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PubMed1990

Sequence-dependent structural variations of hammerhead RNA enzymes.

The discovery of in vivo catalytic activity for the hammerhead RNA self-cleaving domain has led to the development of a new class of sequence-specific RNA endonucleases. Two such ribozymes have been synthesized using in vitro transcription with T7 polymerase and their structures have been studied by optical spectroscopy, nuclear magnetic resonance and nondenaturing gel electrophoresis. These data show the presence of a stable hairpin consisting of a double helical stem and a tetranucleotide loop in both RNA enzymes. Additional structure, with different stabilities, is also observed in both RNA enzymes. The half-lives for cleavage of the complementary RNA substrates by these two RNA enzymes have been previously shown to differ by a factor of 50. The data presented here suggest that this rate difference may be a result of the formation of catalytically inactive conformations in the RNA enzyme which interfere with formation of the enzyme-substrate complex.

Base Sequence↗
PubMed1992

Fluoroquinolones: relationships between structural variations, mammalian cell cytotoxicity, and antimicrobial activity.

Fluoroquinolones are potent inhibitors of bacterial topoisomerase II (DNA gyrase). They can also inhibit eukaryotic topoisomerases, which could possibly lead to clastogenicity and/or cellular toxicity. Recent studies have demonstrated a correlation between mammalian cell cytotoxicity of the fluoroquinolones and the potential of these compounds to induce micronuclei, a genetic toxicity endpoint. In an effort to identify potent nontoxic quinolone antibacterials, we have examined the structural features of the fluoroquinolones associated with mammalian cell cytotoxicity. An investigation of a wide variety of substituents at the 1, 5, 7, and 8 positions of a quinolone nucleus was conducted. The results indicate that no one position has a controlling effect on the observed cytotoxicity. Instead, a combination of the various substituents contributes to the effects seen. Certain trends were apparent, such as the fact that compounds with pyrrolidines at the R-7 position were more cytotoxic than those with piperazines, and halogens at R-8 (X-position) were associated with more cytotoxicity relative to hydrogen. A general trend also existed between the cytotoxicity of the compounds and their Gram-positive antibacterial activity. A detailed comparison between the various groups and positional variations as they controlled the cytotoxicity and antibacterial activity is presented.

Animals↗
PubMed1987

Inhibitors of cyclic AMP phosphodiesterase. 2. Structural variations of N-cyclohexyl-N-methyl-4-[(1,2,3,5-tetrahydro- 2-oxoimidazo[2,1-b]quinazolin-7-yl)-oxy]butyramide (RS-82856).

A series of analogues of the cyclic AMP phosphodiesterase (PDE) inhibitor N-cyclohexyl-N-methyl-4-[(1,2,3,5-tetrahydro- 2-oxoimidazo[2,1-b]quinazolin-7-yl)oxy]butyramide (RS-82856, 1) was prepared by systematic variation of the side-chain substituent, length, position, connecting atom, and the parent heterocycle itself. The compounds were evaluated as inhibitors of cyclic AMP phosphodiesterase from both human platelets and rat or dog heart tissue and as inhibitors of ADP-induced platelet aggregation. Structure-activity correlations for the analogue series revealed significant limitations on the steric bulk of substituents on the 1,2,3,5-tetrahydroimidazo[2,1-b]quinazolin-2-one heterocycle and the position and length of the side chain. As inhibitors of cyclic AMP phosphodiesterase (PDE), potency steadily increased with increasingly lipophilic side chains. In platelet aggregation inhibition studies, however, a maximum in activity was reached with 1, while more lipophilic compounds were significantly less active. Major changes in the heterocycle itself, represented by isomeric and other carbonyl variations, also decreased activity. The molecular features defined by this series of analogues of 1 correlate to a high degree with current understanding of the chemical and topographical requirements of the active site of the FIII (type IV) form of cyclic AMP PDE. Selective inhibition of this enzyme has been proposed as the principal component of the positive inotropic action of a number of cardiotonic agents.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed1980

Immunoglobulin diversity in the phylogenetically primitive shark, Heterodontus francisci. Suggested lack of structural variation between light chains isolated from different animals.

