using the Clinical and Laboratory Standards Institute broth microdilution method. Structural characterization of these compounds was undertaken by mass spectrometry (MS) and nuclear magnetic resonance (NMR) following HPLC purification. Complete NMR assignments were obtained for the first time for filipins I and II. In vitro haemolytic assays revealed that the haemolytic action of these compounds relies largely on the presence of a hydroxyl function at C26, since derivatives lacking such moiety show remarkably reduced activity. Two of these derivatives, 1′-hydroxyfilipin I and filipin I, show decreased toxicity towards cholesterol-containing membranes while retaining potent antifungal activity, and could constitute excellent leads for the development of efficient pharmaceuticals, particularly against Cryptococcosis.

Function and solution structure of the Arabidopsis thaliana RALF8 peptide.

We report the recombinant preparation from Escherichia coli cells of samples of two closely related, small, secreted cysteine‐rich plant peptides: rapid alkalinization factor 1 (RALF1) and rapid alkalinization factor 8 (RALF8). Purified samples of the native sequence of RALF8 exhibited well‐resolved nuclear magnetic resonance (NMR) spectra and also biological activity through interaction with a plant receptor kinase, cytoplasmic calcium mobilization, and in vivo root growth suppression. By contrast, RALF1 could only be isolated from inclusion bodies as a construct containing an N‐terminal His‐tag; its poorly resolved NMR spectrum was indicative of aggregation. We prepared samples of the RALF8 peptide labeled with 15N and 13C for NMR analysis and obtained near complete 1H, 13C, and 15N NMR assignments; determined the disulfide pairing of its four cysteine residues; and examined its solution structure. RALF8 is mostly disordered except for the two loops spanned by each of its two disulfide bridges.

Complete NMR assignment of a bisecting hybrid-type oligosaccharide transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase

This study describes the complete nuclear magnetic resonance (NMR) spectral assignment of a bisecting hybrid-type oligosaccharide 1, transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase (Endo-M). Through 1H- and 13C-NMR, DQF-COSY, HSQC, HMBC, TOCSY, and NOESY experiments, we determine the structure of the glycoside linkage formed by the Endo-M transglycosylation, i.e., the connection between GlcNAc and GlcNAc in oligosaccharide 1.

Cytotoxic Properties and Complete Nuclear Magnetic Resonance Assignment of Isolated Xanthones from the Root of Garcinia cowa Roxb.

Objective:To isolate compounds from the roots of Garcinia cowa and to evaluated their cytotoxic activity against breast (MCF-7), prostate (DU-145), and lung (H-460) cell lines.Materials and Methods:The ground air-dried root was sequentially macerated with hexane, dichloromethane (DCM), ethyl acetate (EtOAc), and methanol. The DCM soluble extract was fractionated by vacuum liquid chromatography, column chromatography, and radial chromatography over silica gel with hexane, EtOAc and methanol as eluent in progressively increasing polarity manner; to yield three compounds. Their structures were elucidated based on their spectroscopic data and their comparison with those of the literature. The cytotoxicity of isolated compounds was carried out against human cell lines by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide colorimetric assay. The extract was added at various concentrations (0.1, 1, 10 and 100 mg/ml). The level of cytotoxicity was determined by calculating the level of IC50 that was based on the percentage of the cell death following the 24 h incubation with the extract.Results:Phytochemical study on the roots of G. cowa yielded rubraxanthone (3), cowanine (4) and 1,5-dihydroxyxanthone (5). Compound 4 with an IC50 value of 4.1 ± 1.0 μM, 5.4 ± 2.3 μM and 11.3 ± 10.0 μM against MCF-7, H-460, and DU-145, respectively while compound 3 was found to be in active.Conclusion:The results indicate that G. cowa roots could be important sources of natural cytotoxic compounds.SUMMARY Isolation of cytotoxic compounds from Garcinia cowaCowanine is the active constituent from the roots of Garcinia cowaComplete nuclear magnetic resonance assignment of isolated compoundsMS fragmentation of rubraxanthone.

