Measurement of 1H�C15N and 1H�C13C residual dipolar couplings in nucleic acids from TROSY intensities

Analogous to the recently introduced ARTSY method for measurement of one-bond (1)H-(15)N residual dipolar couplings (RDCs) in large perdeuterated proteins, we introduce methods for measurement of base (13)C-(1)H and (15)N-(1)H RDCs in protonated nucleic acids. Measurements are based on quantitative analysis of intensities in (1)H-(15)N and (13)C-(1)H TROSY-HSQC spectra, and are illustrated for a 71-nucleotide adenine riboswitch. Results compare favorably with those of conventional frequency-based measurements in terms of completeness and convenience of use. The ARTSY method derives the size of the coupling from the ratio of intensities observed in two TROSY-HSQC spectra recorded with different dephasing delays, thereby minimizing potential resonance overlap problems. Precision of the RDC measurements is limited by the signal-to-noise ratio, S/N, achievable in the 2D TROSY-HSQC reference spectrum, and is approximately given by 30/(S/N) Hz for (15)N-(1)H and 65/(S/N) Hz for (13)C-(1)H. The signal-to-noise ratio of both (1)H-(15)N and (1)H-(13)C spectra greatly benefits when water magnetization during the experiments is not perturbed, such that rapid magnetization transfer from bulk water to the nucleic acid, mediated by rapid amino and hydroxyl hydrogen exchange coupled with (1)H-(1)H NOE transfer, allows for fast repetition of the experiment. RDCs in the mutated helix 1 of the riboswitch are compatible with nucleotide-specifically modeled, idealized A-form geometry and a static orientation relative to the helix 2/3 pair, which differs by ca 6° relative to the X-ray structure of the native riboswitch.     

The Caenorhabditis elegans A��1�C42 Model of Alzheimer Disease Predominantly Expresses A��3�C42

Transgenic expression of human amyloid β (Aβ) peptide in body wall muscle cells of Caenorhabditis elegans has been used to better understand aspects of Alzheimer disease (AD). In human aging and AD, Aβ undergoes post-translational changes including covalent modifications, truncations, and oligomerization. Amino truncated Aβ is increasingly recognized as potentially contributing to AD pathogenesis. Here we describe surface-enhanced laser desorption ionization-time of flight mass spectrometry mass spectrometry of Aβ peptide in established transgenic C. elegans lines. Surprisingly, the Aβ being expressed is not full-length 1–42 (amino acids) as expected but rather a 3–42 truncation product. In vitro analysis demonstrates that Aβ_3–42 self-aggregates like Aβ_1–42, but more rapidly, and forms fibrillar structures. Similarly, Aβ_3–42 is also the more potent initiator of Aβ_1–40 aggregation. Seeded aggregation via Aβ_3–42 is further enhanced via co-incubation with the transition metal Cu(II). Although unexpected, the C. elegans model of Aβ expression can now be co-opted to study the proteotoxic effects and processing of Aβ_3–42.Numerous studies support a role for aggregating Aβ³ in mediating the toxicity that underlies AD (1, 2). However, several key questions remain central to understanding how AD and Aβ pathology are related. What is the connection between Aβ aggregation and toxicity? Is there a specific toxic Aβ conformation or species? How and why does aging impact on Aβ precipitation? Significant effort to address these questions has been invested in the use of vertebrate and simple invertebrate model organisms to simulate neurodegenerative diseases through transgenic expression of human Aβ (3). From these models, several novel insights into the proteotoxicity of Aβ have been gained (4–7).Human Aβ (e.g. in brain, cerebrospinal fluid, or plasma) is not found as a single species but rather as diverse mixtures of various modified, truncated, and cross-linked forms (8–10). Specific truncations, covalent modifications, and cross-linked oligomers of Aβ have potentially important roles in determining Aβ-associated neurotoxicity. For example, N-terminal truncations of Aβ have increased abundance in AD, rapidly aggregate, and are neurotoxic (9, 11). Furthermore, the N-terminal glutamic acid residue of Aβ_3–42 can be cyclized to pyroglutamate (Aβ_3(pE)-42) (12), which may be particularly important in AD pathogenesis (13, 14). Aβ_3(pE)-42 is a significant fraction of total Aβ in AD brain (15), accounting for more than 50% of Aβ accumulated in plaques (16). Aβ_3(pE)-42 seeds Aβ aggregation (17), confers proteolytic resistance, and is neurotoxic (13). Recently, glutaminyl cyclase (QC) has been proposed to catalyze, in vivo, pyroglutamate formation of Aβ_3(pE)-40/42 (14, 18). Aβ_1–42 itself cannot be cyclized by QC to Aβ_3(pE)-42 (19), unlike Aβ that commences with an N-terminal glutamic acid-residue (e.g. Aβ_3–42 and Aβ_11–42) (20). QC has broad expression in mammalian brain (21, 22), and its inhibition attenuates accumulation of Aβ_3(pE)-42 into plaques and improves cognition in a transgenic mouse model of AD that overexpresses human amyloid precursor protein (14). N-terminal truncations at position 3 have been reported in senile plaques (23, 24); however, the process that generates Aβ_3–42 is unknown. Currently there are no reported animal models of Aβ_3–42 expression.Advances in surface-enhanced laser desorption ionization-time of flight mass spectrometry (SELDI-TOF MS) analysis now facilitate accurate identification of particular Aβ species. Using this technology, we examined well characterized C. elegans transgenic models of AD that develop amyloid aggregates (25, 26) to see whether the human Aβ they express is post-translationally modified.     

