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PubMed1992

Group G streptococcal M protein exhibits structural features analogous to those of class I M protein of group A streptococci.

We have previously studied a collection of group G streptococcal strains isolated from bacteremic human infections and demonstrated that such strains resist phagocytosis by human polymorphonuclear leukocytes but are type specifically opsonized by homologous antiserum. We have now performed Southern hybridization analysis on genomic DNA from eight blood isolates. All eight isolates showed DNA homology to a group A emm24 gene probe. The M-protein gene of one of the isolates, strain 1750, has now been isolated. This gene (emmG1) encodes a polypeptide of 67 kDa (MG1) which is reactive with antibodies to the partially purified M protein of the parent strain. The predicted amino acid structure of MG1 demonstrates significant identity with the carboxy terminus (C, D, and anchor domains) of M6 and M24 but only limited identity with the amino terminus (variable portion) of these group A M proteins. Southern hybridization of genomic DNA of the eight group G blood isolates with an emmG1 gene probe indicated there were at least four emm alleles associated with these strains. These studies indicate that M proteins of group G streptococci, like those of group A, are genetically heterogeneous. Moreover, MG1 appears to conform to the recently proposed class I structure of M-protein molecules and thus shares certain distinct structural features with the M proteins of well-established rheumatogenic group A streptococcal serotypes. Further comparison of the structures of group G and group A M proteins of throat and skin isolates may cast light on those configurations of the M protein molecules which are and are not critical for the expression of rheumatogenicity.

Amino Acid Sequence↗

PubMed1989

Secondary structural features of the bacteriophage Mu-encoded A and B transposition proteins.

The role of the bacteriophage Mu-encoded A and B proteins is to direct the transposition of Mu DNA. These are the first active DNA transposition proteins to have been purified and their mechanism of action at the biochemical level is under intensive study. Structural studies on these proteins, however, have lagged behind their biochemical characterization. We report here near- and far-u.v. c.d. spectra for these proteins and their secondary structural features derived from these data. The Mu A protein appears to be composed of primarily beta-sheet (40%) with 24% alpha-helix, 9% beta-turn and 27% random coil. In contrast, the Mu B protein contains 55% alpha-helix with only 13% beta-sheet and 3+ beta-turn and 29% random coil. The near-u.v. c.d. spectrum of the A protein was not unusual; however, the profile of the B protein suggested either buried or restricted chromophores within the protein or short-range interactions between aromatic residues.

Circular Dichroism↗

PubMed1992

Structural features and biological activity of xyloglucans from suspension-cultured plant cells.

Different xyloglucan (XG) fractions were isolated from Rubus fruticosus cells cultured in suspension. Sequential extraction showed that two distinct xyloglucans existed in the primary walls. The first could be easily extracted in alkali and the second was tightly associated to cellulose. A third fraction was isolated from the extracellular polysaccharides of the culture medium. The alkali-soluble XG and the extracellular XG showed many structural features in common. By use of an anti-XG polyclonal antibody, electron microscopy examination suggests that the extracellular hemicellulose is progressively released from the wall by a sloughing mechanism. Oligosaccharides prepared from the extracellular XG were purified and their structure examined by FAB-ms technique. When the nonasaccharide was added at low concentrations (10(-5) mg/ml) to the culture medium it was able to elicit several different glycanohydrolase activities associated to the cell wall.

Cells, Cultured↗

PubMed1991

Human pre-interleukin 1 alpha and beta: structural features revealed by limited proteolysis.