Complete 1H-NMR and 13C-NMR spectral assignment of five malonyl ginsenosides from the fresh flower buds of Panax ginseng

BackgroundGinsenosides are the major effective ingredients responsible for the pharmacological effects of ginseng. Malonyl ginsenosides are natural ginsenosides that contain a malonyl group attached to a glucose unit of the corresponding neutral ginsenosides. MethodsMedium-pressure liquid chromatography and semipreparative high-performance liquid chromatography were used to isolate purified compounds and their structures determined by extensive one-dimensional- and two-dimensional nuclear magnetic resonance (NMR) experiments. ResultsA new saponin, namely malonyl-ginsenoside Re, was isolated from the fresh flower buds of Panax ginseng, along with malonyl-ginsenosides Rb1, Rb2, Rc, Rd. Some assignments for previously published 1H- and 13C-NMR spectra were found to be inaccurate. ConclusionThis study reports the complete NMR assignment of malonyl-ginsenoside Re, Rb1, Rb2, Rc, and Rd for the first time.

Functional analysis of filipin tailoring genes from Streptomyces filipinensis reveals alternative routes in filipin III biosynthesis and yields bioactive derivatives.

BackgroundStreptomyces filipinensis is the industrial producer of filipin, a pentaene macrolide, archetype of non-glycosylated polyenes, and widely used for the detection and the quantitation of cholesterol in biological membranes and as a tool for the diagnosis of Niemann–Pick type C disease. Genetic manipulations of polyene biosynthetic pathways have proven useful for the discovery of products with improved properties. Here, we describe the late biosynthetic steps for filipin III biosynthesis and strategies for the generation of bioactive filipin III derivatives at high yield.ResultsA region of 13,778 base pairs of DNA from the S. filipinensis genome was isolated, sequenced, and characterized. Nine complete genes and two truncated ORFs were located. Disruption of genes proved that this genomic region is part of the biosynthetic cluster for the 28-membered ring of the polyene macrolide filipin. This set of genes includes two cytochrome P450 monooxygenase encoding genes, filC and filD, which are proposed to catalyse specific hydroxylations of the macrolide ring at C26 and C1′ respectively. Gene deletion and complementation experiments provided evidence for their role during filipin III biosynthesis. Filipin III derivatives were accumulated by the recombinant mutants at high yield. These have been characterized by mass spectrometry and nuclear magnetic resonance following high-performance liquid chromatography purification thus revealing the post-polyketide steps during polyene biosynthesis. Two alternative routes lead to the formation of filipin III from the initial product of polyketide synthase chain assembly and cyclization filipin I, one trough filipin II, and the other one trough 1′-hydroxyfilipin I, all filipin III intermediates being biologically active. Moreover, minimal inhibitory concentration values against Candida utilis and Saccharomyces cerevisiae were obtained for all filipin derivatives, finding that 1′-hydroxyfilipin and especially filipin II show remarkably enhanced antifungal bioactivity. Complete nuclear magnetic resonance assignments have been obtained for the first time for 1′-hydroxyfilipin I.ConclusionsThis report reveals the existence of two alternative routes for filipin III formation and opens new possibilities for the generation of biologically active filipin derivatives at high yield and with improved properties.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-015-0307-4) contains supplementary material, which is available to authorized users.

Complete NMR assignments of undegraded asterosaponins from Asterias amurensis.

Four asterosaponins, thornasteroside A (1), versicoside A (2), anasteroside B (3), and asteronylpentaglycoside sulfate (4), were isolated from the predatory starfish Asterias amurensis Lütken. Unlike previous studies focusing on structure elucidation by degradation of the complex saponin molecules, complete nuclear magnetic resonance (NMR) assignment for the intact molecules was accomplished using 600MHz high magnetic field NMR. The complete set of NMR assignments can help in the structure elucidation of asterosaponins isolated in low yields without resorting to chemical degradation. Furthermore, this approach can be extended to other complex steroidal saponins, which may accelerate the discovery of bioactive secondary metabolites from this invasive starfish species.