Protease-Activated Receptor�C1 Expression in Rat Microglia after Trimethyltin Treatment

In the nervous system, protease-activated receptors (PARs), which are activated by thrombin and other extracellular proteases, are expressed widely at both neuronal and glial levels and have been shown to be involved in several brain pathologies. As far as the glial receptors are concerned, previous experiments performed in rat hippocampus showed that expression of PAR-1, the prototypic member of the PAR family, increased in astrocytes both in vivo and in vitro following treatment with trimethyltin (TMT). TMT is an organotin compound that induces severe hippocampal neurodegeneration associated with astrocyte and microglia activation. In the present experiments, the authors extended their investigation to microglial cells. In particular, by 7 days following TMT intoxication in vivo, confocal immunofluorescence revealed an evident PAR-1-related specific immunoreactivity in OX-42-positive microglial cells of the CA3 and hilus hippocampal regions. In line with the in vivo results, when primary rat microglial cells were treated in vitro with TMT, a strong upregulation of PAR-1 was observed by immunocytochemistry and Western blot analysis. These data provide further evidence that PAR-1 may be involved in microglial response to brain damage.     

Molecular Cloning of Pigeon UDP-galactose:��-d-Galactoside ��1,4-Galactosyltransferase and UDP-galactose:��-d-Galactoside ��1,4-Galactosyltransferase, Two Novel Enzymes Catalyzing the Formation of Gal��1�C4Gal��1�C4Gal��1�C4GlcNAc Sequence

We previously found that pigeon IgG possesses unique N-glycan structures that contain the Galα1–4Galβ1–4Galβ1–4GlcNAc sequence at their nonreducing termini. This sequence is most likely produced by putative α1,4- and β1,4-galactosyltransferases (GalTs), which are responsible for the biosynthesis of the Galα1–4Gal and Galβ1–4Gal sequences on the N-glycans, respectively. Because no such glycan structures have been found in mammalian glycoproteins, the biosynthetic enzymes that produce these glycans are likely to have distinct substrate specificities from the known mammalian GalTs. To study these enzymes, we cloned the pigeon liver cDNAs encoding α4GalT and β4GalT by expression cloning and characterized these enzymes using the recombinant proteins. The deduced amino acid sequence of pigeon α4GalT has 58.2% identity to human α4GalT and 68.0 and 66.6% identity to putative α4GalTs from chicken and zebra finch, respectively. Unlike human and putative chicken α4GalTs, which possess globotriosylceramide synthase activity, pigeon α4GalT preferred to catalyze formation of the Galα1–4Gal sequence on glycoproteins. In contrast, the sequence of pigeon β4GalT revealed a type II transmembrane protein consisting of 438 amino acid residues, with no significant homology to the glycosyltransferases so far identified from mammals and chicken. However, hypothetical proteins from zebra finch (78.8% identity), frogs (58.9–60.4%), zebrafish (37.1–43.0%), and spotted green pufferfish (43.3%) were similar to pigeon β4GalT, suggesting that the pigeon β4GalT gene was inherited from the common ancestors of these vertebrates. The sequence analysis revealed that pigeon β4GalT and its homologs form a new family of glycosyltransferases.     

