Ovomucoid intervening sequences specify functional domains and generate protein polymorphism

Two thirds of the natural chicken ovomucoid gene has been sequenced, including all exons and the intron sequences surrounding all fourteen intron/ exon junctions. The junction sequences surrounding four of the introns are redundant; however, the sequences surrounding the other three introns contain no redundancies and thus the splicing sites at either end of these three introns are unambiguous. The splicing in all cases conforms to the GT-AG rule. The ovomucoid gene sequence around intron F can be used to predict the cause of an internal deletion polymorphism in the ovomucoid protein, which is an apparent error in the processing of the ovomucoid pre-mRNA. We also compare the structural organization of the ovomucoid gene with the ovomucoid protein sequence to examine theories of the evolution of ovomucoids as well as the origin of intervening sequences. This analysis suggests that the present ovomucoid gene evolved from a primordial ovomucoid gene by two separate intragenic duplications. Furthermore, sequence analyses suggest that introns were present in the primordial ovomucoid gene before birds and mammals diverged, about 300 million years ago. Finally, the positions of the introns within the ovomucoid gene support the theory that introns separate gene segments that code for functional domains of proteins and provide insight on the manner by which eucaryotic genes were constructed during the process of evolution.     

PEGylated Nanoparticles based on a polyaspartamide. preparation, physico-chemical characterization, and intracellular uptake

Nanoparticles with different surface PEGylation degree were prepared by using as starting material alpha,beta-poly(N-2-hydroxyethyl)-d,l-aspartamide (PHEA). PHEA was functionalized with a PEG amino-derivative for obtaining PHEA-PEG(2000) copolymer. Both PHEA and PHEA-PEG(2000) were derivatized with methacrylic anhydride (MA) for obtaining poly(hydroxyethylaspartamide methacrylated) (PHM) and poly(hydroxyethylaspartamide methacrylated)-PEGylated (PHM-PEG(2000)), respectively. Nanoparticles were obtained by UV irradiation of an inverse microemulsion, using as internal phase an aqueous solution of PHM alone or of the PHM/PHM-PEG(2000) mixture at different weight ratio and as external phase a mixture of propylene carbonate and ethyl acetate. Obtained nanoparticles were characterized by FT-IR analysis, dimensional analysis, and TEM micrography. XPS analysis and zeta potential measurements demonstrated the presence of PEG onto the nanoparticle surface. Moreover, the partial degradation of nanoparticles in the presence of esterase as a function of time was demonstrated. Finally, nanoparticles did not possess any cytotoxic activity against K-562 cells and were able to escape from phagocytosis depending on the surface PEGylation degree.     

Ovomucoid third domains from 100 avian species: isolation, sequences, and hypervariability of enzyme-inhibitor contact residues

Ovomucoids were isolated from egg whites of 100 avian species and subjected to limited proteolysis. From each an intact, connecting peptide extended third domain was isolated and purified. These were entirely sequenced by single, continuous runs in a sequencer. Of the 106 sequences we report (five polymorphisms and chicken from the preceding paper [Kato, I., Schrode, J., Kohr, W. J., & Laskowski, M., Jr. (1986) Biochemistry (preceding paper in this issue)]), 65 are unique. In all cases except ostrich (which has Ser45), the third domains are either partially or fully glycosylated at Asn45. The majority of the third domain preparations we isolated are carbohydrate-free. Alignment of the sequences shows that their structurally important residues are strongly conserved. On the other hand, those residues that are in contact with the enzyme in turkey ovomucoid third domain complex with Streptomyces griseus proteinase B [Read, R., Fujinaga, M., Sielecki, A. R., & James, M. N. G. (1983) Biochemistry 22, 4420-4433] are not conserved but instead are by far the most variable residues in the molecule. These findings suggest that ovomucoid third domains may be an exception to the widely accepted generalization that in protein evolution the functionally important residues are strongly conserved. Complete proof will require better understanding of the physiological function of ovomucoid third domains. This large set of variants differing from each other in the enzyme-inhibitor contact area and augmented by several high-resolution structure determinations is useful for the study of our sequence to reactivity (inhibitory activity) algorithm. It is also useful for the study of several other protein properties. In the connecting peptide fragment most phasianoid birds have the dipeptide Val4-Ser5, which is absent in most other orders. This dipeptide is often present in only 70-95% of the molecules and appears to arise from ambiguous excision at the 5' end of the F intron of ovomucoid. Connecting peptides from the ovomucoids of cracid birds contain the analogous Val4-Asn5 peptide. In laughing kookaburra ovomucoid third domain we found (in 91% of the molecules) Gln5A, which we interpret as arising from ambiguous intron excision at the 3' end of the F intron.     

