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At least 487 records · Page 27Linked to original sources
PubMed2004

Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozyme and its substrate.

The kinetic pathway of a trans-acting delta ribozyme includes an essential structural rearrangement involving the P1 stem, a stem that is formed between the substrate and the ribozyme. We performed cross-linking experiments to determine the substrate position within the catalytic center of an antigenomic, trans-acting, delta ribozyme. Substrates that included a 4-thiouridine either in position -1, +4, or +8 (i.e., adjacent to the cleavage site, or located either in the middle of or at the 3'-end of the P1 stem, respectively) were synthesized and shown to be efficiently cleaved. Examination of the cross-linking conditions, the use of various mutated ribozymes, as well as the probing and characterization of the resulting ribozyme-substrate complexes, revealed several new features of the molecular mechanism: (1) the close proximity of several bases between nucleotides of the substrate and ribozyme; (2) the active ribozyme-substrate complex folds in a manner that docks the middle of the P1 stem on the P3 stem, while concomitantly the scissile phosphate is in close proximity to the catalytic cytosine; and, (3) some complexes appear to be compatible with being active intermediates along the folding pathway, while others seem to correspond to misfolded structures. To provide a model representation of these data, a three-dimensional structure of the delta ribozyme was developed using several RNA bioinformatic software packages.

Base Sequence↗
PubMed1991

Structural features of allergens large and small with emphasis on recombinant allergens.

The application of recombinant DNA techniques to the study of allergen structure has increased our knowledge of primary structures and B- and T-cell determinants. Thus, knowledge of the molecular bases of isoallergens and allergenic cross-reactivities is about to be rapidly expanded. Findings from the early applications of molecular cloning strategies to the study of some polypeptide allergens, together with a summary of our current knowledge of drug allergenic determinants, are presented here.

Allergens↗
PubMed1991

Structural features of stomach aldehyde dehydrogenase distinguish dimeric aldehyde dehydrogenase as a 'variable' enzyme. 'Variable' and 'constant' enzymes within the alcohol and aldehyde dehydrogenase families.

Stomach aldehyde dehydrogenase was structurally evaluated by analysis of peptide fragments of the human enzyme and comparisons with corresponding parts from other characterized aldehyde dehydrogenases. The results establish a large part of the structure, confirming that the stomach enzyme is identical to the inducible or tumor-derived dimeric aldehyde dehydrogenase. In addition, species variations between identical sets of different aldehyde and alcohol dehydrogenases reveal that stomach aldehyde dehydrogenase exhibits a fairly rapid rate of evolutionary changes, similar to that for the likewise 'variable' classical alcohol dehydrogenase, sorbitol dehydrogenase, and cytosolic aldehyde dehydrogenase but in contrast to the 'constant' class III alcohol dehydrogenase and mitochondrial aldehyde dehydrogenase. This establishes that rates of divergence in the aldehyde and alcohol dehydrogenases are unrelated to subunit size or quaternary structure, highlights the unique nature of class III alcohol dehydrogenase, and positions the stomach aldehyde dehydrogenase in a group with more ordinary features.

Aldehyde Dehydrogenase↗
PubMed1977

Structural features of rat cardiac ferritins.

Ferritin extracted from rat heart containes two species separable by gel electrophoresis. These were purified and examined for structural characteristics. As in gel electrophoresis, cardiac ferritin preparations yielded only two bands on isoelectric focusing in gels, with pI values of 4.6 and 4.8. After separation by preparative electrophoresis, the two species were found to have a different amino acid composition from each another and from liver ferritin. Similarly, peptide maps showed several components not found in liver ferritin. On dissociation and electrophoresis with sodium dodecyl sulfate, heart ferritins were found to contain subunits of the same sizes as in other rat ferritins but also some larger components. Since cardiac ferritins have apparent molecular weights greater than those of other ferritins, it is concluded they probably contain more subunits, and possibly some of larger size not present in ferritins of other tissues.

