Application of hammerhead ribozymes for structural studies of ribosomal 5S RNAs

We evaluated the possibility that distinct proteolytic pathways contribute to the down-regulation of a novel (epsilon) or conventional (alpha) isoform of protein kinase C (PKC) in nonimmortalized human fibroblasts. Inhibitors of calpains and other cysteine proteinases, vesicle trafficking, or lysosomal proteolysis did not affect the down-regulation of PKC-alpha or -epsilon produced by bryostatin 1 (Bryo). Lactacystin (Lacta) and certain terminal aldehyde tripeptides or tetrapeptides, which selectively inhibit the proteasome, preserved substantial PKC-alpha and -epsilon protein from down-regulation by Bryo or phorbol-12-myristate-13-acetate. Lacta preserved active kinase in vivo, as shown by the retention of Bryo-induced autophosphorylated PKC-alpha. Concomitant with down-regulation, Bryo produced PKC-alpha and -epsilon species that were larger than the native proteins (80 and 90 kDa, respectively). Western blot analysis showed that the larger PKC-alpha species were ubiquitinylated. Treatment with Bryo plus Lacta synergistically increased multiubiquitinylated PKC-alpha, as expected if Bryo induces ubiquitinylation of PKC-alpha and Lacta blocks its degradation. Bryo also produced a 76-kDa, nonphosphorylated form of PKC-alpha and an 86-kDa form of PKC-epsilon. Phosphatase inhibitors decreased production of 76- and 86-kDa PKC-alpha and -epsilon by Bryo and preserved 80- and 90-kDa PKC-alpha and -epsilon, respectively. Our results suggest that the down-modulation of PKC-alpha and -epsilon occurs principally via the ubiquitin/ proteasome pathway. Dephosphorylation seems to predispose PKC to ubiquitinylation.     

High-pressure scheelite-type polymorph of SmCrO4: synthesis, structural characterization and magnetic properties

The new scheelite form of SmCrO4 oxide was obtained by heating the zircon-type SmCrO4 oxide at 4 GPa and 803 K.X-ray diffraction revealed that this scheelite SmCrO4 phase crystallized with tetragonal symmetry,S.G.141/a and lattice parameters:a=0.50776(3)nm and c=1.15606(2)nm.This structural phase transition from zircon to scheelite involved a decreasing of around 10% in the unit cell volume.Although the Cr-O and Sm-O distances did not change very much in both zircon and scheelite polymorphs,the changes occurred in the bond angles were remarkable that appear to support the proposed reconstructive model to explain this structural zircon-scheelite phase transition.Magnetic susceptibility and magnetization measurements revealed that the scheelite SmCrO4 oxide behaved an antiferromagnetic material,where the Sm3+and Cr5+were simultaneously ordered.The estimated Neel temperature,TN,was 16 K and the critical field at 12 K associated with the memmagnetic transition was 3.2 T.     

Purification, cloning, and preliminary characterization of a Spiroplasma citri ribosomal protein with DNA binding capacity

The rpsB-tsf-x operon of Spiroplasma citri encodes ribosomal protein S2 and elongation factor Ts, two components of the translational apparatus, and an unidentified X protein. A potential DNA-binding site (a 20-base pair (bp) inverted repeat sequence) is located at the 3' end of rpsB. Southwestern analysis of S. citri proteins, with a 30-bp double-stranded oligonucleotide probe (IRS), containing the 20-bp inverted repeat sequence and the genomic flanking sequences, detected an IRS-binding protein of 46 kDa (P46). P46 protein, which displays preferential affinity for the IRS, was purified from S. citri by a combination of affinity and gel filtration chromatographies. The native form of P46 seems to be homomultimeric as estimated by SDS-polyacrylamide gel electrophoresis analysis and gel filtration. A 3.5-kilobase pair S. citri DNA fragment comprising the P46 gene and flanking sequences was cloned and sequenced. Sequence analysis of this DNA fragment indicated that the P46 gene is located within the S10-spc operon of S. citri at the position of the gene coding for ribosomal protein L29 in the known S10-spc operons. The similarity between the N-terminal domain of P46 and the L29 ribosomal protein family and the presence of a 46-kDa IRS-binding protein in S. citri ribosomes indicated that P46 is the L29 ribosomal protein of S. citri. We suggest that P46 is a bifunctional protein with an L29 N-terminal domain and a C-terminal domain involved in IRS binding.     