Both pre-interleukin 1 alpha and beta (pre IL 1 alpha and beta) are proteolytically processed into extracellular mature forms of IL 1 alpha and beta. Since pre IL 1 alpha is shown to be biologically active, there may be other reasons for the proteolytic processing of IL 1 alpha and presumably, for IL 1 beta also. In order to examine the possibility that structural stabilization may be associated with the proteolytic processing of pre IL 1 alpha and beta, we investigated the structural features of pre IL 1 alpha and beta by the combination of limited proteolysis and immunoprecipitation with antibodies to the NH2-terminal halves or COOH-terminal halves of pre IL 1 alpha or beta. Both trypsin and V8 protease digested the NH2-terminal halves of pre IL 1 alpha and beta more easily than the COOH-terminal halves of pre IL 1 alpha and beta, yielding structurally stabilized "mature" forms of IL 1. Both trypsin and V8 protease yielded a fragment similar in size to mature IL 1 alpha from pre IL 1 alpha. In contrast, trypsin digested pre IL 1 beta into fragments smaller in size than mature IL 1 beta, while V8 protease yielded a fragment similar in size to mature IL 1 beta. Furthermore, mature IL 1 beta, once processed and released from cells, was resistant to trypsin.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1992

The beta subunit of tomato fruit polygalacturonase isoenzyme 1: isolation, characterization, and identification of unique structural features.

We have purified and isolated cDNAs encoding the beta subunit of tomato fruit polygalacturonase isoenzyme 1 (PG1), a cell wall protein that associates with, and apparently regulates, the catalytic PG2 polypeptides. Expression of the beta subunit is fruit specific and temporally separated from the expression of PG2 during fruit development. The 37- to 39-kD beta subunit is encoded as a 69-kD precursor protein containing a signal sequence and two propeptide domains. The mature protein is composed almost entirely of the novel 14-amino acid motif FTNYGxxGNGGxxx in which many of the phenylalanine residues are post-translationally modified. The unique structural features of the motif suggest an important role in the function of the protein and hence in the activity of PG1. The beta subunit may represent a class of bifunctional plant proteins that interact both with structural components of the cell wall and catalytic proteins to localize and/or regulate metabolic activities within the cell wall.

Amino Acid Sequence↗

PubMed1989

Processing endoprotease recognizes a structural feature at the cleavage site of peptide prohormones. The pro-ocytocin/neurophysin model.

Pro-ocytocin/neurophysin convertase is a divalent cation-dependent endoprotease isolated from both bovine corpus luteum and neurohypophyseal secretory granules. The putative pro-ocytocin/neurophysin converting enzyme cleaves the Arg12-Ala13 bonds of both pro-ocytocin/neurophysin (1----20) and pro-ocytocin/neurophysin obtained by hemisynthesis. The minimal efficient substrate structure allowing recognition by this processing endoprotease was defined by measuring its cleavage efficiency and the inhibitory properties of a set of 34 selectively modified derivatives of the (1----20) NH2-terminal domain of the ocytocin/neurophysin precursor. The data demonstrate that: (i) the basic Lys11-Arg12 doublet, although necessary, is not sufficient; (ii) a minimal substrate length of nine amino acids (residues 7-15 or 8-16) is essential; (iii) those amino acids around the Lys-Arg doublet which contribute to the formation of a possible beta-turn-alpha-helix secondary structure are critical; (iv) substrate recognition by the enzyme may involve several subsites in which structural determinants, situated on both sides of the basic doublet, participate; (v) the NH2-terminal sequence of neurophysin plays a critical role in the correct reading of the cleavage sequence by the processing endoprotease. It is proposed, first, that this type of structural feature may constitute the basis of a general coding system for endoproteases involved in the processing of polypeptide hormone precursors; second, that in addition to its role in the intragranular packaging of the nonapeptide hormone, neurophysin plays a key role in the correct processing of its common precursor with ocytocin.

Amino Acid Sequence↗

PubMed1990

Predominant structural features of the cell wall arabinogalactan of Mycobacterium tuberculosis as revealed through characterization of oligoglycosyl alditol fragments by gas chromatography/mass spectrometry and by 1H and 13C NMR analyses.

