Affinity extraction of proteins by means of reverse micellar phases containing a metal-chelating surfactant

Summary The principle of metal chelate-protein interaction was applied for protein extraction by means of reverse micellar phases. For this purpose, an affinity surfactant was synthesized exposing iminodiacetic acid as the hydrophilic moiety. The application of this substance as a cosurfactant leads to enhanced extraction of proteins exhibiting histidine groups on their surface.     

Metabolite profiling and fingerprinting of commercial cultivars of Humulus lupulus L. (hop): a comparison of MS and NMR methods in metabolomics

Hop (Humulus lupulus L. Cannabaceae) is an economically important crop. In addition to its role in beer brewing, its pharmaceutical applications have been of increasing importance in recent years. Bitter acids (prenylated polyketides), prenylflavonoids and essential oils, are the primary phytochemical components that account for hop medicinal value. An integrated approach utilizing nuclear magnetic resonance (NMR) and mass spectrometry (MS) techniques was used for the first large-scale metabolite profiling in Humulus lupulus. Resins and extracts prepared from 13 hop cultivars were analysed using NMR, liquid chromatography (LC)-MS and fourier transform ion cyclotron resonance (FTICR)-MS in parallel and subjected to principal component analysis (PCA). A one pot extraction method, compatible with both MS and NMR measurement was developed to help rule out effects due to differences in extraction protocols. Under optimised conditions, we were able to simultaneously quantify and identify 46 metabolites including 18 bitter acids, 12 flavonoids, 3 terpenes, 3 fatty acids and 2 sugars. Cultivars segregation in PCA plots generated from both LC-MS and NMR data were found comparable and mostly influenced by differences in bitter acids composition among cultivars. FTICR-MS showed inconsistent PCA loading plot results which are likely due to preferential ionisation and also point to the presence of novel isoprenylated metabolites in hop. This comparative metabolomic approach provided new insights for the complementariness and coincidence for these different technology platform applications in hop and similar plant metabolomics projects.     

Loss of Function of Glucocerebrosidase GBA2 Is Responsible for Motor Neuron Defects in Hereditary Spastic Paraplegia

Spastic paraplegia 46 refers to a locus mapped to chromosome 9 that accounts for a complicated autosomal-recessive form of hereditary spastic paraplegia (HSP). With next-generation sequencing in three independent families, we identified four different mutations in GBA2 (three truncating variants and one missense variant), which were found to cosegregate with the disease and were absent in controls. GBA2 encodes a microsomal nonlysosomal glucosylceramidase that catalyzes the conversion of glucosylceramide to free glucose and ceramide and the hydrolysis of bile acid 3-O-glucosides. The missense variant was also found at the homozygous state in a simplex subject in whom no residual glucocerebrosidase activity of GBA2 could be evidenced in blood cells, opening the way to a possible measurement of this enzyme activity in clinical practice. The overall phenotype was a complex HSP with mental impairment, cataract, and hypogonadism in males associated with various degrees of corpus callosum and cerebellar atrophy on brain imaging. Antisense morpholino oligonucleotides targeting the zebrafish GBA2 orthologous gene led to abnormal motor behavior and axonal shortening/branching of motoneurons that were rescued by the human wild-type mRNA but not by applying the same mRNA containing the missense mutation. This study highlights the role of ceramide metabolism in HSP pathology.     

Secretion of phosphoproteins associated with neoplastic transformation and with the action of transforming growth factors

Incubation of conditioned media derived from mammary epithelial cells and from fibroblasts with [gamma-32P]ATP revealed much higher intensities of labeled polypeptides in transformed cells compared to normal cells. Conditioned media from human mammary carcinoma cells have in common the presence of characteristic phosphoproteins with molecular masses of about 37,22 and 19.5 kDa. Ehrlich Ascites Mammary Carcinoma Cells secrete a dominant 32 kDa phosphoprotein. Normal fibroblasts secrete elevated levels of phosphoproteins after treatment with transforming growth factors. A phosphoprotein with molecular mass of about 37 kDa becomes secreted preferentially if cell-conditioned media were labeled in vivo. The results indicate that the phosphoproteins comprise a family of secretory polypeptides associated with early steps of transformation.     

DNA binding properties of human Cdc45 suggest a function as molecular wedge for DNA unwinding

The cell division cycle protein 45 (Cdc45) represents an essential replication factor that, together with the Mcm2-7 complex and the four subunits of GINS, forms the replicative DNA helicase in eukaryotes. Recombinant human Cdc45 (hCdc45) was structurally characterized and its DNA-binding properties were determined. Synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering and atomic force microscopy revealed that hCdc45 exists as an alpha-helical monomer and possesses a structure similar to its bacterial homolog RecJ. hCdc45 bound long (113-mer or 80-mer) single-stranded DNA fragments with a higher affinity than shorter ones (34-mer). hCdc45 displayed a preference for 3′ protruding strands and bound tightly to single-strand/double-strand DNA junctions, such as those presented by Y-shaped DNA, bubbles and displacement loops, all of which appear transiently during the initiation of DNA replication. Collectively, our findings suggest that hCdc45 not only binds to but also slides on DNA with a 3′–5′ polarity and, thereby acts as a molecular ‘wedge’ to initiate DNA strand displacement.     

Shiga toxin B-subunit sequential binding to its natural receptor in lipid membranes

Shiga toxin B-subunit (STxB), a protein involved in the cell-binding and intracellular trafficking of Shiga holotoxin, binds to a specific glycolipid, the globotriaosyl ceramide (Gb₃). Tryptophan residues of STxB, located at the protein-membrane interface, allow one to study its interaction with model membranes by means of spectroscopic methods with no need for chemical derivatisation with a fluorophore. The protein emits maximally around 346 nm and a blue shift of about 8 nm, as well as the occurrence of changes in the emission fluorescence intensity spectra, is indicative of insertion and partition into the membrane. However, the interaction seems to take place without pentamer dissociation. Acrylamide quenching experiments confirm tryptophan residues become less exposed to solvent when in the presence of vesicles, and the use of lipophilic probes suggests that they are located in a shallow position near the water/membrane interface. Fluorescence intensity and lifetime measurements upon STxB titration with Gb₃-containing vesicles suggest a complex STxB/Gb₃ docking mechanism involving static quenching in the later stages. Based on our observations, a model of the protein-membrane interaction is proposed and the STxB membrane partition and binding constants were calculated.     

Calculation and use of protein-derived conformation-related spectra for the estimate of the secondary structure of proteins from their infrared spectra

This paper probes the calculation of conformation-related basis spectra from infrared spectra (amide I′band) of reference proteins of known conformational composition and, with their aid, the computation of conformations from the amide I′ band of globular proteins using in both approaches a least-squares, curve-fitting computer program for the analysis of the spectra. The following results were obtained. The infrared basis spectra for the α-helix conformation, the β-(antiparallel-chain pleated sheet) conformation and the ρ-conformation were calculated and their physical reality was substantiated. The basis spectra were shown to be similar when the absorption contributions of the side chains of amino acids were either neglected or taken into account (uncorrected or corrected basis spectra). The mutual correlation of the basis spectra, quantified by the roots of the diagonal elements of the inverse matrix, was found to be low enough only for the β-conformation to allow a statistically reliable estimate of the β-conformation content of proteins. The comparison of the percentages of the β-conformation derived from x-ray structural analysis or calculated from infrared spectra showed the suitability of the basis spectra for the rough estimate of the β-conformation percentages of proteins. The results were not significantly different when using the uncorrected or corrected basis spectra.