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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↗

PubMed1990

Structural features of the cytoplasmic region of CD4 required for internalization.

CD4, the T cell surface antigen, is phosphorylated and internalized when T cells are activated or treated with a phorbol ester, PMA. The actual phosphorylation sites have been identified and the role of phosphorylation of each on CD4 internalization investigated. Seven different mutants, in each of which one, two or all three of the serine residues of the cytoplasmic region was modified to alanine(s) (CD4.SA mutants) and one mutant in which the whole amino acid sequence from Gln421 to the C-terminal Ile433 was changed (CD4.EP mutant) were constructed and used to determine the effect of phosphorylation on CD4 internalization. Ser408 was the most efficiently phosphorylated by PMA treatment, Ser415 next and Ser431 to a minor extent. The effect of mutation on internalization was well matched with the effect on extent of phosphorylation, i.e. Ser408 was the residue most important for internalization. However, complete inhibition of CD4 internalization was achieved only by mutating all three serine residues. Interestingly, the mutant CD4.EP in which Ser408 was present and phosphorylated was not measurably internalized, suggesting that phosphorylation of Ser408 induces CD4 internalization only when other structural features of the cytoplasmic domain remain intact. In addition, the data suggest the existence of an additional minor pathway for CD4 internalization which is phosphorylation independent.

Amino Acid Sequence↗

PubMed1992

Structural features of the pore formed by Staphylococcus aureus alpha-toxin inferred from chemical modification and primary structure analysis.

Staphylococcus aureus alpha-toxin makes cells and model membranes permeable to ions and uncharged molecules by opening oligomeric pores of uniform size. Its primary sequence reveals peculiar features which give some hints on the structure of the pore. A flexible region separating the toxin into two halves, several amphiphilic beta-strands and two amphiphilic alpha-helices long enough to span the hydrophobic core of the lipid bilayer are predicted. In analogy to bacterial porins, we propose that the inner walls of the pore are, at least in part, built by an amphiphilic beta-barrel. The model is consistent with circular dichroism data and with the electrophysiological properties of the pore. Functional information on this toxin were obtained by chemical modification of its four histidine residues. Specific carbethoxylation suggested they have different roles: one is required for specific receptor binding, one for oligomerisation and two for unspecific lipid binding. A tentative assignment of each histidine to its specific role is done on the basis of the structural predictions. A functionally related hemolysin, Aeromonas hydrophyla aerolysin, reveals remarkably similar features including the presence and location of histidines involved in receptor binding and oligomerisation.

Bacterial Toxins↗

PubMed1977

[Structural features of the brain stem reticular formation, hippocampus and limbic region of the cortex].

The paper compares the structural reorganization of reticular formation of the brain stem with the cortical structures of the limbic system--hippocamp and limbic cortex in the mammalian comparative order (a hedgehog, a rabbit, a cat, a dog, a dolphin, a monkey, a man). In all the studied links of the limbico-reticular system the author revealed general regularity: the main trend of a structural development is expressed in the intensification of their structural heterogeneity: nuclei are divided in subnuclei, areas in subareas, layers in sublayers. In all structures these features are expressed more vividly in their phylogenetic new parts. Besides, changes of the brain caudal sections--reticular formation are relatively less expressed than the rostral sections, i.e. hippocamp and limbic cortex.

Animals↗

PubMed1989

Short and long spacer sequences and other structural features of zinc binding sites in zinc enzymes.

The crystal structures of eleven zinc enzymes have served to identify common features of their Zn binding sites. Two of them have non-catalytic Zn sites, both of which contain four cysteine ligands closely spaced in the linear sequence of the protein with no bound water. In contrast, all the catalytic Zn sites have three protein ligands and, in addition, one coordinated, 'activated' water. Histidine is the predominant ligand. The spacing between the first two ligands (1-3 amino acids), the short spacer, ensures a nucleus for Zn binding. The third ligand, separated by from approximately 20 to approximately 120 amino acids, the long spacer, not only completes the coordination but also aligns protein residues for interaction with the substrate. The short and long spacing observed for catalytic zinc sites may also pertain to Fe and Cu proteins.