Making and structural features of Ti-N-B and Ti-N-C nanocomposites

The paper examines the high-pressure sintering of nanograined ceramic polycrystals based on TiN-TiB₂ and TiC_0.5N_0.5 refractory compounds. Using the optimum pressure (up to 4 GPa) allows keeping the initial nanostate (TiN-TiB₂ and TiC_0.5N_0.5) and obtaining high-density ceramics with enhanced mechanical properties. An x-ray structural analysis is used to examine how the TiN-TiB₂ and TiC_0.5N_0,5 crystalline structure evolves during temperature-pressure treatment, which produces new ceramic materials. Based on the properties of the polycrystalline materials obtained, the temperature-time mode for the consolidation of initial nanopowders is determined to ensure favorable parameters of sintered nanograined ceramics. __________ Translated from Poroshkovaya Metallurgiya, Vol. 47, No. 1–2 (459), pp. 62–72, 2008.     

Purification and structural characterization of bovine cathelicidins, precursors of antimicrobial peptides

Cathelicidins are a novel family of antimicrobial peptide precursors from mammalian myeloid cells. They are characterized by a conserved N-terminal region while the C-terminal antimicrobial domain can vary considerably in both primary sequence and length. Four cathelicidins, proBac5, proBac7, prododecapeptide and proBMAP-28, have been concurrently purified from bovine neutrophils, using simple and rapid methodologies. The correlation of ES-MS data from the purified proteins with their cDNA-deduced sequences has revealed several common features of their primary sequence, such as the presence of N-terminal 5-oxoproline (pyroglutamate) residues and two disulfide bridges in a 1-2, 3-4 arrangement. The N-terminal domains of the cathelicidins present one or two Asp-Pro bonds, which are particularly acid-labile in proBac5 and proBac7, but stable in prododecapeptide. This suggests that the spatial organization around these bonds may vary in different cathelicidins, and favour hydrolysis in some cases. An unexpected feature of the prododecapeptide is that it exists as dimers formed by three possible combinations of its two isoforms. The isolation of a truncated, monomeric form of this protein, lacking the cysteine-containing antimicrobial dodecapeptide, indicates that dimerization occurs via disulfide bridge formation at the level of the C-terminal domain and that the dodecapeptide is likely released as a dimer from its precursor. Sequence-based secondary structure predictions and CD results indicate for cathelicidins a 30-50% content of extended conformation and <20% content of alpha-helical conformation, with the alpha-helical segment placed near the N-terminus. Finally, similarity searching and topology-based structure prediction underline a significant sequential and structural similarity between the conserved N-terminal domain of cathelicidins and cystatin-like domains, placing this family within the cystatin superfamily. When assayed against cathepsin L, unlike the potent cystatin inhibitors, three of the four cathelicidins show only a poor inhibitory activity (Ki = 0.6-3 microM).     

Mammalian mitochondrial ribosomal proteins. N-terminal amino acid sequencing, characterization, and identification of corresponding gene sequences

The integrity of healthy mitochondria is supposed to depend largely on proper mitochondrial protein biosynthesis. Mitochondrial ribosomal proteins (MRPs) are directly involved in this process. To identify mammalian mitochondrial ribosomal proteins and their corresponding genes, we purified mature rat MRPs and determined 12 different N-terminal amino acid sequences. Using this peptide information, data banks were screened for corresponding DNA sequences to identify the genes or to establish consensus cDNAs and to characterize the deduced MRP open reading frames. Eight different groups of corresponding mammalian MRPs constituted from human, mouse, and rat origin were identified. Five of them show significant sequence similarities to bacterial and/or yeast mitochondrial ribosomal proteins. However, MRPs are much less conserved in respect to the amino acid sequence among species than cytoplasmic ribosomal proteins of eukaryotes and bacteria.     

Eimeria tenella: cloning and characterization of cDNA encoding a S3a ribosomal protein

We determined the genomic organization of human CRF type-1 receptor (hCRF-R1). The gene coding for hCRF-R1 consists of at least 14 exons and spans over 20 kilobases. hCRF-R1's three reported isoforms originate from the same gene by alternative splicing. The first hCRF-R1, which binds to CRF with the highest affinity and transduces the most sensitive cAMP accumulation in response to CRF, is encoded in a total of 13 exons, the only one excluded being exon 6. The second isoform contains an additional 29-amino acid sequence which corresponds to exon 6. Unlike the first isoform, the third lacks a 40-amino acid sequence, corresponding to exon 3. Exon-intron boundaries are the same as that of the consensus sequence. Locations of introns in the coding sequence are similar to human CRF-R1, rat CRF-R1, human CRF-R2alpha and others belonging to the human glucagon receptor family.     

