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PubMed1982

Universal structural features of prokaryotic and eukaryotic ribosomal 5S RNA derived from comparative analysis of their sequences.

An extensive comparative analysis of more than fifty available sequences of ribosomal 5S RNA has been made. Both for prokaryotic and eukaryotic 5S RNA a generalized secondary structure is presented which is similar to that suggested by Nishikawa and Takemura modified in few positions only. Both generalized secondary structures contain five main helical regions and a high base-pairing content of about 65 +/- 5%. The general structural architecture of prokaryotic and eukaryotic 5S RNA molecules appears to be very similar with minor modifications within particular subgroups of organisms. Conserved and semiconserved nucleotides are accumulated in the single stranded parts of 5S RNA. Functional importance was suggested for some of these regions; other short conserved nucleotide stretches may be involved in the folding of 5S RNA molecules. In particular, we propose a tertiary base-pairing interaction between the universal invariant GUA sequence (positions 76-78 and 75-77 in prokaryotic and eukaryotic 5S RNA, respectively) and the complementary conserved CPuU sequence (positions 38-40 and 36-38) in a parallel manner. A molecular model of the 5S RNA of human KB cells was constructed, which verifies the proposed tertiary interaction, probably stabilizing the two neighboured helices E and D and a stacking arrangement of the bases in the sequence positions 67-108 (and 70-106) in eukaryotic (and prokaryotic) 5S RNAs, respectively.

Animals↗

PubMed1998

Molecular and structural features of the proton-coupled oligopeptide transporter superfamily.

Work in the area of molecular biology of transport proteins has unveiled the presence of a distinct peptide transporter superfamily whose members extend from the prokaryotic to the eukaryotic kingdom. There are two subgroups within this superfamily, one subgroup harnessing the energy necessary for active transport from a transmembrane H+ gradient and the other subgroup relying directly on ATP hydrolysis. In addition to the use of different driving forces, the two subgroups are also distinguishable with regard to molecular structure and operational mechanism. This review is intended to analyze critically the molecular nature of the members of the H+ gradient-dependent peptide transporter subgroup, with emphasis on the cloning strategies utilized in the isolation of the individual transporter cDNAs or genes; on the structural patterns, motifs, and conserved amino acid residues common to constituent members of the subgroup; and on the characteristic topological features of the individual members.

ATP-Binding Cassette Transporters↗

PubMed1994

Cloning of casbene synthase cDNA: evidence for conserved structural features among terpenoid cyclases in plants.

A near-full-length casbene synthase cDNA clone, pCS7, was isolated by using a partial cDNA clone, pCS4, to probe a lambda gt10 library constructed from poly(A)+ RNA from elicited castor bean seedlings. The cDNA insert had a length of 1983 bases with a polyadenylate tail of 19 bases. Translation of the cDNA sequence revealed an open reading frame encoding a 601-aa protein with a predicted M(r) of 68,960. Search of the GenBank data base with the deduced translation product revealed 42% identity and 65% similarity with 5-epi-aristolochene synthase from tobacco and 31% identity and 53% similarity with limonene synthase from spearmint. Each of the three proteins catalyzes an intramolecular cyclization of a prenyl diphosphate substrate to a specific cyclic terpenoid hydrocarbon product. The proposed reaction mechanisms for the three catalytic processes share common chemical features, even though the products being formed are members of three different classes of terpenoid compounds. Analysis of the alignment of the three proteins suggests that both primary and secondary structural elements are conserved. These similarities suggest that the genes that encode terpenoid cyclization enzymes of this type in angiosperms have undergone divergent evolution from an ancestral progenitor gene. In support of this proposition, the locations of five of the six introns in the casbene synthase gene align very closely with those of the five introns in the 5-epi-aristolochene synthase gene.

Amino Acid Sequence↗

PubMed1999

Structural features of the rat GFAP gene and identification of a novel alternative transcript.