Binding Sites↗

PubMed1987

Structural features which distinguish estrogen agonists and antagonists.

The molecular structures of compounds that compete for the estrogen binding site suggest that when estradiol is bound to the receptor, there is a close fit only at the A-ring end of the steroid. The most potent antagonists have phenolic rings capable of mimicking the estradiol A-ring in promoting high affinity binding to the receptor. They fail to stabilize the conformational change or molecular interaction needed to achieve hormonal response because they either lack an essential functional group (hydrogen bond donor) or they present a steric block or topological feature incompatible with transformation or interaction subsequent to the initiation of binding by the A-ring or A-ring analogues. X-Ray analyses of 12 triphenylethylene derivatives demonstrate the stability of a specific conformation that is unaffected by crystal packing forces. This conformation has a pinwheel-like orientation of phenyl rings, the direction of which is correlated with a 10 degrees twist about the central double bond and appears to depend upon the orientation of the non-phenyl substituent relative to the double bond. Empirical energy calculations are insensitive to this intramolecular structural dependence and incorrectly predict that the pinwheel of the opposite direction is of lower energy.

Animals↗

PubMed1992

Structural features of carbohydrate moieties in snake venom glycoproteins.

The structures of the carbohydrate moieties of glycoproteins in snake venoms are largely unknown. In the present study, we have analyzed venoms of several species of snakes as well as plasma and tissue glycoproteins from one species of cobra (Naja naja kaouthia) by lectin affinity staining of Western blots. The data demonstrate that glycoproteins in cobra venom invariably contain terminal alpha-galactosyl residues with negligible proportions of sialic acids. Interestingly, however, terminal alpha-galactosyl residues are present in significantly lower proportions in cobra tissues such as brain, liver, lung, kidney, spleen, muscle, and totally absent in cobra plasma glycoproteins. In sharp contrast to cobras, venom glycoproteins of other snakes do not contain terminal alpha-galactosyl residues but do contain terminal 2,3- and/or 2,6-linked sialic acids as well as beta-galactosyl residues. Cobra venom also contains high molecular weight heavily glycosylated proteins bearing poly-N-acetyllactosaminyl oligosaccharides, the majority of which appear to be linked to the protein core via O-glycosidic bonds.

Animals↗

PubMed1985

Local base dynamics and local structural features in RNA and DNA duplexes.

Local base motion and local structural base information are derived with a simple motional model from site specifically spin-labeled polyribo- and polydeoxyribonucleotides. The model was developed earlier for some nucleic acids and has now been applied to analyze 22 different nucleic acid systems. We conclude that the base motion of the spin-labeled nucleotide in single-stranded RNA, DNA, or non-base-paired bases in duplexes is of the order of 1 ns and that its base mobility decreases by about a factor of 4 upon base pairing. Also, the tether motion of the probe is slower in an RNA than in a DNA duplex.

DNA↗

PubMed1975

Characteristic structural features of fibrous rings and their connexion with the human cardiac conduction system.

In surgical treatment of acquired defects of mitral, aortic, and tricuspid valves, in many instances severe disturbances of cardiac conduction are observed. With due regard to the individual and typical anatomical features of human heart, the author investigated the structures of fibrous rings and triangles and their interrelationships with the cardiac conduction system. The material studied consisted of 230 hearts obtained from persons aged 20-80 years. The author assumes that within the heart cavity "dangerous zones" have to bbe singled out, whose traumatization in heart surgery may produce a disturbance of elements of the conduction system. The "dangerous zones" are situated at the base of the right-side surface of the interatrial septum above the fibrous ring of the septal cusp of the tricuspid valve, along the base of the membranous segment of the interventricular septum, in front of the posterior fibrous triangle, and at the fibrous ring encircling the bases of the posterior and right aortic semilunar valves.