Amino Acids↗
PubMed1988

Ara-tiazofurin: conservation of structural features in an unusual thiazole nucleoside.

Tiazofurin (2-beta-D-ribofuranosylthiazole-4-carboxamide, NSC 286193) is a C-glycosyl thiazole nucleoside with antitumor activity. Crystal structures of tiazofurin and its alpha,2'-deoxy and xylo analogues all show close contacts between the thiazole sulfur (S) and the furanose ring oxygen (O1'). These contacts have been interpreted in terms of an attractive intramolecular S-O interaction in the thiazole nucleosides. Ara-tiazofurin (2-beta-D-arabinofuranosylthiazole-4-carboxamide, ara-T) is the inactive arabinose analogue of tiazofurin. The crystal structure of ara-T is reported. This structure provides evidence for an attractive S-O interaction not seen in the other thiazole nucleosides. The conformation about the C-glycosyl bond in ara-T is such that close contacts are formed between the thiazole sulfur and both O1' and the 2'-hydroxyl oxygen O2'. This conformation is interpreted in terms of an additional attractive interaction between S and O2'. This interpretation is supported by comparison of the conformation of ara-T with those of other ara-nucleosides. These findings provide further evidence for an attractive S-O interaction in the thiazole nucleosides. Ara-T also demonstrates a second conformational feature found in these compounds: the carboxamide nitrogen remains cis to the thiazole nitrogen. Implications of these potentially constrained conformational features are discussed in terms of the mechanism of activity of tiazofurin.

Chemical Phenomena↗
PubMed1988

Quantitation of structural features characterizing weight- and less-weight-bearing regions in articular cartilage: a stereological analysis of medial femoral condyles in young adult rabbits.

The structural organization of articular cartilage from the medial femoral condyle of young adult rabbits has been examined after processing according to an improved fixation procedure. By using recently developed stereological methods, a quantitative analysis of chondrocyte number, surface area, volume, and matrix volume per cell was carried out in the light microscope; at the electron microscopic level, quantities of cytoplasmic components within chondrocytes (including organelles) were estimated. These measurements were made for each of the four zones from the (articular cartilage) surface down to the tidemark, and the results (for each zone) were compared between weight- and less-weight-bearing regions. In general, articular cartilage revealed considerable heterogeneity in structure throughout its depth. The number of cells per unit volume is maximal beneath the surface and decreases toward the tidemark. The size of chondrocytes, and the mean matrix volume surrounding each, increases from the surface toward the deeper zones. Comparison between weight- and less-weight-bearing regions reveals striking differences. The numerical volume density of cells in the superficial zone of regions bearing high physiological load is less than half of that in less-weight-bearing regions, chondrocyte death being principally responsible for this reduction. A comparison between the midzones of weight- and less-weight-bearing areas reveals that the former is characterized by a decrease in cell density and an approximately threefold increase in cell size in relation to the latter. The increase in cell volume is attributable principally to an accumulation of intermediate filaments and glycogen particles, and represents an adaptation to increased functional requirements. Near the tidemark, numerical volume densities of chondrocytes in both weight- and less-weight-bearing locations are similar, but the larger cell size in the former still persists.

Animals↗
PubMed1989

Structural features of some diphenhydramine analogues that determine the interaction with rat liver cytochrome P-450.

The aim of this study was to define the structural characteristics in a series of 21 analogues of the anti-histaminergic drug diphenhydramine which are important for the interaction with cytochrome P-450. The compounds gave substrate (type I) binding spectra with rat hepatic microsomal cytochrome P-450. The main findings were: (1) two phenyl rings are needed for strong binding: saturation or elimination of one ring, or restriction of two phenyls with a two-carbon bridge results in a decrease of binding, (2) substitution on one or both aromatic rings has only a small influence on binding, (3) an amine nitrogen contributes to better binding; decrease or absence of basicity weakens binding, and (4) a chain of 4 to 7 atoms connecting the basic centre with the aromatic part is needed; reduction of the chain length, or restriction of it to a cyclic structure causes decrease or loss of binding ability.

