Molecular cloning and functional characterization of the Xenopus Ca(2+)-binding protein frequenin.

Frequenin was originally identified in Drosophila melanogaster as a Ca(2+)-binding protein facilitating transmitter release at the neuromuscular junction. We have cloned the Xenopus frequenin (Xfreq) by PCR using degenerate primers combined with low-stringency hybridization. The deduced protein has 70% identity with Drosophila frequenin and about 38-58% identity with other Ca(2+)-binding proteins. The most prominent features are the four EF-hands, Ca(2+)-binding motifs. Xfreq mRNA is abundant in the brain and virtually nondetectable from adult muscle. Western blot analysis indicated that Xfreq is highly concentrated in the adult brain and is absent from nonneural tissues such as heart and kidney. During development, the expression of the protein correlated well with the maturation of neuromuscular synapses. To determine the function of Xfreq at the developing neuromuscular junction, the recombinant protein was introduced into Xenopus embryonic spinal neurons by early blastomere injection. Synapses made by spinal neurons containing exogenous Xfreq exhibited a much higher synaptic efficacy. These results provide direct evidence that frequenin enhances transmitter release at the vertebrate neuromuscular synapse and suggest its potential role in synaptic development and plasticity.

Molecular cloning and characterization of a conserved nuclear serine(threonine) protein kinase.

Human, Drosophila melanogaster, and Caenorhabditis elegans cDNA clones encoding homologues of a serine(threonine) protein kinase (EC 2.7.1.37) (designated Ndr protein kinase) have been isolated and sequenced. The human and Drosophila cDNAs predict polypeptides of 54 kDa and 52 kDa, respectively, which share approximately 80% amino acid similarity. Northern analysis of human tissues revealed a ubiquitously expressed 3.9-kb transcript. Recombinant GST-Ndr underwent intramolecular autophosphorylation on serine and threonine residues in vitro but failed to transphosphorylate several standard protein kinase substrates. Transfection of the human cDNA into COS-1 cells resulted in the appearance of an intense nuclear staining in cells analyzed by indirect immunofluorescence; deletion mutagenesis identified a short basic peptide, KRKAETWKRNRR, responsible for the nuclear accumulation of Ndr. Thus, Ndr is a conserved and widely expressed nuclear protein kinase. The closest known relative of this previously uncharacterized kinase is Dbf2, a budding yeast protein kinase required for the completion of nuclear division.

Molecular cloning and characterization of cDNA encoding the alpha subunit of the rat protein synthesis initiation factor eIF-2B.

Eukaryotic initiation factor 2B (eIF-2B) is an essential component of the pathway of peptide-chain initiation in mammalian cells, yet little is known about its molecular structure and regulation. To investigate the structure, regulation, and interactions of the individual subunits of eIF-2B, we have begun to clone, characterize, and express the corresponding cDNAs. We report here the cloning and characterization of a 1510-bp cDNA encoding the alpha subunit of eIF-2B from a rat brain cDNA library. The cDNA contains an open reading frame of 918 bp encoding a polypeptide of 305 aa with a predicted molecular mass of 33.7 kDa. This cDNA recognizes a single RNA species approximately 1.6 kb in length on Northern blots of RNA from rat liver. The predicted amino acid sequence contains regions identical to the sequences of peptides derived from bovine liver eIF-2B alpha subunit. Expression of this cDNA in vitro yields a peptide which comigrates with natural eIF-2B alpha in SDS/polyacrylamide gels. The predicted amino acid sequence exhibits 42% identity to that deduced for the Saccharomyces cerevisiae GCN3 protein, the smallest subunit of yeast eIF-2B. In addition, expression of the rat cDNA in yeast functionally complements a gcn3 deletion for the inability to induce histidine biosynthetic genes under the control of GCN4. These results strongly support the hypothesis that mammalian eIF-2 alpha and GCN3 are homologues. Southern blots indicate that the eIF-2B alpha cDNA also recognizes genomic DNA fragments from several other species, suggesting significant homology between the rat eIF-2B alpha gene and that from other species.

Human acetyl-CoA carboxylase: characterization, molecular cloning, and evidence for two isoforms.