Adult↗

PubMed1991

Structural features of the cell-wall polysaccharides of Asparagus officinalis seeds.

The fine structure of a beta-)1----4)-linked glucomannan from Asparagus officinalis has been determined by n.m.r. analysis of the oligosaccharides obtained by acidic and enzymic hydrolyses. Cleavage of the glucomannan with beta-D-mannase from Aspergillus niger and purification by h.p.l.c. gave oligosaccharide fractions that contained Man (mannose), GlcMan (beta-glucopyranosylmannose), Man2, Glc2Man, and Glc3Man as the major components. Simulated digestion of a polymer composed of randomly distributed monomers with the same Glc:Man ratio as glucomannan from A. officinalis led to the same polysaccharides. The random distribution of the monomers of glucomannan from A. officinalis was corroborated by the diffraction diagram of the raw flour, which indicated that the "in situ" glucomannan was amorphous, whereas both cellulose and mannans are crystalline.

Acids↗

PubMed1987

Structural features of antigenic determinants on variant surface glycoproteins from Trypanosoma brucei.

The immunochemical structure of two variant surface glycoproteins (VSGs) from Trypanosoma brucei has been studied using monoclonal and polyclonal antibodies. These two VSGs, WaTat 1.1 and WaTat 1.12 have been shown to possess cross-reactive surface-exposed antigenic determinants [Barbet et al., Nature 300, 53-57 (1982)] and similar N-terminal amino acid sequences [Olafson et al., Molec. Biochem. Parasit. 12, 287-298 (1984)]. Monoclonal and polyclonal antibodies were raised against the soluble forms of the two VSGs and against their reduced, alkylated and cyanogen bromide (CNBr) cleaved forms. None of the monoclonal antibodies which bound to the surface of living trypanosomes bound to CNBr fragments of the VSGs nor to denatured VSGs. Polyclonal antibodies raised against denatured and cleaved VSG did not bind to the surface of the living trypanosomes. These results suggest that the variable surface exposed antigenic determinants of VSG are topographically assembled structures. It was also shown that the conserved amino terminal peptides of WaTat 1.1 and WaTat 1.12 do not contain antigenic determinants.

Animals↗

PubMed1988

Analysis of structural features responsible for the sweetness of the sesquiterpene, hernandulcin.

The relationship between sweetness and structure was studied for several analogues of the intensely sweet sesquiterpene, hernandulcin. These derivatives were prepared synthetically, and were spectroscopic and conformational analysis. With the exception of the parent substance, none of the derivatives tested proved to be sweet. Evidence gathered in this study suggests that hernandulcin binds to its putative receptor through a three-point interaction, involving the C-1 carbonyl and C-1' hydroxyl groups, and the double bond between C-4' and C-5'. In the course of a preliminary safety assessment, the 3-desmethyl derivative of hernandulcin was found to be mutagenic toward Salmonella typhimurium strain TM677.

Chemical Phenomena↗

PubMed1991

Structural features of an exocyclic adduct positioned opposite an abasic site in a DNA duplex.

Structural studies have been extended to dual lesions where an exocyclic adduct is positioned opposite an abasic site in the center of a DNA oligomer duplex. NMR and energy minimization studies were performed on the 1,N2-propanodeoxyguanosine exocyclic adduct (X) positioned opposite a tetrahydrofuran abasic site (F) with the dual lesions located in the center of the (C1-A2-T3-G4-X5-G6-T7-A8-C9).(G10-T11-A12-C-13-F14-C15 -A16-T17-G-18) X.F 9-mer duplex. Two-dimensional NMR experiments establish that the X.F 9-mer helix is right-handed with Watson-Crick A.T and G.C base pairing on either side of the lesion site. NOEs are detected from the methylene protons of the exocyclic ring of X5 to the imino protons of G4.C15 and G6.C13 which flank the lesion site, as well as to the H1' and H1" protons of the cross strand F14 tetrahydrofuran moiety. These NMR results establish that the exocyclic adduct X5 is positioned between flanking G4.C15 and G6.C13 base pairs and directed toward the abasic lesion F14 on the partner strand. These studies establish that the exocyclic ring of the 1,N2-propanodeoxyguanosine adduct fits into the cavity generated by the abasic site.

