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PubMed1990

Structural features associated with alpha- anomeric in oligo-alpha-thymidylates.

Comparison between gel electrophoresis migrations of oligo-alpha-thymidylates and oligo-beta-thymidylates indicates that the migration of alpha-oligonucleotides under native conditions is different from the migration of beta-oligonucleotides when the number of thymines, part of the sequence, is higher than 5. Such difference disappears when the gels are run under denaturing conditions. This, together with UV spectra, indicates that the structure of alpha-oligonucleotides is more organized than the structure of beta-oligonucleotides and that such an organisation appears for a length higher than 5 monomeric units.

Electrophoresis, Polyacrylamide Gel↗
PubMed1995

X-ray absorption studies and homology modeling define the structural features that specify the nature of the copper site in rusticyanin.

Rusticyanin, a blue copper protein, possessing the highest redox potential among this class of proteins and a high stability at acidic pH reveals homology with the C-terminal end of the other single copper containing blue proteins and an interesting homology to parts of the blue copper domain of the multi-copper proteins such as the nitrite reductases. Extended X-ray absorption fine structure (EXAFS) data at pH 2.0 reveal that Cu is ligated to two His and a Cys in the inner coordination sphere, similar to other blue copper centers. Modeling studies suggest that His85 is the ligating histidine from the N-terminal end. Its neighboring residue is a serine rather than the asparagine found in all known blue Cu proteins. The high stability of the copper site may arise in part due to this substitution. The Cu binding site is surrounded by aromatic residues which may provide further protection for the metal in an acidic environment. In addition, the high number of solvent-exposed uncompensated lysine residues is likely to be of functional relevance under low pH conditions. EXAFS data show a very small change (relative to azurin) in the copper site upon reduction, consistent with a more constrained copper center in rusticyanin compared to azurin and a higher redox potential.

Absorptiometry, Photon↗
PubMed2003

Yeast V1-ATPase: affinity purification and structural features by electron microscopy.

V1-ATPase from the yeast Saccharomyces cerevisiae was purified via a FLAG affinity tag introduced into the N terminus of the G subunit. The preparation migrated as a single band in native gel electrophoresis and contained subunits ABCDEFGH (with subunit C present at substoichiometric amounts) as determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The initial specific Ca-ATPase activity was approximately 6 micromol/min/mg. The structure of the yeast V1-ATPase was studied by electron microscopy of negatively stained and frozen hydrated samples. A 25-A resolution three-dimensional model of the complex was calculated from two-dimensional projections by the angular reconstitution technique. The model shows six elongated densities arranged in pseudo-3-fold symmetry around a large central cavity. At the top of the molecule, various protrusions can be seen. At the bottom of the complex, two large masses are visible that are connected to the main body of the molecule. Comparison of the yeast V1 structure with the structure of the intact V1V0-ATPase from bovine brain clathrin-coated vesicles (Wilkens, S., Vasilyeva, E., and Forgac, M. (1999) J. Biol. Chem. 274, 31804-31810) indicates that the structure of the isolated V1 from yeast is very similar to the structure of the V1 domain in the intact V-ATPase complex.

Chromatography, Affinity↗
PubMed1980

[Structural features of isolated and perfused neurons of Helix pomatia mollusks].

Ultrastructural features of the intact normal neurons of Helix pomatia L., were studied and compared with those of isolated and perfused neurons. The perfusion of the isolated neurons had no definite influence on the intracellular organelia membranes--endoplasmic reticulum, Golgi complex, the neurosecretary granules, pigment bodies. Some changes were manifested in the vacuolization of the structures, increase in the number of cytosomes and lysosomes, modification of the size and shape of the neurosecretory granules. No visible ultrastructural changes of the superficial membrane, submembrane parts of cytoplasm were observed after intracellular perfusion. The obtained data confirm the use of perfused neurons as a model for the investigation of electrophysiological properties of the somatic membrane.

Animals↗
PubMed2026

Mitochondrial genomes of Dactylogyrus wunderi (Monopisthocotyla: Dactylogyridae): structural features, codon usage patterns, and phylogenetic implications.