We have cloned and sequenced the cDNA coding for human HepG2 acetyl-CoA carboxylase (ACC; EC 6.4.1.2). The sequence has an open reading frame of 7038 bp that encode 2346 amino acids (M(r), 264,737). The C-terminal 2.6-kb sequence is very different from that recently reported for human ACC (Ha, J., Daniel, S., Kong, I.-S., Park, C.-K., Tae, H.-J. & Kim, K.-H. [1994] Eur. J. Biochem. 219, 297-306). Northern blot analysis revealed that the ACC mRNA is approximately 10 kb in size and that its level varies among the tissues tested. Evidence is presented to show that the human ACC gene is 200-480 kbp in size and maps to chromosome 17q12. We also provide evidence for the presence of another ACC-like gene with similarly sized mRNA but tissue-specific expression different from that of the ACC gene reported herein. That this second ACC-like gene encodes the 280-kDa carboxylase is not ruled out.

Molecular cloning and characterization of a cDNA encoding monoclonal nonspecific suppressor factor.

The monoclonal nonspecific suppressor factor (MNSF) is a lymphokine product of a murine T-cell hybridoma that inhibits the generation of lipopolysaccharide-induced immunoglobulin-secreting cells in an antigen-nonspecific manner. A cDNA clone encoding MNSF beta (an isoform of MNSF) was isolated and expressed in bacteria. The sequence obtained is virtually identical to the Fau protein, a product of the ubiquitously expressed fau gene with unknown function. Northern blot analysis demonstrated a single, 0.6-kb transcript. Specific polyclonal antibodies against synthetic peptides corresponding to the deduced amino acid sequences were elicited in rabbits. Immunoprecipitation experiments with these antibodies showed that MNSF beta is released extracellularly in an aggregate form, albeit it lacks a signal peptide sequence. The anti-MNSF beta affinity eluate from the MNSF-producing murine hybridoma (E17) and concanavalin A-activated splenocyte culture supernatants inhibited the immunoglobulin production by lipopolysaccharide-activated splenocytes. Recombinant MNSF beta also showed a similar biologic activity. Thus, ubiquitin-like protein(s) may be involved in the regulation of the immune responses.

Molecular cloning and characterization of chitinase genes from Candida albicans.

Chitinase (EC 3.2.1.14) is an important enzyme for the remodeling of chitin in the cell wall of fungi. We have cloned three chitinase genes (CHT1, CHT2, and CHT3) from the dimorphic human pathogen Candida albicans. CHT2 and CHT3 have been sequenced in full and their primary structures have been analyzed: CHT2 encodes a protein of 583 aa with a predicted size of 60.8 kDa; CHT3 encodes a protein of 567 aa with a predicted size of 60 kDa. All three genes show striking similarity to other chitinase genes in the literature, especially in the proposed catalytic domain. Transcription of CHT2 and CHT3 was greater when C. albicans was grown in a yeast phase as compared to a mycelial phase. A transcript of CHT1 could not be detected in either growth condition.

Characterization of Carbon Molecular Sieve Membranes Supported on Ceramic Tubes

Carbon molecular sieve membranes have been analyzed in supported and unsupported configurations in this experimental study. The membranes were used to adsorb CO2, N2 and CH4, and their adsorption data were analyzed to establish differences in rate and capacity of adsorption between the two types of samples (supported and unsupported). Experimental results show an important effect of the support, which can be considered as an additional parameter to tailor pore size on these carbon membranes. Immersion calorimetry values were measured by immersing the membranes into liquids of different molecular dimensions (dichloromethane, benzene, n-hexane, 2,2-dimethylbutane). Similarities were found between adsorption and calorimetric analysis. The pore volume of the samples analyzed ranged from 0.016 to 0.263 cm3/g. The effect of the pyrolysis temperature, either 550 or 700 °C, under N2 atmosphere was also analyzed. Quantification of the pore-size distribution of the support was done by liquid-liquid displacement porosimetry. The composite membrane was used for CO2/CH4 separation before and after pore plugging was done. The ideal selectivity factors value (4.47) was over the Knudsen theoretical factor (0.60) for membrane pyrolyzed at 600 °C, which indicates the potential application of these membranes for the separation of low-molecular weight gases.