Base Composition↗

PubMedDate not supplied

[Structural features of the integration site of foreign DNA in the transgenic mouse genome].

The structure of the transgenic mouse DNA region containing an integrated transgene (fragment of pBR322 sequence) was analysed. In one of the sequences flanking the transgene, short direct and inverted overlapping repeats were revealed at a distance of 60 bp from the integration site. In the same flanking sequence, there is an extended sequence (3.5 kbp) 0.3-1 kbp away from the transgene. It repeats 100-300 times in the mouse genome and is highly conservative (the homologs of the repeat have been revealed in other mammalian, bird, fish and insect genomes). This up-to-date unknown family of highly-conserved dispersed repeats has been denoted by T1. We believe that both the revealed short inverted repeats capable of forming hairpins with loops and the T1 repeat are structures involved in the process of non-homologous insertion of foreign DNA into the region of the transgenic mouse genome.

Animals↗

PubMed1992

Interaction of the p85 subunit of PI 3-kinase and its N-terminal SH2 domain with a PDGF receptor phosphorylation site: structural features and analysis of conformational changes.

Circular dichroism and fluorescence spectroscopy were used to investigate the structure of the p85 alpha subunit of the PI 3-kinase, a closely related p85 beta protein, and a recombinant SH2 domain-containing fragment of p85 alpha. Significant spectral changes, indicative of a conformational change, were observed on formation of a complex with a 17 residue peptide containing a phosphorylated tyrosine residue. The sequence of this peptide is identical to the sequence surrounding Tyr751 in the kinase-insert region of the platelet-derived growth factor beta-receptor (beta PDGFR). The rotational correlation times measured by fluorescence anisotropy decay indicated that phosphopeptide binding changed the shape of the SH2 domain-containing fragment. The CD and fluorescence spectroscopy data support the secondary structure prediction based on sequence analysis and provide evidence for flexible linker regions between the various domains of the p85 proteins. The significance of these results for SH2 domain-containing proteins is discussed.

Amino Acid Sequence↗

PubMed1987

Antigelling and antisickling bisphenyl oligopeptides and peptide analogues have similar structural features.

Single-crystal X-ray diffraction was used to determine the three-dimensional structures of two antigelling oligopeptides, L-lysyl-L-phenylalanyl-L-phenylalanine and L-phenylalanylglycylglycyl-D-phenylalanine, and two antisickling peptide analogues, L-phenylalanine benzyl ester and N-phenylacetyl-L-phenylalanine. Although these bisphenyl compounds are chemically quite different from one another, they demonstrate unusual structural similarities: The molecules have compact conformations in which the two phenyl rings are positioned approximately 5 A apart with interplanar angles approaching 90 degrees, thereby making intramolecular edge-to-face interactions. In addition, the polar atoms, nitrogen and oxygen, are in close proximity without forming intramolecular hydrogen bonds. The relative spatial distribution of polar and nonpolar atoms renders the structures compact and amphipathic. The intramolecular edge-to-face interaction between two aromatic rings, which brings a hydrogen atom with relative positive charge near the pi-electron cloud with relative negative charge, is enthalpically favorable and maintains the molecules in a compact and amphipathic conformation. Nonbonded potential energy calculations were used to characterize the energetics of the aromatic-aromatic interaction, and they showed that the observed geometry is stabilized enthalpically by a favorable interaction on the order of -1 to -2 kcal/mol. Structural differences between the two antisickling and the two antigelling agents suggest that molecular volume limits red cell membrane passage. These data provide a molecular structural framework from which to design and synthesize amphipathic bisphenyl compounds that both bind to deoxy sickle cell hemoglobin and cross the erythrocyte membrane.

Antisickling Agents↗