BACKGROUND: Codon usage bias (CUB) is a common phenomenon reported among many species and genes, but its unique characteristics in the mitochondrial genome of class Monopisthocotyla remain unknown. METHODS: The complete mitochondrial genome of Dactylogyrus wunderi was sequenced and characterized, and the mitochondrial genome compositions and CUB of six Dactylogyrus species and 35 Monopisthocotyla species were analyzed using bioinformatics methods. RESULTS: The mitochondrial genome of D. wunderi is a typical circular structure in length of 14,920 bp. The A&#x2009;+&#x2009;T contents of the six Dactylogyrus species (58.4% &#xb1; 5.7%) were significantly lower than that of Monopisthocotyla species (71.0% &#xb1; 5.80%, p&#x2009;<&#x2009;0.01). Neutrality plot analysis showed slopes of 0.3136 and 0.389 in the six Dactylogyrus and the 35 Monopisthocotyla species, respectively. Furthermore, 98.3% and 77.4% of the genes in the six Dactylogyrus and the Monopisthocotyla species, respectively, had effective number of codons (ENC) higher than 35, but 23.3% and 0.5% genes of ENC ratio ranged from -&#x2009;0.05 to 0.05 in the six Dactylogyrus and Monopisthocotyla species. Phylogenetic analysis revealed that, within the context of the sampled taxa, the families of Monopisthocotyla were monophyletic groups, except for Ancyrocephalidae. CONCLUSIONS: The nucleotide composition had AT base bias in Monopisthocotyla, and natural selection was the main factor affecting CUB in the mitochondrial genomes of Monopisthocotyla species. These results provided insights into the factors affecting CUB in Monopisthocotyla species and deepened our insight of phylogeny, evolution, and codon usage of Monopisthocotyla.

Genome, Mitochondrial↗
PubMedDate not supplied

On some structural features of ovarian ligaments in domestic animals.

The vascular and nerve components of ovarian ligaments (proper and suspensory) of the sheep, cow and the donkey were examined in order to investigate the presence of blood flow-regulator endovasal devices, artero-venous anastomoses, free and/or encapsulated nerve endings and ganglion cells. Both the ligaments of the investigated species showed the presence of endovasal devices (valvular apparati, intimal and polypoid cushions) and artero-venous anastomoses, the latter structurally ascribed to the first and second type of Conti and Bucciante's classification. Moreover, although not constantly, both the examined districts showed an autonomic nerve support, while four Ruffini's corpuscles were found in the suspensory ligament just in one sheep.

Animals↗
PubMed1993

Mutagenesis of EIAV TAT reveals structural features essential for transcriptional activation and TAR element recognition.

Certain members of the lentivirus subfamily of retroviruses encode unique transcriptional activator (Tat) proteins that modify the transcription complex after binding to the 5' end of nascent viral mRNA. The Tat proteins are modular, containing RNA-binding and activation domains that can be exchanged between different Tat proteins or replaced with heterologous protein fragments. While there is considerable sequence conservation among the divergent Tat proteins, there are also some structural differences that might be informative. For example, a cluster of basic amino acids in HIV-1 Tat is sufficient for RNA binding in vivo and in vitro. The homologous region of EIAV Tat is necessary but not sufficient for recognition of its cognate cis-acting RNA element; the entire C-terminal 26 amino acids of EIAV Tat, including the basic patch, are required. To better understand the structure-function relationships in EIAV Tat, we have generated a battery of expression plasmids encoding insertion, deletion, and missense mutations in the carboxy-terminal region of the tat gene. The plasmids were tested for their ability to trans-activate the EIAV promoter or to trans-inhibit a heterologous Tat protein. A mutation of a glutamine to an arginine in the cluster of basic residues generated a potent trans-dominant inhibitor of both EIAV and HIV-1 Tat, indicating that the mutation abolished RNA binding but did not alter the activation domain. Mutations at the extreme C-terminus of EIAV Tat impaired both RNA binding and activation domain functions, suggesting effects on secondary or tertiary structure.

Amino Acid Sequence↗
PubMed2006

Distinctive structural features of hydroxyamino-1,3,5-triazine ligands leading to enhanced hydrolytic stability of their titanium complexes.

Three bis(homoleptic) titanium complexes of hydroxyamino-1,3,5-triazine ligands were synthesized and characterized, and their kinetic behavior in THF-water solutions was studied at various pH conditions using UV-vis, based on the characteristic Ti-O band at 380 nm. One of these complexes, , was analyzed by X-ray crystallography. Due to the characteristic electronic structure of the triazine rings, high electron density on the nitrogen atoms leads to strong N-Ti bonds, as indicative by the 2.0 A coordinative bond lengths in the X-ray structure. Consequently, these complexes exhibit high hydrolytic stability over a wide pH range, where hydrolysis was observed to be promoted by basic conditions. At neutral pH, t(1/2) was estimated to be >200 h, whereas at pH = 5.5, no hydrolysis was observed for a period of at least three days.

Journal Article↗
PubMed1989

Structural features of the acetyl-CoA carboxylase gene: mechanisms for the generation of mRNAs with 5' end heterogeneity.