Semisynthetic preparation of N-glycolylneuraminic acid containing GM1 ganglioside: chemical characterization, physico-chemical properties and some biochemical features

N-Glycolylneuraminic acid containing GM1, GM1(NeuGc), was prepared by semisynthetic procedure. The procedure makes use of GM1 ganglioside deacetylated at the level of sialic acid residue (deAc-GM1) and of 1,3-dioxalan-2,4-dione. DeAc-GM1 is prepared from GM1 by alkaline hydrolysis in the presence of tetramethylammonium hydroxide and the glycolylating compound by reaction of glycolic acid with phosgene in dioxane, followed by cyclization under vacuum. Mass spectrometric and nuclear magnetic resonance spectroscopy analyses clearly indicated the presence, in the neosynthesized ganglioside of a glycolic group in the sialic acid residue. Laser-light scattering measurements show that GM1(NeuGc) aggregates in aqueous media being present in solution as micelles with a molecular weight of 576,000 and a hydrodynamic radius of 62.4 A as determined at 25 degrees C. GM1(NeuGc) promotes neurite outgrowth in N-2a cells to a similar degree as GM1(NeuAc), but shows different behaviour under treatment with sialidase from Arthrobacter ureafaciens.     

Caspases: preparation and characterization

Caspases and their involvement in programmed cell death have been an area of significant interest since their initial identification in 1992. To facilitate the search for new components involved in cell death, and to aid researchers in understanding the interactions between currently known cell death proteins, we describe a number of techniques commonly used in the preparation and characterization of caspases.     

Unusual wax esters and glycolipids: Biocatalytical formation and physico-chemical characterization

By aid of lipases, e.g. of Mucor michei, in n-hexane wax esters were produced from usual primary fatty alcohols and unusual hydroxy fatty acids (in part of microbial origin). Thus, (S)-17-hydroxyoctadecanoic acid dodecyl ester and (R)-3-hydroxy decanoic acid dodecyl ester were formed. In measurements of the film pressure using a LANGMUIR film balance the monolayers of both compounds indicated good stability compared to the non-hydroxy wax esters. Glycolipids de novo produced by microorganisms did not show suitable wetting properties, but they were able to lower ze surface tension of water to a higher extent than the unusual waxes.     

Target-sensitive immunoliposomes: preparation and characterization

A novel target-sensitive immunoliposome was prepared and characterized. In this design, target-specific binding of antibody-coated liposomes was sufficient to induce bilayer destabilization, resulting in a site-specific release of liposome contents. Unilamellar liposomes were prepared by using a small quantity of palmitoyl-immunoglobulin G (pIgG) to stabilize the bilayer phase of the unsaturated dioleoylphosphatidylethanolamine (PE) which by itself does not form stable liposomes. A mouse monoclonal IgG antibody to the glycoprotein D of Herpes simplex virus (HSV) and PE were used in this study. A minimal coupling stoichiometry of 2.2 palmitic acids per IgG was essential for the stabilization activity of pIgG. In addition, the minimal pIgG to PE molar ratio for stable liposomes was 2.5 X 10(-4). PE immunoliposomes bound with HSV-infected mouse L929 cells with an apparent Kd of 1.00 X 10(-8) M which was approximately the same as that of the native antibody. When 50 mM calcein was encapsulated in the PE immunoliposomes as an aqueous marker, binding of the liposomes to HSV-infected cells resulted in a cell concentration dependent lysis of the liposomes as detected by the release of the encapsulated calcein. Neither uninfected nor Sendai virus infected cells caused a significant amount of calcein release. Therefore, the release of calcein from PE immunoliposomes was target specific. Dioleoylphosphatidylcholine immunoliposomes were not lysed upon contact with infected cells under the same conditions, indicating that PE was essential for the target-specific liposome destabilization.(ABSTRACT TRUNCATED AT 250 WORDS)     

Acetylglucagon: preparation and characterization.