A two-step procedure employing gel filtration and anion exchange chromatography has been utilized to isolate LMW immunoglobulin from the horned shark, Heterodontus francisci. Light chains obtained by complete reduction and alkylation of the parent protein have been compared by several analytical techniques. Amino acid composition data implies a limited degree of variation in the light chains isolated from individual animals. Polyacrylamide gel electrophoresis of the CNBr digests of the light chains reveal indistinguishable banding profiles of the major peptides. Isoelectric focusing indicates limited heterogeneity in the light chain spectrotype and identity in the pI of the majority of bands detectable by staining. The suggested degree of structural similarity in the light chains of this phylogenetically primitive shark is discussed in terms of the evolutionary position of the species and current theories concerning the origins of structural diversity in immunoglobulins.

Amino Acids↗
PubMed2026

RAG-mediated structural variation and its impact on relapse risk in acute lymphoblastic leukemia.

Relapse during treatment of B-cell acute lymphoblastic leukemia (B-ALL) is a harbinger of poor outcomes. Identifying biomarkers for subsequent relapse risk which are detectable at B-ALL diagnosis remains a priority. Off-target recombination-activating gene (RAG)-mediated structural variants (SVs) generate genomic instability that drives leukemogenesis and may underlie treatment resistance. Leveraging sequencing data in 1,496 pediatric B-ALL patients enriched for relapse status (relapse n=532; non-relapse n=964), we characterized RAG-mediated SVs across B-ALL molecular subtypes and examined their association with patient characteristics and their impact on clinical outcomes. Off-target RAG-mediated SVs were overall frequent, particularly in ETV6::RUNX1, ETV6::RUNX1-like, and Ph-like B-ALL subtypes, while increasing age-at-diagnosis was positively associated with burden of off-target RAG-mediated SVs (P<.001). Off-target RAG-mediated SVs with a recombination signal sequence (RSS) at one breakpoint, a hallmark of off-target RAG activity, were significantly more frequent at diagnosis in patients who subsequently relapsed (P=.001). This association remained significant in multivariable regression analysis (per SV odds ratio [OR]:1.08, 95%CI:1.04-1.12), in minimal residual disease (MRD)-negative patients (OR:1.09, 95%CI:1.04-1.14) and across subtypes. Excluding deletions, MRD-negative ETV6::RUNX1 patients with &#x2265;3 off-target RAG-mediated SVs had a >3-fold risk of relapse (hazard ratio:3.47, 95% CI:1.86-6.49). RAG-mediated SVs were also associated with relapse risk in T-cell ALL patients. Off-target RAG-mediated SV burden at diagnosis is a risk factor of relapse in pediatric ALL across molecular subtypes and independent of MRD status.

Journal Article↗
PubMed1989

Phenotypic effects of apolipoprotein structural variation on lipid profiles: II. Apolipoprotein A-IV and quantitative lipid measures in the healthy women study.

Apolipoprotein A-IV (APO A-IV) is a major protein component of mesenteric lymph chylomicrons and very-low-density lipoproteins. It is found in plasma predominantly unassociated with major lipoprotein fractions and in high density lipoproteins. APO A-IV exhibits structural heterogeneity owing to two codominant alleles, APO A-IV*1 and APO A-IV*2, that occur in Caucasian and black populations. In vitro experimental evidence indicates that APO A-IV may be a cofactor for the lecithin:cholesterol acyltransferase enzyme, may be involved in reverse cholesterol transport, and may play an important role in the modulation of lipoprotein lipase activity. In this study we have investigated the effect of two APO A-IV phenotypes, APO A-IV 1-1 and APO A-IV 2-1, on quantitative lipid measures in a group of 453 white women being followed through menopause for changes in cardiovascular risk. At baseline all women were premenopausal. Of the nine lipid measures, triglycerides showed a marginally significant effect caused by phenotype. The APO A-IV 2-1 heterozygotes had lower average triglycerides than the 1-1 homozygotes (P = .053).

Adult↗
PubMed1991

Isolation of chicken-bek and a related gene; identification of structural variation in the ligand-binding domains of the FGF-receptor family.

cDNA clones carrying the chicken-bek gene and a related gene were isolated. Deducing the amino acid sequence of chicken-bek allowed us to predict that it encodes for a receptor tyrosine kinase related to the fibroblast growth factor (FGF) receptor, and that the chicken-bek gene and Cek3 are closely related. However, a significant structural difference was identified between chicken-bek and Cek3 within the putative extracellular region, in such a manner that the structure of the immunoglobulin-like domain was conserved. A probe specific to the altered structure detected mRNA in the tissues as did a probe common to bek and Cek3, indicating heterogeneity in the FGF-receptor family in a novel manner. Furthermore, another bek-like gene was isolated and the expressions of its mRNA and protein product were analysed in tissues and cultured cells.