Animals↗
PubMedDate not supplied

Structural features of the antibody-A chain linkage that influence the activity and stability of ricin A chain immunotoxins.

The importance of the various structural elements constituting a ricin A chain immunotoxin to the stability of the disulfide bond between the antibody and A chain was examined using a panel of immunoconjugates prepared with the mouse monoclonal antibody Fib75. Analogues of the standard ricin A chain immunotoxin prepared with the N-succinimidyl 3-(2-pyridyldithio)propionate disulfide cross-linker included immunoconjugates made with N-succinimidyl 4-[(iodoacetyl)amino]benzoate the thioether cross-linker; with N-succinimidyl 3-(2-pyridyldithio)butyrate, the hindered disulfide cross-linker; with a peptide spacer between the antibody and cross-linker; or with the dodecapeptide corresponding to the C-terminus of ricin A chain. The cytotoxic activities of the immunoconjugates and their susceptibility to reduction by glutathione in vitro were compared. The thioether-linked immunotoxin could not be cleaved by glutathione in vitro and had low cytotoxic potency, consistent with the requirement of a reducible disulfide linkage for activity. The hindered disulfide-linked immunotoxin was 3-fold more stable to reduction than the immunotoxin containing a standard unhindered disulfide linkage, but the cytotoxic activities of the two constructs were indistinguishable. The introduction of a flexible peptide Ala-Ala-Pro-Ala-Ala-Ala-Pro-Ala-Pro-Ala between Fib75 and the disulfide linkage introduced by SPDP had no deleterious effect on cytotoxic activity and no effect on the susceptibility of the disulfide linkage to reduction. This finding suggests that the enforced proximity of the A chain to the antibody caused by the use of a short chemical cross-linker in a conventional immunotoxin has no influence on either of these properties in this system.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1989

Structural features of lipoprotein lipase. Lipase family relationships, binding interactions, non-equivalence of lipase cofactors, vitellogenin similarities and functional subdivision of lipoprotein lipase.

A structural homology between lipoprotein lipase, pancreatic lipase and hepatic lipase is known and indicates that all three lipases are members of a common protein family. Lipoprotein lipase and pancreatic lipase utilize small protein co-factors, apolipoprotein C-II and co-lipase, respectively, but comparisons reveal no homology between the co-factor molecules. Hence, they do not show the same relationship as their target enzymes. Neither do screenings detect any extensive similarities between lipoprotein lipase, serine hydrolases, or apolipoproteins. Scannings against data bank proteins show that a 105-residue segment of lipoprotein lipases exhibits a 35-40% residue identity with a sub-region of Drosophila vitellogenins. One fifth of the conserved amino acid residues (8 of 40) are glycine, a pattern which is typical of distantly related forms of protein families. This supports a true relationship between large segments of Drosophila vitellogenins and lipases. Physiological and functional aspects of the vitellogenin/lipoprotein lipase similarities are given. The region concerned is entirely within the N-terminal domain of lipoprotein lipase and constitutes the segment where the similarity to hepatic and pancreatic lipases is most pronounced. Within this lipase region a 10-residue putative lipid-binding site exists for which further similarities have been found to the otherwise not closely related lingual/gastric lipases, prokaryotic lipases and lecithin-cholesterol acyltransferase. Another segment in lipoprotein lipase, where the heparin-binding site has been mapped, exhibits a correlation between strength of heparin binding and extent of basic residues among members of the lipase family. It further exhibits weak similarities with the 'Zn-finger' DNA-binding segment of steroid hormone receptors and may indicate convergence in a binding interaction. Thus, a functional subdivision of lipoprotein lipase into different segments can be distinguished.

Amino Acid Sequence↗
PubMed1979

Hereditary and acquired cardiomyopathies in experimental animals: mechanical, biochemical, and structural features.