Complete backbone and DENQ side chain NMR assignments in proteins from a single experiment: implications to structure–function studies

Resonance assignment is the first and the most crucial step in all nuclear magnetic resonance (NMR) investigations on structure-function relationships in biological macromolecules. Often, the assignment exercise has to be repeated several times when specific interactions with ligands, substrates etc., have to be elucidated for understanding the functional mechanisms. While the protein backbone serves to provide a scaffold, the side chains interact directly with the ligands. Such investigations will be greatly facilitated, if there are rapid methods for obtaining exhaustive information with minimum of NMR experimentation. In this context, we present here a pulse sequence which exploits the recently introduced technique of parallel detectionof multiple nuclei, e.g. (1)H and (13)C, and results in two 3D-data sets simultaneously. These yield complete backbone resonance assignment ((1)H(N), (15)N, (13)CO, (1)Hα/(13)Cα, and (1)Hβ/(13)Cβ chemical shifts) and side chain assignment of D, E, N and Q residues. Such an exhaustive assignment has the potential of yielding accurate 3D structures using one or more of several algorithms which calculate structures of the molecules very reliably on the basis of NMR chemical shifts alone. The side chain assignments of D, E, N, and Q will be extremely valuable for interaction studies with different ligands; Dand E side chains are known to be involved in majority of catalytic activities. Utility of this experiment has been demonstrated with Ca(2+) bound M-crystallin, which contains largely D, E, N and Q residues at the metal binding sites.

Re-evaluation of physicochemical and NMR data of triol ginsenosides Re, Rf, Rg2, and 20-gluco-Rf from Panax ginseng roots

Ginseng roots were extracted with aqueous methanol, and extracts were suspended in water and extracted successively with ethyl acetate and n-butanol. Column chromatography using the n-butanol fraction yielded four purified triol ginseng saponins: the ginsenosides Re, Rf, Rg2, and 20-gluco-Rf. The physicochemical, spectroscopic, and chromatographic characteristics of the ginsenosides were measured and compared with reports from the literature. For spectroscopic analysis, two-dimensional nuclear magnetic resonance (NMR) methods such as 1H-1H correlation spectroscopy, nuclear Overhauser effect spectroscopy, heteronuclear single quantum correlation, and heteronuclear multiple bond connectivity were employed to identify exact peak assignments. Some peak assignments for previously published 1H- and 13C-NMR spectra were found to be inaccurate. This study reports the complete NMR assignment of 20-gluco-Rf for the first time.

Study of the BPP7a peptide and its β-cyclodextrin complex: physicochemical characterization and complete sequence specific NMR assignments

The BPP7a heptapeptide, p-Glu¹Asp²Gly³Pro4Ile5Pro6Pro7, forms an association complex with β-cyclodextrin in a 1:1 molar ratio. The peptide and its complex were characterized by circular dichroism (CD) and isothermal titration calorimetry (ITC), which showed a very weak interaction between the β-cyclodextrin and the peptide. Assignments of all hydrogen resonances of the peptide alone and as a complex were made using ¹H nuclear magnetic resonance (NMR) experiments at 400 and 600 MHz. High resolution diffusion ordered spectroscopy (HR-DOSY) experiments were carried out to establish the self-aggregation state of BPP7a. It was also shown that the β-cyclodextrin breaks the molecular clusters leading to complex formation. In addition, the anti-hypertensive activity of the BPP7a/β-cyclodextrin complex was evaluated in spontaneous hypertensive rats (SHR), showing increased activity compared to that of pure BPP7a.

Interaction Domain on Thioredoxin for Pseudomonas aeruginosa 5′-Adenylylsulfate Reductase