The peptidoglycan-bound arabinogalactan of a virulent strain of Mycobacterium tuberculosis was per-O-methylated, partially hydrolyzed with acid, and the resulting oligosaccharides reduced and O-pentadeute-rioethylated. The per-O-alkylated oligoglycosyl alditol fragments were separated by high pressure liquid chromatography and the structures of 43 of these constituents determined by 1H NMR and gas chromatography/mass spectrometry. The arabinogalactan was shown to consist of a galactan containing alternating 5-linked beta-D-galactofuranosyl (Galf) and 6-linked beta-D-Galf residues. The arabinan chains are attached to C-5 of some of the 6-linked Galf residues. The arabinan is comprised of at least three major structural domains. One is composed of linear 5-linked alpha-D-arabinofuranosyl (Araf) residues; a second consists of branched 3,5-linked alpha-D-Araf units substituted with 5-linked alpha-D-Araf residues at both branched positions. The non-reducing terminal region of the arabinan was characterized by a 3,5-linked alpha-D-Araf residue substituted at both branched positions with the disaccharide beta-D-Araf-(1----2)-alpha-D-Araf. 13C NMR of intact soluble arabinogalactan established the presence of both alpha- and beta-Araf residues in this domain. This non-reducing terminal motif apparently provides the structural basis of the dominant immunogenicity of arabinogalactan within mycobacteria. A rhamnosyl residue occupies the reducing terminus of the galactan core and may link the arabinogalactan to the peptidoglycan. Evidence is also presented for the presence of minor structural features involving terminal mannopyranosyl units. Models for most of the heteropolysaccharide are proposed which should increase our understanding of a molecule responsible for much of the immunogenicity, pathogenicity, and peculiar physical properties of the mycobacterial cell.

Carbohydrate Conformation↗

PubMed1979

Rat pulmonary circulation after chronic hypoxia: hemodynamic and structural features.

In 55 Sprague-Dawley rats (mean wt, 277 +/- 6.2 g) exposed to hypobaric hypoxia (air at 380 mmHg), and 23 weight-matched controls kept in room air, pulmonary and systemic artery pressures were measured daily for 2 wk via indwelling catheters. After each day of exposure, 1 or 2 hypoxic rats, to a total of 20, and 5 control rats were killed during the experiment. In these rats, the pulmonary arterial tree was injected post mortem with barium-gelatin and inflated with formaldehyde solution, and three structural features were quantified microscopically: 1) abnormal extension of muscle into peripheral arteries where it is not normally present (EMPA); 2) increased wall thickness of the normally muscular arteries, expressed as a percentage of external diameter (%WT); and 3) reduction in artery number expressed as an increase in the ratio of alveoli to arteries (A/a). Mean pulmonary artery pressure (Ppa) rose significantly after day 3 of hypoxic exposure (P less than 0.05) and had doubled by day 14; the mean systemic artery pressure (Psa) of hypoxic rats and Ppa and Psa of control rats were unchanged. The level of Ppa correlated with the degree of structural changes; for EMPA, r = 0.84; for %WT, r = 0.64; and for A/a, r = 0.73 (P less than 0.001 in all.

Animals↗

PubMed2026

Structural Features of DNA in TATA-Containing and TATA-Less Core Promoters of RNA Polymerase II Differ.

Nucleotide motifs in the core promoters of eukaryotic protein-coding genes transcribed by RNA polymerase II (Pol II) play an important role in the transcription process. We analyzed the role of an octanucleotide located in the TATA box position. Depending on whether this octanucleotide can form a complex with the TATA-binding protein (TBP), the promoter is classified as either TATA-containing or TATA-less. We analyzed the differences in the primary and spatial structures, as well as their dynamics, in TATA-containing and TATA-less promoters of mammals and plants. We divided the complete promoter sets of six organisms (H. sapiens, M. musculus, C. familiaris, A. thaliana, Z. mays, and H. vulgare) from the EPDnew database into TATA-containing and TATA-less fractions. The sizes of the TATA-containing promoter fractions are significantly smaller than those of the TATA-less fractions in all studied organisms, except in A. thaliana, where the sizes of both fractions are approximately equal. We characterized promoter architecture using variation profiles of various base-pair step parameters, minor-groove width, and the conformational dynamics of native DNA. The architectures of TATA-containing and TATA-less promoters differ significantly. The possible mechanistic influence of DNA structural features on the formation of the pre-initiation complex (PIC) in both types of promoters is discussed.

Promoter Regions, Genetic↗

PubMed1992

Structural features of the low-molecular-mass human salivary mucin.