Acetylated derivatives of glucagon have been prepared by reacting this hormone under various conditions with acetic anhydride. They have been chemically characterized by the use of a 14C-labeled reagent, by peptide mapping techniques following hydrolysis by pronase and chymotrypsin, and by spectroscopy. Acetylation in sodium acetate (pH 5.5) results in a full substitution of the alpha-amino group of the N-terminal histidyl residue, but in a partial (about 0.3 acetyl group per residue) substitution of the epsilon-amino group of the lysyl residue 12. The monosubstituted (on the alpha-amino group) and the disubstituted (on both amino groups) acetylated components have been separated by chromatography on DEAE-cellulose and CM-cellulose. Acetylation in sodium bicarbonate (pH 8.0) results in a complete substitution of both amino groups and of the hydroxyl groups of the tyrosyl residues 10 and 13. Complete deacetylation of the O-acetyltyrosyl residues occurs upon treatment with hydroxyl-amine. Mono, di and tetraacetylglucagon are homogeneous when analyzed by disc gel electrophoresis; di and tetrasubstituted derivatives show an increased mobility towards the anode. 125I-labeled derivatives of acetylglucagon show higher distribution coefficients in the aqueous two-phase dextran/poly(ethylene glycol) system than do similar derivatives of glucagon. Acetylation decreases in parallel the ability of glucagon to stimulate the activity of adenylate cyclase and to bind to its receptors in liver cell membranes of the rat. The biological potencies of the mono, di and tetrasubstituted derivates are, respectively, about 10, 1 and 0.1% that of native glucagon. The binding properties of the material dissociated from the acetylglucagon-receptor complex suggest that the reduction in biological activity results from a decrease in the intrinsic affinity of the modified glucagon for the receptors, as well as from the presence of small amounts of residual, unreacted glucagon. Studies with 125I-labeled derivatives of glucagon indicate that acetylation decreases the rate of association and increases the rate of dissociation of the hormone-receptor complex.     

Histone-binding domains: Strategies for discovery and characterization

Chromatin signaling dynamics fundamentally regulate eukaryotic genomes. The reversible covalent post-translational modification (PTM) of histone proteins by chemical moieties such as phosphate, acetyl and methyl groups constitutes one of the primary chromatin signaling mechanisms. Modular protein domains present within chromatin-regulatory activities recognize or “read” specifically modified histone species and transduce these modified species into distinct downstream biological outcomes. Thus, understanding the molecular basis underlying PTM-mediated signaling at chromatin requires knowledge of both the modification and the partnering reader domains. Over the last ten years, a number of innovative approaches have been developed and employed to discover reader domain binding events with histones. Together, these studies have provided crucial insight into how chromatin pathways influence key cellular programs. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.     

Design,preparation, and characterization of mixed dimers of inducible nitric oxide synthase oxygenase domains

A limitation of site-directed mutagenesis of homodimeric proteins is that both subunits will carry the same mutation. We have devised a way to prepare mixed dimers, in which only one chain bears a desired mutation, or each chain can bear a different mutation. Using the inducible nitric oxide oxygenase domain as a model, our strategy focused on the co-expression of two differentially tagged versions of the oxygenase domain, with isolation of the desired mixed dimer in two chromatography steps. We evaluated expression vectors encoding polyhistidine (His(6)), cellulose binding domain, glutathione-S-transferase, and polyglutamate (Glu(7))-tagged versions of the oxygenase domain for satisfactory levels of soluble protein expression and for their ability to form mixed dimers. The combination of His(6)- and Glu(7)-tagged subunits was successful in both respects, and the mixed dimers could be separated from either form of homodimer by sequential immobilized metal affinity chromatography and anion exchange chromatography. The UV-Vis spectrum, substrate binding properties, and enzymatic activity were not altered in the mixed dimer wild-type (His(6)/Glu(7)) compared to the two homodimers (His(6)/His(6) and Glu(7)/Glu(7)). We then characterized a mixed dimer variant in which one chain contained an E371A substitution (which prevents binding of the substrate L-arginine) while the other subunit was left unaltered. This species binds L-arginine and has about one-half the activity of the wild-type homodimer. Mutants known to destabilize the iNOS dimer (E411A, D454A, and W188F) were also investigated; in these cases co-expression with the wild-type subunit did not lead to the formation of stable mixed dimers.     