NMR spectroscopy has been used to map the interaction domain on Escherichia coli thioredoxin for the thioredoxin- dependent 5'-adenylylsulfate reductase from Pseudomonas aeruginosa (PaAPR). Seventeen thioredoxin amino acids, all clustered around Cys-32 (the more surface-exposed of the two active-site cysteines), have been located at the PaAPR binding site. The center of the binding domain is dominated by nonpolar amino acids, with a smaller number of charged and polar amino acids located on the periphery of the site. Twelve of the amino acids detected by NMR have non-polar, hydrophobic side chains, including one aromatic amino acid (Trp-31). Four of the thioredoxin amino acids at the PaAPR binding site have polar side chains (Lys-36, Asp-61, Gln-62 and Arg-73), with three of the four having charged side chains. Site-directed mutagenesis experiments have shown that replacement of Lys-36, Asp-61, and Arg-73 and of the absolutely conserved Trp-31 significantly decreases the V(max) for the PaAPR-catalyzed reduction of 5'-adenylylsulfate, with E. coli thioredoxin serving as the electron donor. The most dramatic effect was observed with the W31A variant, which showed no activity as a donor to PaAPR. Although the thiol of the active-site Cys-256 of PaAPR is the point of the initial nucleophilic attack by reduced thioredoxin, mutagenic replacement of Cys-256 by serine has no effect on thioredoxin binding to PaAPR.

Confirmation of Potential Herbicidal Agents in Hulls of Rice, Oryza sativa

An ethyl acetate extract of Oryza sativa (rice) hulls yielded seven compounds: hentriacontane, 1-tetratriacontanol, beta-sitosterol, momilactone A, momilactone B, tricin (a flavonoid), and beta-sitosterol-3-O-beta-D-glucoside. The structures of these compounds were elucidated with 500 MHz nuclear magnetic resonance (NMR), using 1D and 2D spectral methods, aided by electron ionization mass spectrometry (EI-MS), fast atom bombardment mass spectrometry (FAB-MS), infrared (IR), and ultraviolet (UV) spectrophotometry. The complete 1H NMR assignments for momilactone A and B and 13C NMR assignments for tricin are discussed. To the best of our knowledge, hentriacontane, 1-tetratriacontanol, and beta-sitosterol-3-O-beta-D-glucoside were identified for the first time in rice hulls. In biological activity tests using these identified compounds, momilactone A and B showed potent inhibitory activity against duckweed (Lemna paucicostata). 1-Tetratriacontanol and beta-sitosterol-3-O-beta-D-glucoside also showed about 13-20% inhibitory activity based on chlorophyll reduction. Hentriacontane and beta-sitosterol did not show any herbicidal activity. In a germination assay of three weed species (Leptochloa chinenesis L., Amaranthus retroflexus L., and Cyperus difformis L.) in culture tubes both momilactones A and B had high inhibitory effects. Momilactone B completely inhibited germination of all three weed species at 20 ppm. Germination of L. chinensis L. was completely inhibited by a 4 ppm solution of momilactone B.

Enzymatic Production and Complete Nuclear Magnetic Resonance Assignment of the Sugar Lactulose

The enzymatic transgalactosylation from lactose to fructose leading to the prebiotic disaccharide lactulose was investigated using the beta-galactosidase from Aspergillus oryzae and the hyperthermostable beta-glycosidase from Pyrococcus furiosus (CelB). The conditions for highest lactulose yields relative to the initial lactose concentration were established on a 1 mL scale. Dependent on the initial molar ratio of lactose to fructose, more or fewer oligosaccharides other than lactulose were generated. Bioconversions on a 30 mL scale in a stirred glass reactor were performed, and lactulose yields of 46 mmol/L (44% relative to lactose) for CelB and 30 mmol/L (30% relative to lactose) for A. oryzae beta-galactosidase were achieved. Only <5% of other oligosaccharides were detectable. The corresponding productivities were 24 and 16 mmol/L/h, respectively. The molecular structure of lactulose was investigated in detail and confirmed after purification of the reaction solution by LC-MS and 1D and 2D NMR. Lactulose (4-O-beta-D-galactopyranosyl-D-fructose) was unambiguously proved to be the major transglycosylation disaccharide.

Structure and calcium-binding properties of Frq1, a novel calcium sensor in the yeast Saccharomyces cerevisiae.