Characterization of carbon molecular sieves using methane and carbon dioxide as adsorptive probes

Nitrogen adsorption at 77 K is the current standard means for pore size determination of adsorbent materials. However, nitrogen adsorption reaches limitations when dealing with materials such as molecular sieving carbon with a high degree of ultramicroporosity. In this investigation, methane and carbon dioxide adsorption is explored as a possible alternative to the standard nitrogen probe. Methane and carbon dioxide adsorption equilibria and kinetics are measured in a commercially derived carbon molecular sieve over a range of temperatures. The pore size distribution is determined from the adsorption equilibrium, and the kinetics of adsorption is shown to be Fickian for carbon dioxide and non-Fickian for methane. The non-Fickian response is attributed to transport resistance at the pore mouth experienced by the methane molecules but not by the carbon dioxide molecules. Additionally, the change in the rate of adsorption with loading is characterized by the Darken relation in the case of carbon dioxide diffusion but is greater than that predicted by the Darken relation for methane transport. Furthermore, the proposition of inkbottle-shaped micropores in molecular sieving carbon is supported by the determination of the activation energy for the transport of methane and subsequent sizing of the pore-mouth barrier by molecular potential calculations.

The structural characterization of carbon molecular sieve membrane (CMSM) via gas adsorption

The microstructure of a carbon molecular sieve membrane (CMSM) is characterized using adsorption equilibrium information. The pore size distributions of the CMSM derived from N-2 and CH4 adsorption isotherm are found to be consistent with each other and in agreement with the results of gas permeation experiments as well as the general characteristics of such molecular sieve materials. (C) 2003 Elsevier B.V. All rights reserved.

The preparation and characterization of tin(IV) complexes of 2-quinolinecarboxaldehyde Schiff bases of S-methyl- and S-benzyldithiocarbazates and the X-ray crystal and molecular structures of the 2-quinolinecarboxaldehyde Schiff base of S-benzyldithi

New tin(IV) complexes of empirical formula, Sn(NNS)I-3 (NNS = anionic forms of the 2-quinolinecarboxaldehyde Schiff bases of S-methyl- and S-benzyldithiocarbazate) have been prepared and characterized by a variety of physico-chemical techniques. In the solid state, the Schiff bases exist as the thione tautomer but in solution and in the presence of tin(IV) iodide they convert to the thiol tautomer and coordinate to the tin atom in their deprotonated thiolate forms. The structures of the free ligand, Hqaldsbz and its triiodotin(IV) complex, [Sn(qaldsbz)I-3] have been determined by X-ray diffraction. The complex, [Sn(qaldsbz)I-3] has a distorted octahedral structure with the Schiff base coordinated to the tin atom as a uninegatively charged tridentate chelating agent via the quinoline nitrogen atom, the azomethine nitrogen atom and the thiolate sulfur atom. The three iodo ligands are coordinated meridionally to the tin atom. The distortion from an ideal octahedral geometry of [Sn(qaldsbz)I-3] is attributed to the restricted bite size of the tridentate Schiff base ligand. (C) 2004 Elsevier Ltd. All rights reserved.

Pleomorphic lobular carcinoma of the breast: role of comprehensive molecular pathology in characterization of an entity

Immunohistochemical analysis of E-cadherin has changed the way lobular neoplasia is perceived. It has helped to classify difficult cases of carcinoma in situ with indeterminate features and led to the identification of new variants of lobular carcinoma. Pleomorphic lobular carcinoma (PLC) and pleomorphic lobular carcinoma in situ (PLCIS), recently described variants of invasive and in situ classic lobular carcinoma, are reported to be associated with more aggressive clinical behaviour. Although PLC/PLCIS show morphological features of classic lobular neoplasia and lack E-cadherin expression, it is still unclear whether these lesions evolve through the same genetic pathway as lobular carcinomas or are high-grade ductal neoplasms that have lost E-cadherin. Here we have analysed a case of extensive PLCIS and invasive PLC associated with areas of E-cadherin-negative carcinoma in situ with indeterminate features, using immunohistochemistry, chromogenic in situ hybridization, high-resolution comparative genomic hybridization (CGH) and array-based CGH. We observed that all lesions lacked E-cadherin and beta-catenin and showed gain of 1q and loss of 16q, features that are typical of lobular carcinomas but are not seen in high-grade ductal lesions. In addition, amplifications of c-myc and HER2 were detected in the pleomorphic components, which may account for the high-grade features in this case and the reported aggressive clinical behaviour of these lesions. Taken together, these data suggest that at least some PLCs may evolve from the same precursor or through the same genetic pathway as classic lobular carcinomas. Copyright (c) 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Molecular dynamics characterization of n-octyl-beta-D-glucopyranoside micelle structure in aqueous solution