Acetyl-CoA carboxylase [acetyl-CoA:carbondioxide ligase (ADP-forming), EC 6.4.1.2] is the rate-limiting enzyme in the biogenesis of long-chain fatty acids. We have previously characterized five acetyl-CoA carboxylase mRNA species that differ in their 5' untranslated regions but not in the coding region. We have now characterized the exon-intron structure of the genomic DNA that encodes the 5' untranslated region of the mRNA. Generation of different forms of the mRNA is the result of the selective use of two promoters and differential splicing of five different exons. These five exons contain a total of 645 nucleotides and they are scattered over a 50-kilobase-pair genomic DNA region that we have characterized.

Acetyl-CoA Carboxylase↗
PubMed1981

Comparison of the structural features of corticotropin required for stimulation of steroidogenesis and cAMP production in rat and rabbit adrenocortical cells.

The steroidogenic activities of ACTH, alpha-MSH, beta-MSH as well as analogs of the hormones have been compared in rat and rabbit adrenocortical cells. ACTH is equally active in both species and the melanotropins have very low steroidogenic potency in either species. The steroidogenic potencies of the peptide analogs are strikingly similar in the two species, suggesting that the structural requirements for eliciting steroidogenesis are the same in rat and rabbit adrenocortical cells. The analog NPS-ACTH has low, comparable steroidogenic activity in both species. NPS-ACTH is a potent antagonist of ACTH-induced cAMP production in rat adrenocortical cells but acts as a weak partial agonist in rabbit adrenocortical cells. These results suggest that steroidogenesis may be mediated by receptors different from those involved in the cAMP response observed at supraphysiological concentrations of ACTH.

Adrenal Cortex↗
PubMed1975

Somatic antigen of Shigella dysenteriae type 3. Structural features of specific polysaccharide chain.

On mild acid hydrolysis of lipolysaccharide from Shigella dysenteriae type 3 the O-specific polysaccharide (hapten) was obtained which appeared to be acidic branched hexosaminoglycan. The repeating unit of this polysaccharide represents a pentasaccharide composed of two D-galactose residues, N-acetyl-D-galactosamine, D-glucose and unidentified acidic component. On the basis of methylation analysis, periodate oxidation, partial acid hydrolysis and chromic anhydride oxidation it is concluded that the structure of the chemical repeating unit of polysaccharide is (see article) where Glcp is glucopyranose, Galp is galactopyranose, Galf is galactofuranose, GalNAcp is 2-acetamido-2-deoxygalactopyranose and where the configuration of galactofuranoside glycosidic linkage and the structure of the acidic monosaccharide A are not known.

Aluminum↗
PubMed2004

Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers.

Most proteins exist in the cell as multi-component assemblies. However, which proteins need to be present simultaneously in order to perform a given function is frequently unknown. The first step toward this goal would be to predict proteins that can function only when in a complexed form. Here, we propose a scheme to distinguish whether the protein components are ordered (stable) or disordered when separated from their complexed partners. We analyze structural characteristics of several types of complexes, such as natively unstructured proteins, ribosomal proteins, two-state and three-state complexes, and crystal-packing dimers. Our analysis makes use of the fact that natively unstructured proteins, which undergo a disorder-to-order transition upon binding their partner, and stable monomeric proteins, which exist as dimers only in their crystal form, provide examples of two vastly different scenarios. We find that ordered monomers can be distinguished from disordered monomers on the basis of the per-residue surface and interface areas, which are significantly smaller for ordered proteins. With this scale, two-state dimers (where the monomers unfold upon dimer separation) and ribosomal proteins are shown to resemble disordered proteins. On the other hand, crystal-packing dimers, whose monomers are stable in solution, fall into the ordered protein category. While there should be a continuum in the distributions, nevertheless, the per-residue scale measures the confidence in the determination of whether a protein can exist as a stable monomer. Further analysis, focusing on the chemical and contact preferences at the interface, interior and exposed surface areas, reveals that disordered proteins lack a strong hydrophobic core and are composed of highly polar surface area. We discuss the implication of our results for de novo design of stable monomeric proteins and peptides.

Macromolecular Substances↗
PubMed1987

Mapping at the nucleotide level of Xenopus laevis mitochondrial D-loop H strand: structural features of the 3' region.

The D-loop resulting from limited synthesis of the newly replicated heavy (H) strand of mitochondrial DNA provides a good opportunity to examine both the origin and termination of DNA synthesis. We report here the precise determination of the 3' and 5' termini of nascent Xenopus laevis D-loop H strand. We observe two major classes of newly synthesized D-loop H strands, 1641 and 1675 nucleotides long. A stable putative secondary structure located around its 3' end is described. Analogous secondary structures are also found in the same region of the mammalian D-loop mitochondrial DNAs. Moreover a pentanucleotide (5' TACAT 3'), base-paired in these secondary structures and most often present in two copies, is conserved in all vertebrate species so far studied. The termination associated sequence previously described in mammals is part of the putative stop signal represented by the secondary structure except in man. These results show that the mechanism of arrest of H strand synthesis is common to vertebrates.

