The structure and protein binding of amyloid-specific dye reagents

The self-assembling tendency and protein complexation capability of dyes related to Congo red and also some dyes of different structure were compared to explain the mechanism of Congo red binding and the reason for its specific affinity for beta-structure. Complexation with proteins was measured directly and expressed as the number of dye molecules bound to heat-aggregated IgG and to two light chains with different structural stability. Binding of dyes to rabbit antibodies was measured indirectly as the enhancement effect of the dye on immune complex formation. Self-assembling was tested using dynamic light scattering to measure the size of the supramolecular assemblies. In general the results show that the supramolecular form of a dye is the main factor determining its complexation capability. Dyes that in their compact supramolecular organization are ribbon-shaped may adhere to polypeptides of beta-conformation due to the architectural compatibility in this unique structural form. The optimal fit in complexation seems to depend on two contradictory factors involving, on the one hand, the compactness of the non-covalently stabilized supramolecular ligand, and the dynamic character producing its plasticity on the other. As a result, the highest protein binding capability is shown by dyes with a moderate self-assembling tendency, while those arranging into either very rigid or very unstable supramolecular entities are less able to bind.     

Expression of p16 in sporadic primary uveal melanoma

Expression of p16 protein, intragenic mutations of CDKN2A and hypermethylation of CDKN2A promoter region in 41 sporadic primary uveal melanomas were studied. There were 2 cases of spindle cell B histological type, 11 of A + B and 28 of mixed type. All melanomas infiltrated sclera but in 28 cases infiltration was superficial while in 13 profound. In 7 cases the tumor infiltrated the optic nerve. Expression of p16 was studied by immunohistochemistry and recorded by assessment of the proportion of positive tumor cells and staining intensity. Results were expressed as staining index (IRS). Intragenic mutations were studied by PCR-SSCP followed by sequencing, while hypermethylation of the promoter region by CpG methylation assay. In 15% of cases less than 10% of melanoma cells were p16 positive, in 70% of cases less than 50% of cells, while in 7% more than 80% of cells stained for p16 (mean IRS for all cases was 4.87 +/- 2.43). In B type the IRS was 8.5 +/- 0.7, in A + B type 6.0 +/- 2.1 and in the mixed type 4.17 +/- 2.43 (differences statistically significant). In melanomas profoundly infiltrating sclera mean IRS was 4.16, while in those infiltrating optic nerve 3.71 (statistically not significant). Analysis of the intragenic mutations revealed in two patients a GAC/GAT substitution in codon 84--a silent mutation. No hypermethylation of the CpG island of the p16 promoter region was found. In conclusion, we found that the degree of p16 expression is related to the histological type of tumor but not to the histological indicators of tumor invasiveness and that intragenic mutations and promoter hypermethylation are not major mechanisms of p16 inactivation in sporadic uveal melanoma.     

Effects of ivermectin and albendazole against Anisakis simplex in vitro and in guinea pigs

The activity of ivermectin and albendazole against larval Anisakis simplex was tested in vitro and in experimentally infected guinea pigs. Before drug exposure the medium for half of the larvae was adjusted to pH 2.0 with 1 N HCl, whereas the other half was held at pH 7.0. To these solutions, ivermectin was added to full concentrations of 1, 2, 5, 10, 50, 100, or 200 microg/ml, and for albendazole, 300, 400, and 500 microg/ml. Animals from group I were given 0.1 ml of 1% (3.3 mg/kg) ivermectin, whereas guinea pigs from group II were each given 5-7 mg (16.6-23.3 mg/kg) of albendazole orally. The efficacy of both drugs against L, A. simplex was high in vitro and in vivo against the larvae in different organs of guinea pigs.     

The coiled coil region (amino acids 129-250) of the tumor suppressor protein adenomatous polyposis coli (APC). Its structure and its interaction with chromosome maintenance region 1 (Crm-1)

The APC (adenomatous polyposis coli) tumor suppressor protein has many different intracellular functions including a nuclear export activity. Only little is known about the molecular architecture of the 2843-amino acid APC protein. Guided by secondary structure predictions we identified a fragment close to the N-terminal end, termed APC-(129-250), as a soluble and protease-resistant domain. We solved the crystal structure of APC-(129-250), which is monomeric and consists of three alpha-helices forming two separate antiparallel coiled coils. APC-(129-250) includes the nuclear export signal NES-(165-174) at the C-terminal end of the first helix. Surprisingly, the conserved hydrophobic amino acids of NES-(165-174) are buried in one of the coiled coils and are thus not accessible for interaction with other proteins. We demonstrate the direct interaction of APC-(129-250) with the nuclear export factor chromosome maintenance region 1 (Crm-1). This interaction is enhanced by the small GTPase Ran in its activated GTP-bound form and also by a double mutation in APC-(129-250), which deletes two amino acids forming two of the major interhelical interactions within the coiled coil. These observations hint to a regulatory mechanism of the APC nuclear export activity by NES masking.     

Dicarboxylate platinum(II) complexes as inhibitors of plasma membrane H(+)-ATPase in the yeast Saccharomyces cerevisiae

A series of cytotoxic neutral dicarboxylatoplatinum(II) complexes containing D(+), L(-) or DL-malate dianion and ethylenediamine or 1-ethylimidazole as ligands were examined using ATPase activity assays and the proton extrusion test. ATPase activity assays in vitro on plasma membrane H+-ATPase and on mitochondrial ATPase were carried out. The concentrations of compounds inhibiting enzyme activity to 50 per cent (J50) was determined. The new platinum complexes showed a stronger level of inhibition of both ATPases than the reference carboplatin; this inhibitory activity is related to a stereoisomeric form of anionic platinum ligands. ATPase inhibition in vivo was tested by glucose-stimulated proton extrusion and the influence of platinum compounds on this process in yeast cells was determined. Significant differences in activity levels were observed between those complexes with 1-ethylimidazole and those with ethylenediamine.     