The low-molecular-mass human salivary mucin has at least two isoforms, MG2a and MG2b, that differ primarily in their sialic acid and fucose content. In this study, we characterize further these isoforms, particularly their peptide moieties. Trypsin digests of MG2a and MG2b yielded high- and low-molecular-mass glycopeptides following gel filtration on Sephacryl S-300. The larger glycopeptides from MG2a and MG2b had similar amino acid compositions and identical N-terminal sequences, suggesting common structural features between their peptides. An oligonucleotide probe generated from the amino acid sequence of the smaller glycopeptide from MG2a was employed in Northern-blot analysis. This probe specifically hybridized to two mRNA species from human submandibular and sublingual glands. A cDNA clone selected from a human submandibular gland cDNA expression library with antibody generated against deglycosylated MG2a also hybridized to these two mRNA species. In both cases, the larger mRNA was polydisperse, and the hybridization signal was more intense in the sublingual gland. In addition, the N-terminal amino acid sequence of the larger glycopeptide was found to be part of one of the selected MG2 cDNA clones.

Amino Acid Sequence↗

PubMed1989

Constitutive endocytosis of HLA class I antigens requires a specific portion of the intracytoplasmic tail that shares structural features with other endocytosed molecules.

HLA class I antigens present in the human leukemia T-cell line HPB-ALL are shown to be endocytosed in the absence of specific antibodies. In 1 hr, approximately 10% of class I molecules initially present at the cell surface are found intracellularly. Genetically engineered mutants of the HLA-A2 gene lacking exon 6 or 7 or both were used to analyze whether the cytoplasmic region contributes to the internalization. The results indicate that amino acids encoded by exon 7 (spanning amino acid residues 323-340) are required for internalization, while deletion of exon 6 had no effect. In addition, a comparison of the cytoplasmic sequences of receptors that are known to be internalized via coated pits and the present data revealed that they share a structural feature that could constitute a specific signal required for endocytosis.

Antigen-Antibody Complex↗

PubMed1988

Charybdotoxin block of Shaker K+ channels suggests that different types of K+ channels share common structural features.

Charybdotoxin (CTX), a 37 amino acid protein isolated from the venom of L. quinquestriatus, is a high-affinity blocker of various Ca2(+)-activated K+ channels. CTX also blocks Drosophila Shaker (Sh) clone H4 transient K+ currents expressed in Xenopus oocytes with similar affinity (Kd = 3.6 nM). CTX blocks both the open and the closed states of Sh channels with no apparent change in gating behavior. In addition, the block is enhanced as the ionic strength is lowered. These properties are identical to those of CTX block of Ca(+)-activated K+ channels, and these results suggest that the external pore openings of these two functionally dissimilar K+ channels may share common structural features.

Animals↗

PubMed1992

Terminal disorder: a common structural feature of the axial proteins of bacterial flagellum?

We report, based on proteolytic experiments and high resolution 1H nuclear magnetic resonance studies that the terminal regions of the monomeric hook protein are highly mobile and exposed to the solvent. The disordered parts of the hook protein span approximately the first 70 and the last 30 amino acid residues. Although the amino acid sequences of flagellin and hook protein do not resemble each other at all, both proteins have now been shown to contain large disordered terminal regions. Sequential similarities of flagellin and hook protein, especially near the NH2 and COOH termini, to other axial components of bacterial flagellum suggest that terminal disorder may be a common structural feature of the axial proteins of the bacterial flagellum.

Amino Acid Sequence↗

PubMed1989

Isolation of mouse CD44 cDNA: structural features are distinct from the primate cDNA.