The FRQ1 gene is essential for growth of budding yeast and encodes a 190-residue, N-myristoylated (myr) calcium-binding protein. Frq1 belongs to the recoverin/frequenin branch of the EF-hand superfamily and regulates a yeast phosphatidylinositol 4-kinase isoform. Conformational changes in Frq1 due to N-myristoylation and Ca(2+) binding were assessed by nuclear magnetic resonance (NMR), fluorescence, and equilibrium Ca(2+)-binding measurements. For this purpose, Frq1 and myr-Frq1 were expressed in and purified from Escherichia coli. At saturation, Frq1 bound three Ca(2+) ions at independent sites, which correspond to the second, third, and fourth EF-hand motifs in the protein. Affinity of the second site (K(d) = 10 microM) was much weaker than that of the third and fourth sites (K(d) = 0.4 microM). Myr-Frq1 bound Ca(2+) with a K(d)app of 3 microM and a positive Hill coefficient (n = 1.25), suggesting that the N-myristoyl group confers some degree of cooperativity in Ca(2+) binding, as seen previously in recoverin. Both the NMR and fluorescence spectra of Frq1 exhibited very large Ca(2+)-dependent differences, indicating major conformational changes induced upon Ca(2+) binding. Nearly complete sequence-specific NMR assignments were obtained for the entire carboxy-terminal domain (residues K100-I190). Assignments were made for 20% of the residues in the amino-terminal domain; unassigned residues exhibited very broad NMR signals, most likely due to Frq1 dimerization. NMR chemical shifts and nuclear Overhauser effect (NOE) patterns of Ca(2+)-bound Frq1 were very similar to those of Ca(2+)-bound recoverin, suggesting that the overall structure of Frq1 resembles that of recoverin. A model of the three-dimensional structure of Ca(2+)-bound Frq1 is presented based on the NMR data and homology to recoverin. N-myristoylation of Frq1 had little or no effect on its NMR and fluorescence spectra, suggesting that the myristoyl moiety does not significantly alter Frq1 structure. Correspondingly, the NMR chemical shifts for the myristoyl group in both Ca(2+)-free and Ca(2+)-bound myr-Frq1 were nearly identical to those of free myristate in solution, indicating that the fatty acyl chain is solvent-exposed and not sequestered within the hydrophobic core of the protein, unlike the myristoyl group in Ca(2+)-free recoverin. Subcellular fractionation experiments showed that both the N-myristoyl group and Ca(2+)-binding contribute to the ability of Frq1 to associate with membranes.

Structural characterization and topology of the second potential membrane anchor region in the thromboxane A2 synthase amino-terminal domain.

Thromboxane A2 synthase (TXAS) has been proposed to have two membrane-bound regions located in the NH2-terminal domain [Ruan, K.-H., Wang, L.-H., Wu, K. K., and Kulmacz, R. J. (1993) J. Biol. Chem, 268, 19483-19489; Ruan, K.-H., Li, P., Kulmacz, J. R., and Wu, K. K. (1994) J. Biol. Chem, 269, 20938-20942]. To test this hypothesis, a solution structure in membrane mimetic environments of a synthetic peptide corresponding to the second region of the NH2-terminal domain (TXAS residues 33-60) has been investigated by circular dichroism (CD), 2D nuclear magnetic resonance (NMR) spectroscopy, and peptidoliposome reconstitution. CD spectroscopy indicated that the peptide adopted a structure with significant alpha-helical content in 30% trifluoroethanol (TFE) or in dodecylphosphocholine (DPC) micelles, which mimic hydrophobic membrane environment. Through a combination of 2D NMR experiments in the presence of TFE or DPC micelles, complete 1H NMR assignments of the peptide have been obtained and the structure of the peptide has been determined. NH2-terminal segment of the peptide takes on a well-defined alpha-helical conformation; the center segment of the peptide, containing three prolines, adopts a bent conformation, and the C-terminal segment of the peptide exists in a mixture of rapidly interconverting conformations. These results provide direct structural evidence that residues 33-60 of the TXAS NH2-terminal domain contain a second membrane anchor region, with at least residues 35-46 having their helical structure expected for hydrophobic interaction with the membrane. The orientation of the peptide in DPC micelles was evaluated from the effect of incorporation of a spin-label 12-doxylstearate into the micelles. The peptide portions, found to be immersed in the micelles, include the helical segment, the bent segment, and some hydrophobic residues within the C-terminal segment. Two additional synthetic peptides, one corresponding to the NH2-terminal helical segment (TXAS residues 33-46) and the other including the bent and the C-terminal segments (TXAS residues 47-60) were analyzed for their ability to incorporate into peptidoliposomes. The helical peptide readily incorporated into liposomes; the other peptide did not. These results support the presence of a second functional membrane anchor region localized to the helical segment within TXAS residues 33-46, with passive membrane contacts in the bent and the C-terminal segments of the peptide (TXAS residues 47-60) due to immersion of the helical in the membrane.