Low-pH-sensitive PEG-stabilized plasmid-lipid nanoparticles: preparation and characterization

The acid-labile poly(ethyleneglycol)-diorthoester-distearoylglycerol lipid (POD), was used with a cationic lipid-phosphatidylethanolamine mixture to prepare stabilized plasmid-lipid nanoparticles (POD SPLP) that could mediate gene transfer in vitro by a pH triggered escape from the endosome. Nanoparticles of 60 nm diameter were prepared at pH 8.5 using a detergent dialysis method. The DNA encapsulation efficiency in the nanoparticles was optimal between 10 and 13 mol % ratio of cationic lipid and at a POD content of 20 mol %. The apparent zeta potential of the nanoparticles at 1 mM salt and pH 7.5 was positive, indicating cationic lipid on the external surface. However, the external layer of the nanoparticles was depleted in the cationic component compared to the starting mole ratio. Low pH sensitivity of the POD SPLP was characterized by a lag phase followed by a rapid collapse; at pH 5.3 the nanoparticles collapsed in 100 min. Nanoparticles prepared from a pH-insensitive PEG-lipid, PEG-distearoylglycerol had similar physicochemical characteristics as the POD SPLP but did not collapse at low pH. The POD SPLP had up to 3 orders of magnitude greater gene transfer activity than did the pH-insensitive nanoparticles. Both the pH-sensitive and pH-insensitive nanoparticles were internalized to a qualitatively similar extent in a punctate pattern into cultured cells within 2 h of incubation with the cells; thus, increased gene transfer of the POD SPLP was due to a more rapid escape from the endosome rather than to greater cell association of these nanoparticles. These results suggest that the pH-sensitive stabilized plasmid-lipid nanoparticles may be a useful component of a synthetic vector for parenterally administered gene therapy.     

Cobalt cytochrome C: preparation of characterization

Cobalt cytochrome c has been prepared from porphyrin cytochrome c in water/acetic acid solvent. The dominant band in the electrophoresis of the product at pH7 has the same mobility as the native protein. Dithionite changes the ultraviolet/visible spectrum markedly and generates an epr signal with cobalt hyperfine and other superhyperfine features. Nitric oxide removes part of the epr signal. Fractionation on Amberlite CG-50 under NaCl gradient at pH8.0 yields two major components distinguished by their rates of reactivity to dithionite and electrophoretic mobility. Cobalt cytochrome c is reduced by DPNH cytochrome c reductase to produce the same electron paramagnetic resonance signal as that generated by dithionite.     

Fractional and physico-chemical characterization of hemicelluloses from ultrasonic irradiated sugarcane bagasse

The present study was undertaken to investigate the extractability of the hemicelluloses from bagasse obtained by ultrasound-assisted extraction methods. The results showed that the ultrasonic treatment and sequential extractions with alkali and alkaline peroxide under the conditions given led to a release of over 90% of the original hemicelluloses and lignin. This fact as well as the sugar composition and structural features of the isolated seven hemicellulosic fractions indicated that ultrasonication attacked the integrity of cell walls, cleaved the ether linkages between lignin and hemicelluloses, and increased accessibility and extractability of the hemicelluloses. Increasing alkali concentration from 0.5 to 2M and alkaline peroxide percentage from 0.5% to 3.0% resulted in degradation of hemicellulosic backbone as shown by a decrease in their molecular weights from 43,580 to 14,470 and 30,180 to 18,130gmol(-1), respectively. However, there were no significant differences in the structural features of the seven sequential alkali- or alkaline peroxide-soluble hemicellulosic fractions, which are composed mainly of L-arabino-(4-O-methyl-D-glucurono)-D-xylans. Ferulic and p-coumaric acids were found to be chemically linked with hemicelluloses.     