Organic solutes in the deepest phylogenetic branches of the Bacteria: identification of ��(1�C6)glucosyl-��(1�C2)glucosylglycerate in Persephonella marina

The accumulation of organic solutes was investigated in the thermophilic bacteria Persephonella marina and Marinitoga piezophila, two representatives of the deepest lineages in the domain Bacteria. These organisms grow optimally at around 70 °C in medium containing 3 % NaCl. A new disaccharide, accumulating in Persephonella marina, was identified as ??(1?C6)glucosyl-??(1?C2)glucosylglycerate (GGG), by nuclear magnetic resonance. This identification was validated by comparison with the spectra of the compound obtained by chemical synthesis. Besides GGG, the solute pool of Persephonella marina comprised ??-glutamate, di-myo-inositol-1,3??-phosphate and 2-O-??-glucosylglycerate. In contrast, amino acids such as ??-glutamate, proline and alanine were the dominant components of the solute pool of Marinitoga piezophila and sugar derivatives were absent. The ability of GGG to protect protein structure against heat denaturation was assessed using model proteins. A genomic search for the biosynthetic pathways of known ionic solutes in Aquificales and Thermotogales shows the inability of this analysis to predict the nature of compatible solutes and underlines the need for efficient cultivation techniques.     

Characterization of a New ��(1�C3)-Glucan Branching Activity of Aspergillus fumigatus

A new HPLC method was developed to separate linear from β(1–6)-branched β(1–3)-glucooligosaccharides. This methodology has permitted the isolation of the first fungal β(1–6)/β(1–3)-glucan branching transglycosidase using a cell wall autolysate of Aspergillus fumigatus (Af). The encoding gene, AfBGT2 is an ortholog of AfBGT1, another transglycosidase of A. fumigatus previously analyzed (Mouyna, I., Hartland, R. P., Fontaine, T., Diaquin, M., Simenel, C., Delepierre, M., Henrissat, B., and Latgé, J. P. (1998) Microbiology 144, 3171–3180). Both enzymes release laminaribiose from the reducing end of a β(1–3)-linked oligosaccharide and transfer the remaining chain to another molecule of the original substrate. The AfBgt1p transfer occurs at C-6 of the non-reducing end group of the acceptor, creating a kinked β(1–3;1–6) linear molecule. The AfBgt2p transfer takes place at the C-6 of an internal group of the acceptor, resulting in a β(1–3)-linked product with a β(1–6)-linked side branch. The single Afbgt2 mutant and the double Afbgt1/Afbgt2 mutant in A. fumigatus did not display any cell wall phenotype showing that these activities were not responsible for the construction of the branched β(1–3)-glucans of the cell wall.     

Association between circulating interleukin-1 beta (IL-1��) levels and IL-1�� C�C511T polymorphism with cervical cancer risk in Egyptian women

Cancer cervix is one of the leading causes of cancer-related mortality among women worldwide. It is believed that the host genetic factors such as inflammation-induced cytokines may play a role in cervical carcinogenesis. The interleukin-1β (IL-1β) gene contains several single nucleotide polymorphisms. One of them, C-511T, which in the promoter region has been associated with increased IL-1β production and with increased risk of developing cancers. We assessed the association between the IL-1β C-511T polymorphism and cervical cancer risk in a case-control study among 100 histopathologically confirmed Egyptian women with cervical cancer and 50 age-matched, cervical cytology negative, healthy controls by polymerase chain reaction-restriction fragment length polymorphism. Plasma levels of IL-1β were assayed by enzyme-linked immunosorbent assay. There was significant increase in the mean plasma IL-1β level in cervical cancer cases (43.40 ± 25.95 pg/ml) when compared with controls (30.51 ± 18.28 pg/ml, P = 0.002). The plasma levels above the 75th percentile of controls (IL-1β ≥ 45.74 pg/ml) were significantly associated with a 2.49-fold increased risk of cervical cancer. The significant increase in IL-1β concentration in cervical cancer cases was observed only among cervical cancer cases carrying C-511T variant genotypes. T/T genotype of IL-1β polymorphism was significantly higher in cervical cancer cases compared with controls (57 vs. 38%; OR = 2.16; P = 0.028) and the T allele carriage was significantly associated with cervical cancer risk (OR = 2.00, 95% CI = 1.19-3.38, and P = 0.008). In conclusion, plasma IL-1β level and IL-1β C-511T polymorphism may be considered as candidate biomarkers for cervical cancer in Egyptian women.     