Evidence has been presented regarding alterations of contractile behavior muscle biochemistry, and ulstrastructure during the course of the hereditary hamster cardiomyopathy. Also, preliminary structural and mechanical data were presented on the acquired cardiomyopathy of diabetes mellitus in experimental animals. In the hamster model, contractile performance, measured as isometric tension and rate of tension development, was shown to be depressed throughout the course of the disease, whereas normalized force-velocity relationships returned to normal only during the compensated stages of hypertrophy. Force-frequency relationships were depressed in myopathic muscles, indicating the presence of alterations in the muscle activation system, namely, the biochemical and functional integrity of the sarcoplasmic reticulum. Analysis of the contractile proteins in myopathic muscle has revealed depressions of Ca2+ activity in purified myosin in addition to an independently increased neutral protease activity that results in the specific degradation of LC2 of myosin. Sympathetic time and norepinephrine turnover increase progressively during the course of the disease. These changes are accompanied by decreasing tissue levels of neorepinephrine and increasing levels of dopamine, indicating a shift in the rate-limiting step for norepinephrine synthesis. Alterations were also noted in nuclear protein composition and serotonin levels. Microscopically, the myolytic and calcification changes that characterize the hamster cardiomyopathy have been confirmed. In addition, contraction bands and lysosomal changes have been observed that may relate to cateholamine hypersensitivity. In the experimental model of diabetic cardiomyopathy, a significant alteration in relaxation process was demonstrated despite the fact that peak tension development and its rate of development were unaltered. Also, the length dependence of contractile behavior was altered when compared to that of age-matched controls, indicating a potential loss of contractility reserve. When animals with combined hypertension and diabetes were studied, bothe contraction and relaxation processes were affected to a greater degree.

Actomyosin↗
PubMed2005

Structural features of thermozymes.

Enzymes synthesized by thermophiles and hyperthermophiles are known as thermozymes. These enzymes are typically thermostable, or resistant to irreversible inactivation at high temperatures, and thermophilic, i.e. optimally active at elevated temperatures between 60 and 125 degrees C. Enzyme thermostability encompasses thermodynamic stability and kinetic stability. Thermodynamic stability is defined by the enzyme's free energy of stabilization (deltaG(stab)) and by its melting temperature (Tm). An enzyme's kinetic stability is often expressed as its halflife (t1/2) at defined temperature. DeltaG(stab) of thermophilic proteins is 5-20 kcal/mol higher than that of mesophilic proteins. The thermostability mechanisms for thermozymes are varied and depend on the enzyme; nevertheless, some common features can be identified as contributing to stability. These features include more interactions (i.e. hydrogen bonds, electrostatic interactions, hydrophobic interactions, disulfide bonds, metal binding) than in less stable enzymes and superior conformational structure (i.e. more rigid, higher packing efficiency, reduced entropy of unfolding, conformational strain release and stability of alpha-helix). Understanding of the stabilizing features will greatly facilitate reengineering of some of the mesozymes to more stable thermozymes.

Archaea↗
PubMed1982

High-field 1H NMR studies of synthetic analogs of somatostatin. Structural features involving aromatic residues in an active eight-membered ring analog.

360 MHz 1H-NMR data are presented for somatostatin and an analog whose primary structure is cyclo(-Gaba-Asn5-Phe6-Phe7-DTrp8-Lys9-Thr10-Phe11-). This report focuses on the aromatic portion of the spectrum, and this region for the analog is unambiguously assigned, using two experimental approaches: selective deuteration and photo-induced CIDNP. The most prominent feature of the analog aromatic spectrum is a two-proton resonance which exhibits a pronounced upfield shift. Significantly, this feature is also present for somatostatin and other active analogs (unpublished data). Assignments show that this resonance derives from the ortho hydrogens of the Phe6 and that aromatic resonances of Phe6 shift markedly upfield as temperature is decreased. In contrast, the aromatic resonances of Phe7,11 and DTrp8 reveal generally much smaller temperature coefficients and shift primarily downfield as temperature is decreased. Ring-current analysis shows that simple pair-wise parallel pi-stacking alone cannot give rise to the observed data. However, a simple hypothesis involving only two phenylalanine residues is totally consistent with the data if they maintain a time-averaged co-perpendicular orientation. Indirect evidence is offered which implicates only one phenylalanine stacking partner for Phe6, which we tentatively identify as Phe11.