Identification and characterization of structural domains of human ERp57: association with calreticulin requires several domains

The amino acid sequence of ERp57, which functions in the endoplasmic reticulum together with the lectins calreticulin and calnexin to achieve folding of newly synthesized glycoproteins, is highly similar to that of protein disulfide isomerase (PDI), but they have their own distinct roles in protein folding. We have characterized the domain structure of ERp57 by limited proteolysis and N-terminal sequencing and have found it to be similar but not identical to that of PDI. ERp57 had three major protease-sensitive regions, the first of which was located between residues 120 and 150, the second between 201 and 215, and the third between 313 and 341, the data thus being consistent with a four-domain structure abb'a'. Recombinant expression in Escherichia coli was used to verify the domain boundaries. Each single domain and a b'a' double domain could be produced in the form of soluble, folded polypeptides, as verified by circular dichroism spectra and urea gradient gel electrophoresis. When the ability of ERp57 and its a and a' domains to fold denatured RNase A was studied by electrospray mass analyses, ERp57 markedly enhanced the folding rate at early time points, although less effectively than PDI, but was an ineffective catalyst of the overall process. The a and a' domains produced only minor, if any, increases in the folding rate at the early stages and no increase at the late stages. Interaction of the soluble ERp57 domains with the P domain of calreticulin was studied by chemical cross-linking in vitro. None of the single ERp57 domains nor the b'a' double domain could be cross-linked to the P domain, whereas cross-linking was obtained with a hybrid ERpabb'PDIa'c polypeptide but not with ERpabPDIb'a'c, indicating that multiple domains are involved in this protein-protein interaction and that the b' domain of ERp57 cannot be replaced by that of PDI.     

Anticancer double lipid prodrugs: liposomal preparation and characterization

The escape of encapsulated anticancer drugs from liposomes by passive diffusion often leads to suboptimal drug concentrations in the cancer tissue, therefore calling for effective trigger mechanisms to release the drug at the target. We investigated mixtures of lipid components that not only form stable liposomes, but also can be turned into active drugs by secretory phospholipase A? (sPLA?), an enzyme that is upregulated in various cancer cells, without the necessity for conventional liposome drug loading. The liposomes are composed of a novel lipid-based retinoid prodrug premixed with saturated phospholipids. The prodrug is found to be miscible with phospholipids, and the lipid mixtures are shown to form liposomes with the desired size distribution. The preparation procedure, phase behavior, and physicochemical properties of the formed liposomes are described as a function of lipid composition. We show that the premixing of the prodrug with phospholipids can be used to modify the physicochemical properties of liposomal formulations. The results should prove useful for further exploration of the potential for using these novel lipid prodrugs in liposomal formulations for cancer treatment.     

Phosphoroselenoate oligodeoxynucleotides: synthesis, physico-chemical characterization, anti-sense inhibitory properties and anti-HIV activity.

Oligodeoxynucleotides with a phosphorus atom in which one of the non-bridging oxygen atoms is substituted by selenium were prepared and investigated with respect to their antisense properties. A general synthesis of phosphoroselenoate analogs of oligonucleotides is described using potassium selenocyanate as the selenium donor. The compounds, characterized by 31P NMR, were shown to decompose to phosphate with a half-life of ca. 30 days. Melting temperatures of duplexes between poly(rA) or poly(rI) with oligo(dT) and oligo(dC), respectively, indicate diminished hybridization capability of phosphoroselenoate oligomers relative to both the unmodified phosphodiester oligomers and the phosphorothioate congeners. A phosphoroselenoate 17-mer is a sequence specific inhibitor of rabbit beta-globin synthesis in wheat germ extract and in injected Xenopus oocytes. In contrast phosphoroselenoate analogs are potent non-sequence specific inhibitors in rabbit reticulocyte lysate. In vitro HIV assays were carried out on a phosphoroselenoate sequence and compared with a phosphorothioate analogue that has previously been shown to exhibit anti-HIV activity (Matsukura et al., Proc. Natl. Acad. Sci. (1987) 84, 7706-7710). The phosphoroselenoate was somewhat less active, and was much more toxic to the cells.