CD44 is a glycoprotein that participates in adhesion of lymphocytes to high endothelial cells of lymph organs and likely functions in other intercellular adhesions as well. We have isolated a mouse CD44 cDNA by polymerase chain reaction amplification of cDNA synthesized from total cellular RNA isolated from 38C-13, a B-lymphocyte cell line. The oligonucleotide sequences were based at the 5' end on the baboon CD44 sequence upstream of and including the translation initiator ATG and at the 3' end on a mouse CD44 sequence that was determined from a rare, incomplete cDNA clone. The mouse CD44 DNA sequence is similar to the baboon CD44 sequence but has structural features that are distinct. The external domain has a region that is only 35% similar between the mouse and primate proteins, in contrast to 85%-90% similarity in the rest of the sequence. In addition, just upstream from the predicted cleavage site of the leader peptide, nucleotide insertions result in the addition of two or four amino acids, depending upon the mouse strain. An amino acid replacement between two strains carrying different CD44 (also called Pgp-1) allotypes is likely responsible for the Pgp-1 polymorphism. The most striking aspect of mouse CD44 is that the RNA does not fractionate with polyadenylylated RNA, unlike the CD44 RNA in human, baboon, rat, and chicken.

Amino Acid Sequence↗

PubMed1985

Structural features of rat epididymal epithelial cells in vitro.

Epididymal epithelial fragments, free of stromal elements were isolated from mature rats using two sequential collagenase digestions. Within 24 h these attached efficiently to a variety of substrates including glass, plastic, placental collagen, type IV collagen and epididymal extracellular matrix material. Cells spreading away from the fragments rapidly assumed a flattened, overlapping, monolayer appearance typical of epithelial cells in culture. Cells still associated with the fragments or adjacent to them remained more polarized and more closely resembled epididymal principal cells in vivo than did cells that had migrated to the periphery of the monolayer. Apical microvilli characteristic of these cells in vivo were common during the first 4 days in culture but diminished in number and size thereafter. Cultured cells maintained many of the structural features characteristic of principal cells in vivo, including a well developed Golgi apparatus, coated pits and vesicles, and many multivesicular bodies. An extensive filamentous network, shown immunocytochemically to consist of keratin, was present in the cytoplasm of all cells but was more obvious in flattened cells at the periphery of the monolayer. Rhodamine phalloidin labelling of filamentous actin showed that concentrations of actin occurred corresponding to microvilli on the apical surface, in a continuous ring just below the apical surface, and also in stress fibres at the base of the cells. Cells isolated and cultured from the distal caput epididymidis possessed lobulated nuclei, in contrast to the round or oval nuclei found in cells cultured from the proximal caput epididymidis. Cells from the distal caput epididymidis were also characterized by the presence of many lipid droplets in their cytoplasm. Autofluorescent granules were observed in epithelial cells from both regions but were larger and more numerous in cells isolated from the distal caput epididymidis. Tritiated thymidine incorporation by the cells after 4 days in culture showed that cells adjacent to the parent epithelial fragment were dividing at a greater rate than cells that had migrated to the periphery of the monolayer.

Actins↗

PubMed1986

Proto-oncogene c-ros codes for a molecule with structural features common to those of growth factor receptors and displays tissue specific and developmentally regulated expression.

A recombinant DNA clone containing cellular sequences homologous to the transforming sequence, v-ros, of avian sarcoma virus UR2 was isolated from a chicken genomic DNA library. Heteroduplex mapping and nucleotide sequencing reveal that the v-ros sequences are distributed in nine exons ranging from 65 to 204 nucleotides on cellular ros (c-ros) DNA over a range of 11 kilobases. Comparison of the deduced amino acid sequences of c-ros and v-ros shows two differences: v-ros contains a three-amino-acid insertion within the hydrophobic domain presumed to be involved in membrane association, and (ii) the carboxyl 12 amino acids of v-ros are completely different from those of the deduced c-ros sequence. The deduced amino acid sequence of c-ros bears striking structural features similar to those of insulin and epidermal growth factor receptors, including the presumed hydrophobic membrane binding domain, amino acids flanking the domain, and the distance between the domain and the catalytic region of the kinase activity. The expression of c-ros appears to be under a very stringent control. When tissues at various stages of chicken development were analyzed, only kidney was found to contain a significant level of c-ros RNA. The level of c-ros RNA in kidney tissue is most abundant in 7- to 14-day-old chickens. Finally, nucleotide sequences of c-ros DNA and UR2-associated helper viral genome at regions corresponding to the gag ros recombination site suggest that the junction has been formed by RNA splicing.