The Nuclear Magnetic Resonance Solution Structure of the Mixed Disulfide between Escherichia coli Glutaredoxin(C14S) and Glutathione

The determination of the nuclear magnetic resonance (NMR) solution structure of the mixed disulfide between the mutant Escherichia coli glutaredoxin Grx(C14S) and glutathione (GSH), Grx(C14S)-SG, is described, the binding site for GSH on Grx(C14S) is located, and the non-bonding interactions between -SG and the protein are characterized. Based on nearly complete sequence-specific NMR assignments, 1010 nuclear Overhauser enhancement upper distance constraints and 116 dihedral angle constraints were obtained as the input for the structure calculations, for which the distance geometry program DIANA was used followed by energy minimization in a waterbath with the AMBER force field in the program OPAL. The -SG moiety was found to be localized on the surface of the protein in a cleft bounded by the amino acid residues Y13, T58, V59, Y72, T73 and D74. Hydrogen bonds have been identified between -SG and the residues V59 and T73 of Grx(C14S), and the formation of an additional hydrogen bond with Y72 and electrostatic interactions with the side-chains of D74 and K45 are also compatible with the NMR, conformational constraints. Comparison of the reduced and oxidized forms of Grx with Grx(C14S)-SG shows that the mixed disulfide more closely resembles the oxidized form of the protein. Functional implications of this observation are discussed. Comparisons are also made with the related proteins bacteriophage T4 glutaredoxin and glutathione S-transferase.

Nuclear Magnetic Resonance Solution Structure of Dendrotoxin K from the Venom of Dendroaspis polylepis polylepis

The solution structure of dendrotoxin K (Toxin K), a protein consisting of one polypeptide chain with 57 residues purified from the venom of the black mamba, Dendroaspis polylepis polylepis, was determined by nuclear magnetic resonance (NMR) spectroscopy. On the basis of virtually complete sequence-specific 1H NMR assignments, including individual assignments for 38 pairs of diastereotopic substituents and side chain amide protons, a total of 818 nuclear Overhauser effect distance constraints and 123 dihedral angle constraints were identified. Using this input, the solution structure of Toxin K was calculated with the program DIANA, and refined by restrained energy minimization with a modified version of the program AMBER. The average root-mean-square deviation (r.m.s.d.) relative to the mean atomic co-ordinates of the 20 conformers selected to represent the solution structure is 0·31 Å for all backbone atoms N, Cα and C′, and 0·90 Å for all heavy atoms of residues 2 to 56. The solution structure of Toxin K is very similar to the solution structure of the basic pancreatic trypsin inhibitor (BPTI) and the X-ray crystal structure of the α-dendrotoxin from Dendroaspis angusticeps (α-DTX), with r.m.s.d. values of 1·31 Å and 0·92 Å, respectively, for the backbone atoms of residues 2 to 56. Some local structural differences between Toxin K and BPTI are directly related to the fact that intermolelcular interactions with two of the four internal molecules of hydration water in BPTI are replaced by intramolecular hydrogen bonds in Toxin K.

Determination of the structure of the nucleocapsid protein NCp7 from the human immunodeficiency virus type 1 by 1H NMR.

