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PubMed1983

Renin: structural features of active enzyme and inactive precursor.

To determine the structural basis for the unique catalytic mechanism of renin and the mechanism of activation of inactive renin, renin and inactive renin were isolated in pure form. The active site of renin consists of two aspartyl residues, two tyrosyl residues, and one arginyl residue, analogous to pepsin and other acid proteases. The complete amino acid sequence of mouse submaxillary gland renin was determined. Of the amino acids, 43% were identical to those in porcine pepsin. Combination of various chromatographic techniques permitted the separation of inactive renin from active renin in human plasma and kidney. Inactive renin of hog kidney was completely purified. Inactive renin consists of a single polypeptide chain and is activated by proteolysis but not by dissociative reagents such as 4 M NaCl or detergent. Thus it was concluded that the inactive renin in these tissues is renin zymogen rather than a renin-inhibitor complex.

Amino Acid Sequence↗

PubMed2002

Structural features of prions explored by sequence analysis I. Sequence data.

Animal prion proteins (PrPs) form at the sequence level a very homogenous and 'closed' family. Therefore, few of their structural and functional features can be gleaned from sequence comparison as is now possible on a wide scale for other protein families. To detect putatively related proteins (at the structural and/or functional level), we used a battery of sequence analysis tools. This analysis resulted in (i) the identification of a putative 'prion-like' domain within the envelope of foamy retroviruses, (ii) the detection of putative similarities between prions and an interferon-inducible membrane protein, and (iii) the proposal that of the TATA-box-binding protein is a structural scaffold, which might allow understanding of a key event leading to the structural conversion from PrP(C) (normal cellular prion structure) towards PrP(Sc) (pathogenic structure).

Amino Acid Sequence↗

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↗

PubMedDate not supplied

Freeze-etching and freeze-fracture structural features of cell envelopes in mycobacteria and leprosy derived corynebacteria.

The structural properties of the cell wall and cell membrane of several mycobacteria and of Leprosy Derived Corynebacteria are investigated by freeze-etching and freeze-fracture. In all cases the freeze-fracture split the cell wall in two asymmetric halves. The cell wall fracture faces of the mycobacteria are characterized by a filamentous network which vary with respect to the amount and complexity among microorganism of the same species and even more of different species. In LDC the structure organization of the cell wall and cell membrane differs from that of mycobacteria. The most stricking difference is the presence on the fracture faces of the LDC cell wall of different classes of particulated entities of yet unknown nature. In the mycobacteria and LDC the periseptal annuli likely provide a potential frame for cell envelope and cell membrane assembly.

Animals↗

PubMedDate not supplied

Structural features of vancomycin.

Recent analytical methods have advanced knowledge of the structure of vancomycin from a description of only several molecular fragments to a complete understanding of the intact molecule. The molecular weight is 1,448. The molecule consists of a seven-membered peptide chain that is formed by parts of three phenylglycine systems, two chlorinated tyrosine units, aspartic acid, and N-methylleucine. Two ether bonds and a carbon-carbon bond join the various substituents on the peptide chain into three large rings. A disaccharide, composed of glucose and vancosamine, is also present but is not part of the cyclic structure. Details of the vancomycin structure have been related to hydrogen bonding between the antibiotic and bacterial cell-wall precursors that have a D-alanyl-D-alanine carboxyl terminus; such bonding would provide a molecular basis for the cell-wall mode of action for vancomycin. With one carboxyl, two amino, and three phenolic groups, vancomycin undergoes a variety of ionic interactions in solutions of different pH and composition.

Binding Sites↗

PubMed1981

Relation of structural features to pyrrolic metabolites in livers of rats given pyrrolizidine alkaloids and derivatives.

Levels of pyrrolic metabolites have been measured in the livers of rats given some pyrrolizidine alkaloids and semisynthetic derivatives. Structural and chemical features favouring the formation of such metabolites have been defined. The most important of these were: steric hindrance or chemical properties giving resistance to ester hydrolysis; lipophilic character, allowing access to hepatic microsomal enzymes; a conformation favoring microsomal oxidation of the pyrroline ring in preference to N-oxidation. In addition, the presence of ester groups gave the resulting pyrroles high chemical reactivity, leading to tissue binding. Amounts of pyrroles bound to liver were very low when animals were given either highly water soluble pyrrolizidine derivatives, including non-esterified bases or more-lipophilic esters if these were easily hydrolysed. Compounds prone to hydrolysis gave increased pyrrole levels in rats pretreated to deplete their esterase activity. Whereas heliotridine-based alkaloids usually give more pyrrole than similar retronecine esters, heliotridine ditiglate gave less pyrrole than retronecine ditiglate because the former was more open to hydrolytic attack. Among the carboxylic diesters, the cyclic retronecine diesters, in which the pyrrolizidine nucleus is more exposed to oxidative metabolism, gave the highest pyrrole levels in rats. Liver pyrrole measurements are useful for studying relationships between molecular structure, metabolism and toxicity of pyrrolizidine derivatives. They can be used for screening alkaloids for potential toxicity and for assessing dose levels suitable for toxicity tests when limited material is available.