The glial fibrillary acidic protein (GFAP) is expressed in a cell-specific manner and represents the major subunit of intermediate filaments of astroglial cells. The knowledge of the gene structure is an important step for further understanding the mechanisms of cell-specific expression. In the present study, we report the complete sequence of the rat GFAP gene and provide evidence for the existence, in the rat brain, of a novel alternative transcript. Since three different transcripts, indicated as GFAPalpha, beta, and gamma, have been previously reported (Feinstein et al. [1992] J. Neurosci. Res. 32:1-14; Zelenika et al. [1995] Mol. Brain Res. 30:251-258), we called this novel mRNA isoform GFAPdelta. It is generated by the alternative splicing of a novel exon located in the classic seventh intron. This alternative exon (called VII+) contains a 101-bp coding sequence in frame with exon VII and interrupted by a stop codon TAA at position +5451. Therefore, the novel GFAPdelta transcript encodes for an hypothetical GFAP where the forty-two carboxy-terminal amino acids encoded by exon VIII and IX are replaced by thirty-three amino acids encoded by exon VII+. Northern blot analysis with a specific probe for exon VII+ revealed a 4.2-kb mRNA, expressed in several brain areas, but absent in extracerebral tissues (lung, heart, kidney, liver, spleen). The previously discovered GFAP isoforms (alpha, beta, and gamma) produce hypothetical translation products differing in the amino-terminal Head domain. The present data suggest, for the first time, the possible existence of GFAP isoforms differing in the carboxy-terminal Tail domain.

Alternative Splicing↗

PubMed1989

Fine structural features of the cerebral microvasculature in hydrocephalic human infants: correlated clinical observations.

Four of 30 human cerebral cortex biopsies from infants ranging from four days to about ten years treated for hydrocephalus by shunt operations are described paying special attention to the vascular structures. The biopsy specimens were studied in semi-thin and ultrathin sections. Attention is drawn to the role of pinocytotic vesicles found in capillaries and smaller vessels as a possible transcellular route for the hydrocephalic oedema resolution. No intercellular dehiscences or the so called blisters were observed. With the passage of time, the number of membrane bound vesicles increased and arrays of pinocytotic vesicles were discernible both on the abluminal as well as luminal aspect of the capillary wall. Additionally, larger vacuoles containing electron-dense material, apparently undergoing autolysis, were also detected. The basal lamina was of uneven thickness and at places duplicated. Hypertrophic pericytes exhibited remarkable oedamatous changes, increased vesicular or vascular transport, demonstrating pericyte brain-barrier dysfunction. Swelling of the astrocytic end-feet bordering the capillaries was remarkable. These findings indicate that the CSF or oedema fluid is absorbed into the vascular system via a transendothelial pathway.

Cerebral Cortex↗

PubMed2002

Structural features of prions explored by sequence analysis. II. A PrP(Sc) model.

Prion diseases are neurodegenerative disorders associated with a conformational conversion of the prion PrP protein, in which the beta strand content increases and that of the a helix decreases. However, the structure of the pathogenous form PrP(Sc), occurring after conformational conversion of the normal cellular form PrP(C), is not yet known. From sequence analysis, we have previously proposed that helix H2 of the prion PrP(C) structure might be a key region for this structural conversion. More recently, we identified the TATA box-binding protein fold as a putative scaffold that may locally satisfy the predicted secondary-structure organisation of PrP(Sc). In the present analysis, we detail the schematic construction of PrP(Sc) monomeric and dimeric models, based on this hypothesis. These models are globally compatible with available data and therefore may provide further insights into the structurally and functionally elusive PrP protein. Some comments are also devoted to a comparison of the yeast Ure2p prion and animal prions.

Amino Acid Sequence↗

PubMed1998

Placental ecto-ATP diphosphohydrolase: its structural feature distinct from CD39, localization and inhibition on shear-induced platelet aggregation.