Outer membrane proteome of Prevotella intermedia 17: identification of thioredoxin and iron-repressible hemin uptake loci

Although hemin is an indispensable nutrient for the oral pathogen Prevotella intermedia, not much is known regarding the molecular mechanisms of hemin acquisition. The availability of the genomic sequence of the bacterium allowed us to apply proteomic approaches to identify proteins that may be mediating the hemin acquisition process. As hemin acquisition mechanisms have been shown to be induced in iron-depleted conditions, we applied proteomic approaches to detect those proteins whose expressions were affected by iron. We analyzed 40 protein spots and identified 19 such proteins. Interestingly, two proteins drastically upregulated in iron-depleted conditions, PIN0009 and PINA0611, are homologs of hemin uptake receptors in other bacteria. PIN0009 is predicted to be an outer membrane lipoprotein. It is encoded by a gene that is the first of a seven-gene genomic locus encoding proteins of a novel hemin acquisition system. The second protein, PINA0611, is a homolog of numerous TonB-dependent outer membrane receptors including outer membrane iron uptake receptors of various Gram-negative bacteria. There was also another protein, regulated by iron, that was previously demonstrated to bind hemoglobin in P. intermedia. Finally, we identified a thioredoxin-like protein that has a novel outer membrane location.     

Discovery of a Unique Clp Component,ClpF, in Chloroplasts: A Proposed Binary ClpF-ClpS1 Adaptor Complex Functions in Substrate Recognition and Delivery

Clp proteases are found in prokaryotes, mitochondria, and plastids where they play crucial roles in maintaining protein homeostasis (proteostasis). The plant plastid Clp machinery comprises a hetero-oligomeric ClpPRT proteolytic core, ATP-dependent chaperones ClpC and ClpD, and an adaptor protein, ClpS1. ClpS1 selects substrates to the ClpPR protease-ClpC chaperone complex for degradation, but the underlying substrate recognition and delivery mechanisms are currently unclear. Here, we characterize a ClpS1-interacting protein in Arabidopsis thaliana, ClpF, which can interact with the Clp substrate glutamyl-tRNA reductase. ClpF and ClpS1 mutually stimulate their association with ClpC. ClpF, which is only found in photosynthetic eukaryotes, contains bacterial uvrB/C and YccV protein domains and a unique N-terminal domain. We propose a testable model in which ClpS1 and ClpF form a binary adaptor for selective substrate recognition and delivery to ClpC, reflecting an evolutionary adaptation of the Clp system to the plastid proteome.     

Defoliation of wild native box trees (Buxus sempervirens): Does box rust (Puccinia buxi) infection influence herbivory,survival and growth of the invasive Cydalima perspectalis?

The invasive box‐tree moth Cydalima perspectalis causes damage to horticultural box trees (Buxus spp.) in private gardens and parks in Europe and defoliation of large areas of European native box trees Buxus sempervirens, which grow in the understorey of deciduous forests. In some parts of their distribution area, wild native box trees are infected by the box rust Puccinia buxi, a fungus which does not occur in the native range of C. perspectalis. We examined whether the infection of P. buxi deters grazing by C. perspectalis in 31 wild box‐tree stands in forests in north‐western Switzerland and south‐western Germany. On average, 82.4% of the box trees were infested by P. buxi (among‐site variation 20%–100%), or 18.5% of their leaves. Linear mixed‐effect (LME) models revealed that the percentage of rust‐infected leaves was influenced by the local box‐tree density and the slope aspect of the forest site. 9.5% of the leaves showed grazing damage by C. perspectalis. LME showed that the percentage of leaves with grazing damage was affected by the elevation of the site and the percentage of rust‐infected leaves. The effect of box rust infection on food choice and larval performance (survival and growth rate) was examined in two experiments. In food‐choice tests, larvae of C. perspectalis did not show any preference for uninfected or rust‐infected box‐tree leaves and consumed similar amounts of leaf tissue of either type. However, when larvae were reared on leaves with three different degrees of P. buxi‐infection (and uninfected leaves as control), both survival and growth rate decreased with increasing degree of rust infection. This indicates that larval performance of C. perspectalis is reduced by the box rust. In the case of an outbreak of C. perspectalis, however, larvae may indiscriminately defoliate wild box trees.     

Time-resolved NMR studies of RNA folding

The application of real-time NMR experiments to the study of RNA folding, as reviewed in this article, is relatively new. For many RNA folding events, current investigations suggest that the time scales are in the second to minute regime. In addition, the initial investigations suggest that different folding rates are observed for one structural transition may be due to the hierarchical folding units of RNA. Many of the experiments developed in the field of NMR of protein folding cannot directly be transferred to RNA: hydrogen exchange experiments outside the spectrometer cannot be applied since the intrinsic exchange rates are too fast in RNA, relaxation dispersion experiments on the other require faster structural transitions than those observed in RNA. On the other hand, information derived from time-resolved NMR experiments, namely the acquisition of native chemical shifts, can be readily interpreted in light of formation of a single long-range hydrogen bonding interaction. Together with mutational data that can readily be obtained for RNA and new ligation technologies that enhance site resolution even further, time-resolved NMR may become a powerful tool to decipher RNA folding. Such understanding will be of importance to understand the functions of coding and non-coding RNAs in cells.