Amino Acid Sequence↗
PubMed1984

Promoter helical structure variation at the Escherichia coli polymerase interaction sites.

There is evidence that the Escherichia coli polymerase recognizes and binds to three sites on the promoter DNA: the -10, -35, and -16 regions. Sequence homology was noted among the -10 sites (Pribnow box) and among the -35s with consensus sequences, TATAAT and TTGACA , respectively. Weak nucleotide sequence homology was detected at -16. Since the polymerase recognizes these sites in a multitude of promoters, one expects similarities in the three-dimensional structures. To date, no data directly bearing on such structures exist. Recently, Calladine ( Calladine , C.R. (1982) J. Mol. Biol. 161, 343-352) and, subsequently, Dickerson ( Dickerson , R.E. (1983) J. Mol. Biol. 166, 419-441) suggested "rules" for doublestranded DNA structures which were tested against data from several known crystals. Using these rules, I compare the deviations from "ideal" B-DNA of the twist angles, base pair roll, sideways shift, and propeller suppression in 56 promoters at the three sites. I also appended to these the twist angle computations on additional 77 promoters from the recently published compilation of promoter sequences. For the latter, additional nucleotides from the spacer regions were added. The results display similarities at the -10 site. Equally strong similarities were obtained for the -35 and the -16 contact regions. The existence of structural differences for some sites is likely to account for the different degrees of efficiency of the polymerase recognition and transcriptional regulation.

Base Sequence↗
PubMed1992

Structural variations of different oral basement membranes revealed by cationic dyes and detergent added to aldehyde fixative solution.

The ultrastructural appearance of different types of basement membrane was studied using histochemical methods for visualizing glycosaminoglycans. Samples of rat gingiva and mouse molar germ tissue were fixed either with glutaraldehyde, glutaraldehyde-ruthenium hexammine trichloride (RHT), glutaraldehyde-Cuprolinic Blue (CB) or cetylpyridinium chloride-glutaraldehyde (CPC). Ultrathin sections were stained with uranyl acetate and lead citrate. The results showed that the conventional trilaminar structure of the basement membrane was observed after glutaraldehyde and CB fixation. In contrast, after CPC or RHT fixation, the appearance of the basement membrane was homogeneous without any evidence of a lamina lucida. Furthermore, after single fixation with CPC, the ultrastructure of different basement membranes from oral tissues showed some differences in appearance which were related to their localizations, functions, or both.

Animals↗
PubMed1990

Ligand-dependent structural variations in Escherichia coli F1 ATPase revealed by cryoelectron microscopy.

The Escherichia coli F1 ATPase, ECF1, has been examined by cryoelectron microscopy after reaction with Fab' fragments generated from monoclonal antibodies to the alpha and epsilon subunits. The enzyme-antibody complexes appeared triangular due to the superposition of three anti-alpha Fab' fragments on alternating densities of the hexagonally arranged alpha and beta subunits. The Fab' to the epsilon subunit superimposed on a beta subunit. A density was observed near the center of the structure in the internal cavity. The position of this central density with respect to peripheral sites was not fixed. Sorting of images of ECF1 labeled with the combination of three anti-alpha Fab' fragments plus an Fab' directed to the epsilon subunit gave three classes in each of which the central density was closest to a different beta subunit. The distribution of the central density among the three classes was measured for different ligand-binding conditions. When ATP was present in catalytic sites under conditions where there was no enzyme turnover (i.e., without Mg2+ present), there were approximately equal numbers of images in each of three classes. When ATP and Mg2+ were added and ATP hydrolysis was allowed to proceed, almost two-thirds of the images were in the class in which the central density was closest to the beta subunit superimposed by the epsilon subunit. We conclude that domains within the ECF1 structure, either the central mass or a domain including the epsilon subunit, move in the enzyme in response to ligand binding. We suggest that this movement is involved in coupling catalytic sites to the proton channel in the F0 part of the ATP synthase.

Adenosine Diphosphate↗
PubMed1977

[Morphological and structural variations of the human inguinal region (author's transl)].