Amino Acid Sequence↗
PubMed2003

Thermotropic phase behaviour of alpha-dipalmitoylphosphatidylcholine multibilayers is influenced to various extents by carotenoids containing different structural features--evidence from differential scanning calorimetry.

Carotenoids are the effective modulators of physical properties of model and natural membranes. To demonstrate the relationship between the structure of carotenoids and their effect on the molecular dynamics of membranes, we have investigated the influence of five structurally different carotenoids: beta-carotene, lycopene, lutein, violaxanthin, zeaxanthin and additionally carotane--a fully saturated derivative of beta-carotene, on thermotropic phase behaviour of dipalmitoylphosphatidylcholine (DPPC) multilamellar vesicles by means of differential scanning calorimetry (DSC). The results obtained indicate that the carotenoids used modulated the thermotropic properties of multibilayers to various extents, broadening the pretransition and the main phase transition peaks and shifting them to lower temperatures. Pronounced decrease of pretransition enthalpy (DeltaH(p)) proves that carotenoids very strongly alter the membrane properties in its gel phase. Comparison of the influence of several carotenoids shows that a rigid, polyisoprenoid chain plays a basic role in altering the thermotropic properties of such membranes and the presence of rings without oxygen-containing groups has a minor significance for the observed interactions. Carotenoids containing epoxy and/or hydroxy groups attached to their rings modify the thermotropic phase behaviour of DPPC multilamellar vesicles stronger than carotenes--a result of their orientation in the DPPC bilayer.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1987

Structural features and hydration of a dodecamer duplex containing two C.A mispairs.

X-ray diffraction techniques have been used to characterise the crystal and molecular structure of the deoxyoligomer d(C-G-C-A-A-A-T-T-C-G-C-G) at 2.5A resolution. The final R factor is 0.19 with the location of 78 solvent molecules. The oligomer crystallises in a B-DNA type conformation with two strands coiled about each other to produce a duplex. This double helix consists of four A.T and six G.C Watson-Crick base pairs and two C.A mispairs. The mismatched base pairs adopt a "wobble" type structure with the cytosine displaced laterally into the major groove, the adenine into the minor groove. We have proposed that the two close contacts observed in the C.A pairing represent two hydrogen bonds one of which results from protonation of adenine. The mispairs are accommodated in the double helix with small adjustments in the conformation of the sugar-phosphate backbone. Details of the backbone conformation, base stacking interactions, thermal parameters and the hydration are now presented and compared with those of the native oligomer d(C-G-C-G-A-A-T-T-C-G-C-G) and with variations of this sequence containing G.T and G.A mispairs.

Base Composition↗
PubMed1997

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair.

Adenine↗
PubMed2004

Structural features of the rice chromosome 4 centromere.

A complete sequence of a chromosome centromere is necessary for fully understanding centromere function. We reported the sequence structures of the first complete rice chromosome centromere through sequencing a large insert bacterial artificial chromosome clone-based contig, which covered the rice chromosome 4 centromere. Complete sequencing of the 124-kb rice chromosome 4 centromere revealed that it consisted of 18 tracts of 379 tandemly arrayed repeats known as CentO and a total of 19 centromeric retroelements (CRs) but no unique sequences were detected. Four tracts, composed of 65 CentO repeats, were located in the opposite orientation, and 18 CentO tracts were flanked by 19 retroelements. The CRs were classified into four types, and the type I retroelements appeared to be more specific to rice centromeres. The preferential insert of the CRs among CentO repeats indicated that the centromere-specific retroelements may contribute to centromere expansion during evolution. The presence of three intact retrotransposons in the centromere suggests that they may be responsible for functional centromere initiation through a transcription-mediated mechanism.

Base Sequence↗