The retroviral gag nucleocapsid protein NCp7 (72 amino acids) of HIV-1 (LAV strain), which contains two successive zinc fingers of the Cys-X2-Cys-X4-His-X4-Cys form linked by a stretch of basic residues, promotes viral RNA dimerization and encapsidation and activates annealing of the primer tRNA to the initiation site of reverse transcription. The structure of NCp7 and other shorter fragments was studied by 600 MHz 1H nuclear magnetic resonance (NMR) in aqueous solution to account for its various biological properties. Complete sequence specific 1H NMR assignments of the 13-51 residues of NCp7 encompassing the two zinc fingers was achieved by two-dimensional NMR experiments and the three-dimensional structure of (13-51)NCp7 was deduced from DIANA calculations, using nuclear Overhauser effects as constraints. The structure of the zinc complexed form of NCp7 is characterized by a kink at the Pro31 level in the basic Arg29-Ala-Pro-Arg-Lys-Lys-Gly35 RNA binding linker leading to a proximity of the Lys14-Cys18 to the Gly35-Cys39 sequences, which belong to the folded proximal and distal zinc fingers, respectively. Accordingly, the aromatic residues Phe16 and Trp37 were found to be spatially close. The Lys33 and Lys34 side-chains involved in viral RNA dimerization were solvent exposed. The N- and C-terminal sequences of NCp7 behave as flexible independent domains. The proposed structure of NCp7 might be used to rationally design new anti-viral agents aimed at inhibiting its functions.

Three new D-ring unsaturated sterols from the Mediterranean sponge Topsentia aurantiaca: Structure determination and complete nuclear magnetic resonance assignment

Three novel sterols with a rare D-ring unsaturation were isolated from the marine sponge Topsentia aurantiaca and identified as 5α-cholest-14-ene-3β,16α-diol ( 2), 24R- ethyl-5α-cholest-14-ene-3β,16α-diol ( 3), and 24S- ethyl-5α-cholest-14-ene-3β,16a-diol ( 4). The sponge also elaborates a further D-ring unsaturated sterol, 5α-cholest-15-en-3β-ol ( 1), which has been previously described only as a synthetic product. All the 1H and 13C nuclear magnetic resonances of compounds 1 and 2 were assigned to the relevant protons and carbons by bidimensional COSY, HETCOR, and HMQC nuclear magnetic resonance experiments.

The rate and structural consequences of proline cis-trans isomerization in calbindin D9k: NMR studies of the minor (cis-Pro43) isoform and the Pro43Gly mutant

The EF-hand calcium-binding protein, calbindin D9k, exists in solution in the calcium-loaded state, as a 1:3 equilibrium mixture of two isoforms, the result of cis-trans isomerism at the Gly42-Pro43 peptide bond [Chazin et al. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 2195-2198]. Nuclear magnetic resonance (NMR) studies of the minor (cis-Pro43) isoform and the Pro43----Gly mutant are reported here. The rate of cis----trans isomerization at the Pro43 peptide bond in the wild-type protein was determined by line-shape analysis at elevated temperatures, using a sample in which all amino acids, except Ser and Val, were deuterated. The cis----trans rate is calculated to be 0.2 s-1 at 25 degrees C, corresponding to a free energy of activation, delta G, of 77 kJ/mol. The complete sequence-specific 1H NMR assignments of the cis-Pro43 isoform and the Pro43----Gly mutant in the calcium-loaded state have been obtained by using standard methods combined with comparisons to the previously assigned major (trans-Pro43) isoform. This has permitted detailed comparative analysis of 1H NMR chemical shifts, backbone scalar coupling constants, and nuclear Overhauser effects. The minor isoform has a global fold that is identical with that of the major isoform. Structural changes imposed by cis-trans isomerization at Pro43 are highly localized to the linker loop (containing Pro43) that joins the two EF hands. The Pro43----Gly mutant has a global fold that is identical with the wild-type protein, but does not exhibit conformational heterogeneity. Only very limited structural differences are observed between mutant and wild-type protein, and these are also highly localized to the linker loop. The ion-binding properties of the mutant, as determined by 43Ca and 113Cd NMR, are found to be very similar to the wild-type protein. These results provide crucial evidence that justifies the calculation of high-resolution three-dimensional structures of the Pro43Gly mutant, rather than of the conformationally heterogeneous wild-type protein.