Animals↗

PubMed1998

Growth and structural features of the adult stage of Ascaris suum (Nematoda, Ascaridoidea) from experimentally infected domestic pigs.

For studying the morphogenesis of the adult stage of Ascaris suum, worms were obtained from experimentally infected domestic pigs. Structural and morphometric features of A. suum are analyzed by light and scanning electron microscopy. It was shown that the increase in length of the worm from days 35 to 56 is based on a region-specific lengthening of individual transverse annuli in the cuticle. An increased worm size also results in an increased diameter of different cuticular sense organs. It is shown that a pair of lateral midbody papillae, the centrids, are prominent sensilla in the adult male and female worm. The centrids have an asymmetric placement, the right centrid being more anterior on the worm than the left.

Animals↗

PubMed1998

SnoRNA-guided ribose methylation of rRNA: structural features of the guide RNA duplex influencing the extent of the reaction.

Eukaryotic rRNAs contain a large number of ribose-methylated nucleotides of elusive function which are confined to the universally conserved rRNA domains. Ribose methylation of these nucleotides is directed by a large family of small trans -acting guide RNAs, called box C/D antisense snoRNAs. Each snoRNA targets precisely one of the nucleotides to be methylated within the pre-rRNA sequence, through transient formation of a 10-21 bp regular RNA duplex around the modification site. In this study we have analyzed how different features of the double-stranded RNA guide structure affect the extent of site-specific ribose methylation, by co-expressing an appropriate RNA substrate and its cognate tailored snoRNA guide in transfected mouse cells. We show that an increased GC content of the duplex can make up for the inhibitory effects of a helix truncation or for the presence of helix irregularities such as a mismatched pair or a bulge nucleotide. However, some helix irregularities dramatically inhibit the reaction and are not offset by further stabilization of the duplex. Overall, the RNA duplex tolerates a much larger degree of irregularity than anticipated, even in the immediate vicinity of the methylation site, which offers new prospects in the search for additional snoRNA guides. Accordingly, a few snoRNA-like sequences of uncertain status detected in the yeast Saccharomyces cerevisiae genome now appear as likely bona fide ribose methylation guides.

Animals↗

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↗

PubMed2004

Exploring structural features of the interaction between the scorpion toxinCnErg1 and ERG K+ channels.

The gamma-KTx-type scorpion toxins specific for K+ channels were found to interact with ERG channels on the turret region, while alpha-KTx3.2 Agitoxin-2 binds to the pore region of the Shaker K+ channel, and alpha-KTx5.3 BmP05 binds to the intermediate region of the small-conductance calcium-activated K-channel (SK(Ca)). In order to explore the critical residues for gamma-KTx binding, we determined the NMR structure of native gamma-KTx1.1 (CnErg1), a 42 amino acid residues scorpion toxin isolated from the venom of the Mexican scorpion Centruroïdes noxius Hoffmann, and we used computational evolutionary trace (ET) analysis to predict possible structural and functional features of interacting surfaces. The 1H-NMR three-dimensional solution structure of native ergtoxin (CnErg1) was solved using a total of 452 distance constraints, 13 3J(NH-Halpha) and 10 hydrogen bonds. The structure is characterized by 2 segments of alpha-helices and a triple-stranded antiparallel beta-sheet stabilized by 4 disulfide bridges. The ET and structural analysis provided indication of the presence of two important amino acid residue clusters, one hydrophobic and the other hydrophilic, that should be involved in the surface contact between the toxin and the channel. Some features of the proposed interacting surface are discussed.

Amino Acid Sequence↗

PubMed1997

Structural features of nephritogenic lupus autoantibodies.