Human placental ecto-ATP diphosphohydrolase (ATPDase), an 82 kDa single-chain glycoprotein, was purified to high specific activity using a specific murine monoclonal antibody MK33 (IgG1-kappa). Structurally, protein-based analysis showed this enzyme to be almost identical to that of CD39 lymphoid cell activation antigen deduced by cDNA sequencing (Maliszewski CR, et al, J Immunol 1994; 153:3574); but differing in the NH2-terminal amino acid sequence, suggesting that placental ecto-ATPDase is most likely an isoform of CD39 generated by alternative splicing of the pre-mRNA. Functionally, placental ecto-ATPDase totally inhibits the secondary platelet aggregation induced by agonists at a final concentration (f.c.) of 1 microgram/ml. The purified enzyme (1 microgram/ml, final), pre-incubated with washed platelets prior to alpha-thrombin stimulation, completely inhibits the activation of platelet glycoprotein (GP) IIb/IIIa, thereby blocking the binding of fibrinogen or von Willebrand factor to platelets. Further, under different shear stresses, the enzyme modulates platelet aggregation differently. Low shear stress-induced platelet aggregation is blocked by this enzyme in a dose-dependent manner and is totally blocked at f.c. 0.5 microgram/ml. Under high shear stress, however, this protein at a f.c. of 0.5 microgram/ml mediates almost complete disaggregation of platelets without affecting the initial aggregation. Using immunohistochemical analysis, this enzyme was observed to be localized at the syncytiotrophoblasts of placental microvilli and the endothelial cells (ECs) of the umbilical vein obtained at full-term normal delivery, but scarcely at the ECs of the umbilical artery.

Adenosine Triphosphatases↗

PubMed1997

The modern face of prejudice and structural features that moderate the effect of cooperation on affect.

Facial muscle activity and self-reports were examined for racial bias in 3 studies. In the first 2 experiments, While participants imagined cooperating with a Black or White partner. Experiment 1 manipulated reward structure in the context of cooperating with a deficient partner. Experiment 2 manipulated partner deficiency and willingness to expend compensatory effort. On both facial EMG and self-report measures, joint rewards produced more negative affect than independent rewards. However, all partners were liked more when they were willing to try to compensate for their deficits. In addition, more liking was reported for Black partners, but EMG activity indicated bias against Blacks. Experiment 3 investigated individual differences in prejudice. Again, a greater preference for Blacks than Whites occurred on self-report measures, but in their facial muscle activity, high-prejudiced participants exhibited bias against Blacks.

Adult↗

PubMed1984

Antigenic and structural features of goblet-cell mucin of human small intestine.

With the use of a newly developed solid-phase radioimmunoassay method, the major antigenic determinants of human small-intestinal goblet-cell mucin were investigated and related to the overall tertiary structure of the mucin. Preliminary hapten inhibition studies with various oligosaccharides of known sequence and structure suggested that the determinants did not reside in carbohydrate. Exhaustive thiol reduction, however, almost abolished antigenicity, caused breakdown of the mucin into small heterogeneous glycopeptides, and liberated a 'link' peptide of Mr 118000. Western 'blots' of reduced mucin from polyacrylamide gels on to nitrocellulose sheets showed that a small amount of residual antigenicity remained in large-Mr glycopeptides (Mr greater than 200000). The 'link' peptide was not antigenic. Timed Pronase digestion of native mucin resulted in a progressive loss of antigenic determinants. Gel electrophoresis revealed that after 8h of digestion the 118000-Mr peptide had disappeared, whereas antigenicity, which was confined to large-Mr glycopeptides, was destroyed much more slowly with time (70% by 24h, 100% by 72h). Despite the loss of antigenicity, 72h-Pronase-digested glycopeptides retained all of the carbohydrate of the native mucin. Therefore the antibody to human small-intestinal mucin appears to recognize a 'naked' (non-glycosylated and Pronase-susceptible) peptide region(s) of mucin glycopeptides. For full antigenicity, however, disulphide bonds are required to stabilize a specific three-dimensional configuration of the 'naked' region.

Amino Acids↗

PubMed1990

T cell receptor V beta gene usage in a human alloreactive response. Shared structural features among HLA-B27-specific T cell clones.