In the inguinal region, numerous muscular and fibrous alterations are described. They are related to the unconstant position of the pubic tubercle in relation io the interspinous diameter (linea bi-spinalis). The pubic tubercle can be observed in two different locations: either high or low. The high location is characterized by the presence of the pubic tubercle at a distance of 5 to 7.5 cm below the interspinous diameter. It must be considered as normal and is found in 65% of the subjects. In the low locations, the distance between spinous tubercle and interspinous diameter reaches 7,5 to 12 cm. It is an important abnormality which interests 35% of the subjects. The lower the pubic tubercle are located, the more often morphological alterations are to be found in the following structures: obliquus externus, obliquus internus, transversus and cremaster muscles as well as fascia transversalis. Nevertheless, the pyramidalis muscle as well as the inguinal ligamentary formation, Hesselbach's interfoveolar ligament and Thompson's iliopubic tract do not follow that rule, since the important morphological variations of these deep fibrous components can never be related to the distance between pubic tubercle and interspinous diameter. The functional signification of the inguinal region and especially of the inguinal canal is modified by those ostelogical, muscular and ligamentary variations.

Humans↗
PubMed1981

Structural variation among human beta-tubulin genes.

A chicken beta-tubulin cDNA probe has been used to screen two independently generated human genomic libraries. Of 13 EcoRI fragments detectable in a human genomic Southern blot experiment, 7 correspond in size to EcoRI fragments isolated from recombinant bacteriophage. The location of beta-tubulin-specific regions and the direction of transcription were determined within each cloned fragment. One clone (5 beta) contained a beta-tubulin-specific region of 6.8 kilobase pairs (kbp) that included three intervening sequences as well as a number of inverted repeat structures. The remaining clones contained beta-tubulin-specific sequences that were close to or, in two cases, substantially less than 1.9 kbp long. Because mature human beta-tubulin mRNA is approximately 1.9 kbp long, these short DNA regions cannot on their own encode a functional beta-tubulin mRNA. Analysis using 3'- and 5'-specific probes derived from the chicken cDNA clone showed the presence of both of these end regions within one truncated tubulin-like sequence. A second short tubulin-specific region failed to hybridize with a 3'-specific probe. These short sequences are therefore likely to be examples of pseudogenes that have arisen by loss of a portion of DNA essential to the production of functional human beta-tubulin mRNA.

Animals↗
PubMed1981

Fetal lung hypoplasia: biochemical and structural variations and their possible significance.

Quantitative biochemical criteria for lung growth and maturation were compared with the histological appearances in hypoplastic lungs from 20 fetuses and newborn infants. Cases associated with oligohydramnios showed a characteristic series of changes with narrow airways, retardation of epithelial and interstitial growth, delay in development of blood-air barriers, and low concentrations of phospholipid phosphorus, lecithin phosphorus, total palmitate, and lecithin palmitate. The growth and maturation arrest appeared to affect the peripheral part of the acinus. Examples of other types of lung hypoplasia showed different features. Hypoplastic lungs from infants with normal or increased amniotic fluid were of mature structure with phospholipid concentrations similar to those of infants with normally developed lungs at term. The hypoplastic left lung in 2 cases of congenital diaphragmatic hernia had an immature structure with low phospholipid concentrations, whereas the right lung has structurally and biochemically more mature. It is suggested that fetal lung growth may be impaired by any influence which reduces thoracic volume but that maturation arrest is due specifically to loss of the ability to retain lung liquid.

DNA↗
PubMed1984

Primary structural variation among serologically indistinguishable DS antigens: the MB3-bearing molecule in DR4 cells differs from the MB3-bearing molecule in DR5 cells.

HLA-DS molecules bearing the MB3 supertypic specificity have been isolated from two DR4 and two DR5 homozygous cell lines by using the monoclonal antibody IVD12 . Limited amino-terminal amino acid sequence analysis of these molecules demonstrates polymorphism of the HLA-DS subregion. Although the distribution of amino-terminal tyrosine residues in the alpha-chains of all IVD12 -reactive molecules was identical, amino-terminal amino acid sequence differences existed between DS beta-chains isolated from these two groups of cell lines bearing different DR specificities. These studies indicate that two DS molecules bearing the same serologic determinant ( MB3 ), although similar to one another, may be structurally distinct.

Amino Acid Sequence↗