Animals↗
PubMed1997

Evolutionary shifts in three major structural features of the mitochondrial genome among iguanian lizards.

A phylogenetic tree for major lineages of iguanian lizards is estimated from 1,488 aligned base positions (858 informative) of newly reported mitochondrial DNA sequences representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Two well-supported groups are defined, the Acrodonta and the Iguanidae (sensu lato). This phylogenetic hypothesis is used to investigate evolutionary shifts in mitochondrial gene order, origin for light-strand replication, and secondary structure of tRNACys. These three characters shift together on the branch leading to acrodont lizards. Plate tectonics and the fossil record indicate that these characters changed in the Jurassic. We propose that changes to the secondary structure of tRNACys may destroy function of the origin for light-strand replication which, in turn, may facilitate shifts in gene order.

Animals↗
PubMed2000

The structural features of concanavalin A governing non-proline peptide isomerization.

The reversible binding of manganese and calcium to concanavalin A determines the carbohydrate binding of the lectin by inducing large conformational changes. These changes are governed by the isomerization of a non-proline peptide bond, Ala-207-Asp-208, positioned in a beta-strand in between the calcium binding site S2 and the carbohydrate specificity-determining loop. The replacement of calcium by manganese allowed us to investigate the structures of the carbohydrate binding, locked state and the inactive, unlocked state of concanavalin A, both with and without metal ions bound. Crystals of unlocked metal-free concanavalin A convert to the locked form with the binding of two Mn(2+) ions. Removal of these ions from the crystals traps metal-free concanavalin A in its locked state, a minority species in solution. The ligation of a metal ion in S2 to unlocked concanavalin A causes bending of the beta-strand foregoing the S2 ligand residues Asp-10 and Tyr-12. This bending disrupts conventional beta-sheet hydrogen bonding and forces the Thr-11 side chain against the Ala-207-Asp-208 peptide bond. The steric strain exerted by Thr-11 is presumed to drive the trans-to-cis isomerization. Upon isomerization, Asp-208 flips into its carbohydrate binding position, and the conformation of the carbohydrate specificity determining loop changes dramatically.

Calcium↗
PubMed1988

Structural features of potent inhibitors of rat kidney histamine N-methyltransferase.

Three antimalarial drugs amodiaquine, quinacrine and chloroquine were compared side-by-side with the antiseptic agent chlorhexidine and the neuromuscular blocker alcuronium for their capacity to competitively inhibit in vitro the activity of the enzyme histamine N-methyltransferase (HMT) from rat kidney over the concentration range 10(-3)-10(-8). Amodiaquine was clearly the most potent HMT inhibitor followed by quinacrine, chlorhexidine, alcuronium and chloroquine. Investigation of the structure-activity relationships by examining space-filling models revealed marked similarities in the conformations of the arrangement of three N atoms in histamine and in each of the compounds tested.

Alcuronium↗
PubMed2004

Specific structural features of heparan sulfate proteoglycans potentiate neuregulin-1 signaling.

Neuregulins are a family of growth and differentiation factors that act through activation of cell-surface erbB receptor tyrosine kinases and have essential functions both during development and on the growth of cancer cells. One alternatively spliced neuregulin-1 form has a distinct heparin-binding immunoglobulin-like domain that enables it to adhere to heparan sulfate proteoglycans at key locations during development and substantially potentiates its activity. We examined the structural specificity needed for neuregulin-1-heparin interactions using a gel mobility shift assay together with an assay that measures the ability of specific oligosaccharides to block erbB receptor phosphorylation in L6 muscle cells. Whereas the N-sulfate group of heparin was most important, the 2-O-sulfate and 6-O-sulfate groups also contributed to neuregulin-1 binding in these two assays. Optimal binding to neuregulin-1 required eight or more heparin disaccharides; however, as few as two disaccharides were still able to bind neuregulin-1 to a lesser extent. The physiological importance of this specificity was shown both by chemical and siRNA treatment of cultured muscle cells. Pretreatment of muscle cells with chlorate that blocks all sulfation or with an siRNA that selectively blocks N-sulfation significantly reduced erbB receptor activation by neuregulin-1 but had no effect on the activity of neuregulin-1 that lacks the heparin-binding domain. These results suggest that the regulation of glycosaminoglycan sulfation is an important biological mechanism that can modulate both the localization and potentiation of neuregulin-1 signaling.

Animals↗