Expression of Somatostatin and Somatostatin Receptor Subtypes 1�C5 in Human Normal and Diseased Kidney

Somatostatin mediates inhibitory functions through five G protein–coupled somatostatin receptors (sst_1–5). We used immunohistochemistry, immunofluorescence, and RT-PCR to determine the presence of somatostatin receptors sst₁, sst_2A, sst_2B, sst₃, sst₄, and sst₅ in normal and IgA nephropathy human kidney. All somatostatin receptors were detected in the thin tubules (distal convoluted tubules and loops of Henle) and thick tubules (proximal convoluted tubules) in the tissue sections from nephrectomy and biopsy samples. Immunopositive sst₁ and sst₄ staining was more condensed in the cytoplasm of tubular epithelial cells. In normal kidney tissue sections, podocytes and mesangial cells in the glomeruli stained for sst₁, sst_2B, sst₄ and sst₅, and stained weakly for sst₃. In IgA kidney tissue, the expression of somatostatin receptors was significantly increased with particular immmunopositive staining for sst₁, sst_2B, sst₄, and sst₅ within glomeruli. In the epithelial cells, the staining for sst_2B and sst₄ in proximal tubules and sst₁, sst_2B, and sst₅ in distal tubules was increased. The mRNA expression of sst_1–5 was also detected by RT-PCR. Somatostatin and all five receptor subtypes were ubiquitously distributed in normal kidney and IgA nephropathy. The increased expression of somatostatin receptors in IgA nephropathy kidney might be the potential pathogenesis of inflammatory renal disease. (J Histochem Cytochem 56:733–743, 2008)     

Dynamic properties of pH-dependent structural organization of the amyloidogenic ��-protein (1�C40)

The structural organization of the amyloidogenic β-protein containing 40 amino acid residues (Aβ40) was studied by the high temperature molecular dynamics simulations in the acidic (pH ∼ 3) and basic (pH ∼ 8) pH regions. The obtained data suggest that the central Ala21-Gly29 segment of Aβ40 can adopt folded and partially unfolded structures. At the basic pH, this segment forms folded structures stabilized by electrostatic interactions and hydrogen bonds. At the acidic pH, it forms partially unfolded structures. Two other segments flanking to the central segment exhibit the propensity to adopt unstable interconverting α-helical, 3₁₀-helical and turn-like structures. One of these segments is comprised of the Ala30-Val36 residues at both of the considered pHs. The second segment is comprised of the Glu11-Phe20 at the basic pH and of the Glu11-Val24 residues at the acidic pHs. The revealed pH-dependent structuration of the Aβ40 allowed us to suggest a possible scenario for initial Aβ aggregation. According to this scenario, the occurrence of the partially unfolded states of the Ala21-Gly29 segment plays main role in the Aβ oligomerization process.Key words: amyloid-β protein, Alzheimer disease, oligomerization, fibril, electrostatic interactions, molecular dynamics simulations     

Deoxygenated Disaccharide Analogs as Specific Inhibitors of ��1�C4-Galactosyltransferase 1 and Selectin-mediated Tumor Metastasis