Amino Acid Sequence↗

PubMed1991

Sequence analysis of the S RNA of the African arenavirus Mopeia: an unusual secondary structure feature in the intergenic region.

Mopeia virus is an apparently nonpathogenic African arenavirus which can protect animals from subsequent challenge by the closely related Lassa virus. As a step toward understanding these differences in pathogenicity and the means by which Mopeia virus infection can protect against subsequent Lassa virus infection, cDNA clones corresponding to 3419 nucleotides of Mopeia virus S RNA were isolated and sequenced. Two open reading frames, encoding the glycoprotein precursor (GPC) and nucleocapsid (N) proteins, were located in the ambisense arrangement characteristic of the arenaviruses. Comparison of the amino acid sequences of the translation products with those of two Lassa virus strains showed considerable conservation, with 74 and 80% identity for the two glycoproteins G1 and G2, and 74% identity for the N protein. The putative dibasic site of GPC cleavage (R-R) was conserved, as were the potential N-linked glycosylation sites. A striking difference between Mopeia virus and Lassa virus was identified in the noncoding intergenic region. Instead of the single hairpin structure formed by base-pairing of complementary sequences which is usually found, the Mopeia virus S RNA has the potential to form two hairpins. These hairpins were similar in sequence and may have been formed in a duplication event during RNA replication. The possible contribution of this secondary structure feature to differences in pathogenicity between Mopeia and Lassa viruses is discussed.

Amino Acid Sequence↗

PubMed1992

The sequence HGLGHGHEQQHGLGHGH in the light chain of high molecular weight kininogen serves as a primary structural feature for zinc-dependent binding to an anionic surface.

The histidine-glycine-rich region of the light chain of cleaved high molecular weight kininogen (HK) is thought to be responsible for binding to negatively charged surfaces and initiation of the intrinsic coagulation, fibrinolytic, and kinin-forming systems. However, the specifically required amino acid sequences have not been delineated. An IgG fraction of a monoclonal antibody (MAb) C11C1 to the HK light chain was shown to inhibit by 66% the coagulant activity and by 57% the binding of HK to the anionic surface of kaolin at a concentration of 1.5 microM and 27 microM, respectively. Proteolytic fragments of HK were produced by successive digestion with human plasma kallikrein and factor XIa (FXIa). Those polypeptides that bound tightly (Kd = 0.77 nM) to a C11C1 affinity column were eluted at pH 3.0 and purified by membrane filtration. On 15% SDS polyacrylamide electrophoresis, the approximate M(r) was 7.3 kDa (range 6.2-8.1 kDa). Based on N-terminal sequencing, this polypeptide (1(2)), which extends from the histidine residue 459 to a lysine at position 505, 509, 511, 512, 515, or 520, inhibits by 50% the coagulant activity expressed by HK at a concentration of 22 microM. The synthetic peptide HGLGHGH representing the N-terminal of the 1(2)) fragment was synthesized, tested, and found at 4 mM to inhibit the procoagulant activity of HK 50%. A synthetic heptadecapeptide, HGLGHGHEQQHGLGHGH (residues 459-475) included within the 1(2) fragment, and with the ability to bind zinc, inhibited 50% of the HK coagulant activity at a concentration of 325 microM in the absence and presence of added Zn2+ (30 microM). The specific binding of 125I-HK to a negatively charged surface (kaolin) was inhibited 50% by unlabeled HK (5 microM). HGLGHGH, at a concentration of 7.0 mM, inhibited the binding to kaolin by 50%. The heptadecapeptide inhibited the specific binding of 125I-HK to kaolin by 50%, at a concentration of 2.3 mM, in the absence of Zn2+. In contrast, when Zn2+ was added, the concentration to achieve 50% inhibition decreased to 630 microM, indicating that Zn2+ was required to attain a favorable conformation for binding. Moreover, the 1(2) fragment was found to inhibit 50% of the 125I-HK binding to kaolin at a concentration of 380 microM. These results suggest that residues contained within the 1(2) fragment, notably HGLGHGHEQQHGLGHGH, serves as a primary structural feature for binding to a negatively charged surface.

Amino Acid Sequence↗