The hemidesmosome: new fine structural features revealed by freeze-fracture techniques

Hemidesmosomes along the dermal-epidermal junction of larval and post-metamorphic newt skin have been examined in freeze-fracture replica images correlated with electron micrographs of sectioned material. Larval hemidesmosomal sites are characterized by large (200-300 A) intramembranous granules arranged into clusters, each of which is aligned with a cytoplasmic hemidesmosomal plaque. In unfixed epidermis the granules remain attached to the A-face, while after glutaraldehyde fixation they are found on both A- and B-faces. Following metamorphosis the clusters are less distinct and localized. Replicas of unfixed B-faces and nearby cytoplasm display elongate, filamentous profiles which traverse the cytoplasmic leaflet and extend onto the B-face. The possibility that these components constitute a filamentous network serving to link tonofilaments, hemidesmosomal plaque, and basal plasmalemma is considered in view of the evidence to date. Hemidesmosomal fine structure as revealed by these studies is compared to features of desmosomes as detailed in the following report.     

Two cytosolic protein families implicated in lipid-binding: main structural and functional features

1. According to the important biological role of fatty acids and phospholipids in cell membranes, two cytosolic proteins implicated in their binding and transport in brain were considered, namely: Fatty Acid-Binding Protein and basic 21 kDa protein. 2. They were reviewed as well as their related protein families. 3. Although the two protein groups do not present significant sequence homologies, they share several similar properties and might thus be implicated in common physiological functions.     

Cloning and characterization of cDNAs encoding S-RNases from almond (Prunus dulcis): primary structural features and sequence diversity of the S-RNases in Rosaceae

The ability of histamine H3 receptor ligands to interact with 5-HT3 receptors in NG108-15 cells was studied using the whole cell patch clamp recording technique. Imetit, a histamine H3 receptor agonist, generated inward currents and exhibited weak partial agonist activity at the 5-HT3 receptor (EC50 = 11.8 microM). Imetit-induced currents were slow to desensitize and at a high concentration reduced in size. The histamine H3 receptor antagonists iodophenpropit and thioperamide did not generate inward currents but were able to inhibit 5-hydroxytryptamine (5-HT) responses with an IC50 of 1.57+/-0.3 microM and 13.7+/-3.5 microM, respectively. Thioperamide is probably a non-competitive antagonist which may have more than one binding site on the receptor.     

Conserved structural features between HLA-DO beta and -DR beta

HLA-DO is a non-classical MHC class II molecule presumed to play a specialized role in the antigen processing pathway. We have modeled the HLA-DO beta-chain and found its overall structure compatible with the one of DR beta. Functional studies further highlighted the similarity between these beta-chains of the class II family of proteins. Indeed, a mixed heterodimer composed of the DR alpha and a chimeric DO beta-chains presented bacterial superantigens to T cells and was shown to interact with CD4. The implications of such structural conservation for the in vivo functions of HLA-DO are discussed.     

Physicochemical and structural features of mono- and polycrystalline manganese-zinc ferrites

Studies carried out using various methods — x-ray structural and spectral, electromagnetic, gravimetric, nuclear -resonance, and nuclear magnetic resonance — revealed that the crystal-chemical structure of mono-and polycrystalline manganese — zinc ferrites used in video tape recorders and color television sets possess defects, with various degrees of localization (point, plane, and cluster), existing simultaneously in both the cation and anion sublattices. Differences in the structure of mono- and polycrystalline specimens were observed, but the specimens were similar with respect to the nature of the clustered defects. A relationship between the defect structure and specified electromagnetic properties of the ferrites was established. It is concluded that more information is needed concerning the actual crystal-chemical structure of ferrites containing defects of different types and dimensions (micro, meso, macro).VNII Reaktivélektron, Donetsk. Translated from Poroshkovaya Metallurgiya, No. 5–6, pp. 89–93, May–June, 1994.     