A strategy, based on using V beta family-specific oligonucleotides, was developed for specific amplification and direct sequencing of human TCR V beta genes. With this strategy, it was possible to undertake a structural analysis of TCRs from human T cell clones in specific responses. 12 HLA-B27-specific cytotoxic clones were examined. The results reveal a nonrandom use of V beta gene diversity in this alloreactive response in that: (a) the clones express a restricted number of V beta segments, including a subset of V beta families that are significantly more related to one another than to most other V beta families; (b) five of seven clones having a particular reaction pattern with HLA-B27 subtypes possess Alanine at the D-J junction; and (c) identical J beta segments are found associated in several instances with identical or highly homologous V beta gene segments. In addition, two new V beta 13 members are reported.

Amino Acid Sequence↗

PubMed1993

Structural features of two T-cell-specific genes that suggest a potential role in HTLV-I-associated pathology.

The Rpt-1 gene product is an intranuclear protein expressed by CD4+ T-cells, which may regulate expression of the interleukin-2 receptor. Structural analysis of Rpt-1 reveals structural motifs that are shared by a group of transcriptional regulatory proteins with oncogenic potential. We suggest that altered expression of Rpt-1 may be associated with HTLV-I-dependent T-cell leukemias.

Amino Acid Sequence↗

PubMed1986

Internal structural features of E. coli glycyl-tRNA synthetase examined by subunit polypeptide chain fusions.

In contrast to most aminoacyl-tRNA synthetases which are monomers or oligomers of a single polypeptide, Escherichia coli glycyl-tRNA synthetase has an alpha-2, beta-2 structure. The enzyme requires both subunits for catalysis of either adenylate or aminoacyl-tRNA synthesis. The head-to-tail arrangement of the alpha- and beta-chain coding regions in the genome suggests that the two-subunit protein may be tantamount to a single chain. We fused the carboxyl terminus of the alpha-chain to the amino terminus of the beta-chain, through a short peptide linker. Five different amino acid substitutions were placed in the linker. In all instances, the fusion polypeptide is stable in maxicell extracts. In a glyS null strain, a gene encoding any of the fusion proteins substitutes for the wild-type gene. Assays confirm that, in vitro, the engineered polypeptide fusion is active to within 2- to 3-fold of the wild-type, unfused chains. Oligomers of the fusion protein are observed and may be required for activity. Because the creation and limited manipulation of the artificial peptide linker region does not destroy the activity, we also conclude that the C-terminal part of the alpha-chain and the amino-terminal part of the beta-chain are not important for activity.

Amino Acyl-tRNA Synthetases↗

PubMed1987

The immunoglobulin heavy chain switch: structural features of gamma 1 recombinant switch regions.

The immunoglobulin heavy chain isotype switch is mediated by a DNA rearrangement involving specific genomic segments referred to as switch regions. Switch regions are composed of tandemly repeated simple sequences. The role of the tandemly repeated structure of switch regions in the switch recombination process is not understood. We mapped eight recombination sites--six in the gamma 1 and two in the gamma 3 tandem arrays. In addition, we obtained molecular clones representing three of the six gamma 1 rearrangements, and determined the nucleotide sequences of the recombination sites in each. In general, the rearrangements are confined to the tandem repeat units, and are not clustered in a particular portion of either the gamma 3 or gamma 1 switch region. Nucleotide sequence analysis of one of the recombinant clones, gamma M35, reveals evidence for a successive switch event wherein a recombination between S mu and S gamma 3 was followed by recombination 57 bp downstream with S gamma 1. gamma 1 sequence data from the molecular clones we obtained, together with similar data from other investigators regarding the gamma 1, gamma 2b, and gamma 2a switch regions, reveals that recombinations tend to occur at homologous positions of the respective gamma-unit repeats, adjacent to the elements AGCT and GGGG found in each. This finding suggests that the cutting and religation step of the recombination process is mediated by a recombinase common to the four gamma-isotypes.