The disaccharide peracetylated GlcNAcβ1–3Galβ-O-naphthalenemethanol (disaccharide 1) diminishes the formation of the glycan sialyl Lewis X (Neu5Acα2–3Galβ1–4(Fucα1–3) GlcNAc; sLe^X) in tumor cells. Previous studies showed that the mechanism of action of disaccharide 1 involves three steps: (i) deacetylation by carboxyesterases, (ii) action as a biosynthetic intermediate for downstream enzymes involved in sLe^X assembly, and (iii) generation of several glycans related to sLe^X. In this report, we show that GlcNAcβ1–3Galβ-O-naphthalenemethanol binds to the acceptor site of human β1–4-galactosyltransferase much like the acceptor trisaccharide, GlcNAcβ1–2Manβ1–6Man, which is present on N-linked glycans. The 4′-deoxy analog, in which the acceptor hydroxyl group was replaced by -H, did not act as a substrate but instead acted as a competitive inhibitor of the enzyme. The acetylated form of this compound inhibited sLe^X formation in U937 monocytic leukemia cells, suggesting that it had inhibitory activity in vivo as well. A series of synthetic acetylated analogs of 1 containing -H, -F, -N₃, -NH₂, or -OCH₃ instead of the hydroxyl groups at C-3′- and C-4′-positions of the terminal N-acetylglucosamine residue also blocked sLe^X formation in cells. The reduction of sLe^X by the 4′-deoxy analog also diminished experimental tumor metastasis by Lewis lung carcinoma in vivo. These data suggest that nonsubstrate disaccharides have therapeutic potential through their ability to bind to glycosyltransferases in vivo and to alter glycan-dependent pathologic processes.The sialylated, fucosylated tetrasaccharide, sLe^X,³ is a common carbohydrate determinant present in many O-GalNAc-linked mucins and N-linked glycans that act as selectin ligands (see Ref. 1 and references therein). Expression of sLe^X endows tumor cells with the capacity to bind to platelets and endothelial cells in the vasculature via P- and E-selectins, thus facilitating hematogenous metastasis possibly through protection against innate immune cells and by adhesion to the blood vessel wall. Strategies for blocking selectin-carbohydrate interactions include (i) competition by soluble recombinant forms of selectins, glycoprotein ligands, and glycolipids, (ii) peptides based on the primary sequence of the carbohydrate binding site, (iii) anti-selectin antibodies, (iv) oligosaccharides related to Lewis^X, (v) inositol polyanions and sulfated sugars, (vi) heparin, and (vii) molecular mimics of sLe^X, including oligonucleotides (reviewed in Refs. 2 and 3). Analogs of acceptor substrates of the various glycosyltransferases involved in glycan biosynthesis provide another class of potential inhibitors (reviewed in Refs. 4 and 5). Although many of these analogs are effective in vitro, they generally do not exhibit inhibitory activity in cells due to poor membrane permeability. The large number of polar hydroxyl groups and the lack of membrane transporters for oligosaccharides in most cells presumably prevent their uptake (6).In contrast to many of the inhibitors described above, peracetylated disaccharides (e.g. acetylated Galβ1–4GlcNAcβ-O-naphthalenemethanol (NM), acetylated Galβ1–3GalNAcα-O-NM, and acetylated GlcNAcβ1–3Galβ-O-NM) inhibit sLe^X biosynthesis in cells (6–9). These compounds are taken up by cells by passive diffusion and acted on by cytoplasmic or membrane-associated carboxyesterases, which remove the acetyl groups. The compounds gain access to the biosynthetic enzymes located in the Golgi complex, where they serve as substrates, priming oligosaccharide synthesis and generating products related to O-GalNAc-linked mucin oligosaccharides. Priming in this manner diverts the assembly of the O-linked chains from endogenous glycoproteins, resulting in inhibition of expression of terminal Lewis antigens that are recognized by selectins. Inhibition occurs at a much lower dose than for monosaccharide-based agents, such as GalNAcβ-O-benzyl (∼25 μm versus 1–2 mm, respectively) (10, 11). Furthermore, the disaccharides appear to selectively affect sLe^X formation, since sLe^a expression was unaffected (12). By blocking selectin ligand expression, these compounds block both experimental and spontaneous metastasis (12, 13).In this study, we have examined acetylated disaccharide analogs that have been modified so that after deacetylation their activity as substrates would be altered. Characterization of the 4′-deoxy derivative using β1–4-galactosyltransferase 1 as a model showed that it acts by competitively inhibiting the enzyme. Interestingly, the peracetylated form of this analog maintains the capacity to inhibit sLe^X expression in U937 lymphoma cells and Lewis lung carcinoma (LLC) cells and block tumor formation in vivo. Thus, the deoxy analog presumably inhibits one or more galactosyltransferases in vivo, thereby blocking sLe^X formation and experimental tumor cell metastasis without generation of oligosaccharide products.     

Implications for Collagen Binding from the Crystallographic Structure of Fibronectin 6FnI1�C2FnII7FnI

Collagen and fibronectin (FN) are two abundant and essential components of the vertebrate extracellular matrix; they interact directly with cellular receptors and affect cell adhesion and migration. Past studies identified a FN fragment comprising six modules, ⁶FnI^1–2FnII^7–9FnI, and termed the gelatin binding domain (GBD) as responsible for collagen interaction. Recently, we showed that the GBD binds tightly to a specific site within type I collagen and determined the structure of domains ^8–9FnI in complex with a peptide from that site. Here, we present the crystallographic structure of domains ⁶FnI^1–2FnII⁷FnI, which form a compact, globular unit through interdomain interactions. Analysis of NMR titrations with single-stranded collagen peptides reveals a dominant collagen interaction surface on domains ²FnII and ⁷FnI; a similar surface appears involved in interactions with triple-helical peptides. Models of the complete GBD, based on the new structure and the ^8–9FnI·collagen complex show a continuous putative collagen binding surface. We explore the implications of this model using long collagen peptides and discuss our findings in the context of FN interactions with collagen fibrils.