Stability of cis, trans, and nonplanar peptide groups

Conformational energy calculations using ECEPP (Empirical Conformational Energy Program for Peptides) were performed on the molecular fragment Calpha1C'ONHCalpha2, on N-methylacetamide, and on several peptide molecules including N-acetyl-N'-methylglycineamide (Gly single residue), N-acetyl-N',N'-dimethylglycine-amide, and N-acetyl-N'-methylamide dipeptides of Gly-Gly and Gly-Pro. Energy minimization was carried out with peptide groups taken in both the cis and trans conformations, and the librational entropy and conformational free energy were determined at each minimum. It was found that the instability of cis in Gly-Gly comes primarily from interactions of the Calpha1 and HCalpha1 atoms with the Calpha2 and HCalpha2 atoms, and also from avorable interactions present in the trans form which are disallowed in the cis form, and from conformational entropy. The instability of cis in Gly-Pro is much less than in Gly-Gly because unfavorable interactions of the type CalphaH-CalphaH present in the cis conformation of Gly-Gly are present in both the cis and trans forms of Gly-Pro. The instability of cis in Gly-Pro arises mainly from the change in electrostatic energy caused by the restricted rotation about the N-Calpha bond of Pro. Entropy accounts for about 0.5 kcal/mol of the instability of cis in Gly-Pro compared with about 1.5 kcal/mol in Gly-Gly. The calculated fraction (4%) of cis in Gly-pro is in good agreement with the experimental value (5%) for related peptides in nonpolar solvents. When the dihedral angle omega of the central peptide bond in these dipeptides is allowed to vary during energy minimization, the deviations from planarity are only 1-3 degrees in low-energy minima of Gly-Gly but as much as 10 degrees in Gly-Pro. A comparison of these results with calculations in which the peptide bond was held fixed in the planar trans conformation shows that conformation-dependent properties of blocked dipeptides can be represented adequately without allowing omega to vary.     

Enzyme-assisted synthesis and structural characterization of nitrocatechol glucuronides

OBJECTIVE: To investigate the effect of improved air quality on IVF and subsequent embryo development. DESIGN: Retrospective cohort study. SETTING: Hospital-based IVF facility composed of an anteroom, a cleanroom, and an adjacent operating room. PATIENT(S): Two-hundred seventy-five couples requesting IVF between 1993 and 1997. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Particle counts (sizes 0.3, 0.5, 1.0, and 5.0 microm); IVF rates; and embryo quality (stage and grade). RESULT(S): Clinical pregnancy rates decreased from 35% in 1993 to 16% in 1994 (numerous construction odors were detected during 1994) and increased steadily after the cleanroom was built (rates for 1995-1997 were 20%, 32%, and 59%, respectively). Fertilization rates decreased between 1993 (74%) and 1994 (60%) and then steadily increased after cleanroom installation (62% in 1995, 71% in 1996, and 69% in 1997). The proportion of embryos past the four-cell stage decreased from 66% in 1993 to 61% in 1994 but then increased steadily in the years after the cleanroom was built (78%, 77%, and 83% in 1995, 1996, and 1997, respectively). During the same 5-year period, there were no differences in embryo quality or number of embryos transferred. CONCLUSION(S): Construction of a Class 100 cleanroom improved air quality and IVF rate and increased the number of embryos past the four-cell stage available for transfer.     

Halophilic class I aldolase and glyceraldehyde-3-phosphate dehydrogenase: some salt-dependent structural features

Aldolase and glyceraldehyde-3-phosphate dehydrogenase from the extremely halophilic archaebacterium Haloarcula vallismortis are stable only in high concentrations of KCl present within the physiological environment. Data concerning the structural changes in the two enzymes as a result of lowering of salt concentration and changes in pH were obtained by monitoring the intrinsic protein fluorescence in the presence of quenchers. When the KCl concentrations were lowered below 2 M or in the presence of 6 M guanidine hydrochloride, the emission maximum shifted to a longer wavelength, indicating enhanced exposure of tryptophyl residues to the solvent. The spectral characteristics of the two proteins in guanidine hydrochloride and 0.4 M KCl were identical. However, these denatured states appear to be different than those observed after acid denaturation. Further perturbation of fluorescence was observed due to I-, and application of the Stern-Volmer law showed that the total fluorescence was available to the quenchers only in 0.4 M KCl solutions. The unfolding of proteins in 0.4 M KCl was a gradual process which was accompanied by a time-dependent loss in enzyme activity. The activity loss was complete within 30 min for aldolase whereas in the case of GAPDH nearly 3 h was required for the destruction of activity. For both enzymes, inactivation and protein denaturation were strongly correlated. The data on activity and thermostability measurements of the two enzymes in varying concentrations of KCl and potassium phosphate revealed that though both proteins are halophilic, the forces in the maintenance of their stability could be different.(ABSTRACT TRUNCATED AT 250 WORDS)