Animals↗

PubMed1985

Experiment acknowledged the Watson-Crick hypothesis: a review of B-DNA double helix structural features at atomic resolution.

The dodecamer d(CGCGAATTCGCG) forms a right-handed B-DNA double helix of a Watson-Crick type both in crystal and solution. It is the first piece of DNA longer than one helix turn whose molecular structure has become known at the atomic resolution. The article reviews qualitative aspects of its structure with a special emphasis on local variations in the disposition of base pairs in the double helix.

Cisplatin↗

PubMed1981

Structural features of PGBX (a prostaglandin polymer) deduced by analogies with dimers derived from 15-keto-prostaglandin B.

The polymeric prostaglandin, PGBX, has a beneficial effect on oxidative phosphorylation of damaged mitochondria in vitro and has manifested interesting effects in vivo. Its chemical structure has been partially elucidated by comparison of its 13C-NMR (nuclear magnetic resonance) spectrum with the spectra of prostaglandin monomers. Reported here is subsequent comparison of PGBX with two prostaglandin dimers derived from 15-keto-PGB1, which provide more complete structural information. The two prostaglandin dimers were synthesized and analyzed by 13C-MNR and by other techniques, with particular attention to positions of linkages between the two monomeric prostaglandin subunits of the dimers. Based on these data, some proposals are presented regarding probable locations of linkages between prostaglandin monomeric subunits in the polymeric PGBX.

Magnetic Resonance Spectroscopy↗

PubMed1992

Topographical requirements for delta opioid ligands: common structural features of dermenkephalin and deltorphin.

We propose a common topographical model for the bioactive conformation of deltorphin and dermenkephalin at the delta opioid receptor. In this model a hydrophilic surface from the N- to C-termini is surrounded by lipophilic residues ("hot dog" structure). The important element that orients the N-terminal tyramine is the interaction of the N-terminal amino group, with the carboxyl group of Asp4 in deltorphin I and with Asp7 through His4 (as a triad) in dermenkephalin. The biological properties of synthetic analogues designed to test this model demonstrate that the hydrophilic amino acid residues of these peptides are interchangeable. In addition, incorporation of Aib residues that change the lipophilic topography of these molecule, strongly reduces affinity for the delta opioid receptor.

Amino Acid Sequence↗

PubMed1993

The unusual metal clusters of nitrogenase: structural features revealed by x-ray anomalous diffraction studies of the MoFe protein from Clostridium pasteurianum.

Nitrogenase (EC 1.18.6.1) catalyzes the conversion of dinitrogen to ammonia, the central reaction of biological nitrogen fixation. X-ray anomalous diffraction data were analyzed to probe the structures of the metal clusters bound by nitrogenase MoFe protein. In addition to one FeMo cofactor, each half-molecule of MoFe protein binds one large FeS cluster of a type not previously observed in a protein. The FeS cluster contains roughly eight Fe atoms, comprises two subclusters, and is separated from the FeMo cofactor by an edge-to-edge distance of 14 A. The inorganic framework of the FeMo cofactor is not resolved into subclusters, but the Mo atom is located at its periphery. FeMo cofactors in different half-molecules are 70 A apart and cannot promote binuclear activation of dinitrogen by two Mo atoms.

Clostridium↗

PubMed1988

Structural features of human monoamine oxidase A elucidated from cDNA and peptide sequences.

Monoamine oxidase (MAO), an important enzyme for the degradation of amine neurotransmitters, has been implicated in neuropsychiatric illness. The amino acid sequence for one form of the enzyme, MAO-A, has been deduced from human cDNA clones and verified against proteolytic peptides. The covalent binding site for the flavin adenine dinucleotide (FAD) cofactor is near the C-terminal region. The presence of features characteristic of the ADP-binding fold suggests that the N-terminal region is also involved in the binding of FAD. These cDNAs should facilitate the study of the structure, function, and intracellular targeting of MAO, as well as the analysis of its expression in normal and pathological states.

Adenosine Diphosphate↗