n-Octyl-beta-D-glueopyranoside (OG) is a non-ionic glycolipid, which is used widely in biotechnical and biochemical applications. All-atom molecular dynamics simulations from two different initial coordinates and velocities in explicit solvent have been performed to characterize the structural behaviour of an OG aggregate at equilibrium conditions. Geometric packing properties determined from the simulations and small angle neutron scattering experiment state that OG micelles are more likely to exist in a non-spherical shape, even at the concentration range near to the critical micelle concentration (0.025 M). Despite few large deviations in the principal moment of inertia ratios, the average micelle shape calculated from both simulations is a prolate ellipsoid. The deviations at these time scales are presumably the temporary shape change of a micelle. However, the size of the micelle and the accessible surface areas were constant during the simulations with the micelle surface being rough and partially elongated. Radial distribution functions computed for the hydroxyl oxygen atoms of an OG show sharper peaks at a minimum van der Waals contact distance than the acetal oxygen, ring oxygen, and anomeric carbon atoms. This result indicates that these atoms are pointed outwards at the hydrophilic/hydrophobic interface, form hydrogen bonds with the water molecules, and thus hydrate the micelle surface effectively. (c) 2005 Elsevier Inc. All rights reserved.

Molecular cloning and characterization of the mouse Na+ sulfate cotransporter gene (Slc13a4): structure and expression

Sulfate is an essential ion required for numerous functions in mammalian physiology. Due to its hydrophilic nature, cells require sulfate transporters on their plasma membranes to allow entry of sulfate into cells. In this study, we identified a new mouse Na+-sulfate cotransporter (mNaS2), characterized its tissue distribution and determined its cDNA and gene (Slc13a4) structures. mNaS2 mRNA was expressed in placenta, brain, lung, eye, heart, testis, thymus and liver. The mouse NaS2 cDNA spans 3384 nucleotides and its open frame encodes a protein of 624 amino acids. Slc13a4 maps to mouse chromosome 6131 and contains 16 exons, spanning over 40 kb in length. Its 5'-flanking region contains CART- and GC-box motifs and a number of putative transcription factor binding sites, including GATA-1, MTF-1, STAT6 and HNF4 consensus sequences. This is the first study to define the tissue distribution of mNaS2 and resolve its cDNA and gene structures, which will allow us to investigate mNaS2 gene expression in vivo and determine its role in mammalian physiology.

Characterization of the structure of RAMP1 by mutagenesis and molecular modeling

Receptor activity modifying proteins (RAMPs) are a family of single-pass transmembrane proteins that dimerize with G-protein-coupled receptors. They may alter the ligand recognition properties of the receptors (particularly for the calcitonin receptor-like receptor, CLR). Very little structural information is available about RAMPs. Here, an ab initio model has been generated for the extracellular domain of RAMP1. The disulfide bond arrangement (Cys 27-Cys82, Cys40-Cys72, and Cys 57-Cys104) was determined by site-directed mutagenesis. The secondary structure (a-helices from residues 29-51, 60-80, and 87-100) was established from a consensus of predictive routines. Using these constraints, an assemblage of 25,000 structures was constructed and these were ranked using an all-atom statistical potential. The best 1000 conformations were energy minimized. The lowest scoring model was refined by molecular dynamics simulation. To validate our strategy, the same methods were applied to three proteins of known structure; PDB:1HP8, PDB:1V54 chain H (residues 21-85), and PDB:1T0P. When compared to the crystal structures, the models had root mean-square deviations of 3.8 Å, 4.1 Å, and 4.0 Å, respectively. The model of RAMP1 suggested that Phe93, Tyr 100, and Phe101 form a binding interface for CLR, whereas Trp74 and Phe92 may interact with ligands that bind to the CLR/RAMP1 heterodimer. © 2006 by the Biophysical Society.