We have identified monoclonal antibodies derived from MRL-lpr/lpr lupus-prone mice that produced nephritis after passive transfer to normal mice. Our present goal was to elucidate the structural and immunochemical features of nephritogenic Ig that facilitate immune deposition. For this purpose the antigen binding properties, capacity to form immune deposits, and nucleotide sequence of a genetically related autoantibody subgroup were compared. The prototype, H147 (an IgG encoded by 7183/81X VH gene), produced glomerular and tubular basement membrane, mesangial immune deposits, and proliferative glomerulonephritis after passive transfer to normal mice. For comparison three other 7183/81X encoded anti-DNA IgG (H257, H171, and H8a) were evaluated (predicted heavy chain aa homology >75%). H257 produced similar types of immune deposits as H147, and this was associated with nephritis; H8a produced predominantly mesangial deposits, whereas H171 did not produce significant deposits. Although their antigen binding profile to a panel of soluble autoantigens was variable, only H147 and H257 bound to both mesangial and aortic endothelial cell surfaces. V gene sequence analysis of the IgG suggests that individual residues, motifs, and conformations influence the autoantigen binding specificities that contributed to the observed differences in immune deposit formation.

Amino Acid Sequence↗

PubMed1996

Structural features of crayfish phasic and tonic neuromuscular terminals.

We examined the fine structure of terminals of the phasic and tonic excitatory axon to the crayfish limb extensor muscle. The phasic terminals are known to release 50-100 times more transmitter for a small length of terminal for a single impulse. Phasic terminals labeled with horseradish peroxidase (HRP) were relatively thin and contained a single unbranched mitochondrion; tonic terminals were much thicker, and their varicosities contained several multibranched mitochondria. Tonic terminals devoted a larger proportion of their total volume to mitochondria. The percentage volume of clear synaptic vesicles was slightly higher in phasic axon terminals, but as the tonic axon terminals were fivefold larger in volume, the total synaptic volume is much greater in tonic than phasic terminals. The number of synapses per length of terminal, and the total number of active zones per length of terminal, were greater for tonic terminals, and individual synapses were, on average, slightly larger in surface contact area for tonic terminals. In contrast, individual active zones were, on average, longer in phasic synapses. A higher proportion (50%) of phasic synapses had multiple active zones than was the case for tonic synapses (16%), and pairs of closely spaced active zones were more frequently found on phasic synapses. These findings clearly rule out synapse and active zone number as a factor contributing to higher transmitter output, but suggest that active zone size and synaptic complexity, as evidenced by multiple closely spaced active zones in a single synapse, are likely to play a causal role in the greater transmitter release of the phasic terminal. Even synapse complexity would not be enough to account fully for the large difference in terminal transmitter output, and additional factors may include electrical and biochemical differences.

Animals↗

PubMed1994

Common structural features of the Ro RNP associated hY1 and hY5 RNAs.

The secondary structures of human hY1 and hY5 RNAs were determined using both chemical modification techniques and enzymatic structure probing. The results indicate that both for hY1 and for hY5 RNA the secondary structure largely corresponds to the structure predicted by sequence alignment and computerized energy-minimization. However, some important deviations were observed. In the case of hY1 RNA, two regions forming a predicted helix appeared to be single-stranded. Furthermore, the pyrimidine-rich region of hY1 RNA appeared to be very resistant to reagents under native conditions, although it was accessible to chemical reagents under semi-denaturing conditions. This may point to yet unidentified tertiary interactions for this region of hY1 RNA. In the case of hY5 RNA, two neighbouring internal loops in the predicted structure appeared to form one large internal loop.

Animals↗

PubMed1994

Nucleotide sequence and structural features of the group III citrus viroids.

The nucleotide sequence and secondary structure of two representative variants from the Group III citrus viroids. CVd-IIIa (297 bases) and CVd-IIIb (294 bases) were determined. The variants are related to the apple scar skin viroid (ASSVd) family. Although smaller in size than any of the ASSVd-related viroids, the central conserved region as well as most of the terminal conserved region of ASSVd is retained. The rod-like structural configuration (characteristic of ASSVd) of the variants as predicted by minimum free energy analysis is presented.

Base Composition↗

PubMed1983

Structural features of epidermal keratin filaments reassembled in vitro.

We have studied the structure of epidermal keratin filaments polymerized in vitro, addressing two different levels of organization. First, we have determined the amino acid sequence of a mouse epidermal keratin subunit from the nucleotide sequence of a cDNA clone. The subunit contains a large central region, representing about 50 percent, whose sequence strongly suggests that it assumes a coiled-coil alpha-helical conformation. This is flanked on the amino and carboxyl terminals by long glycine-rich sequences. Second, we have used scanning transmission electron microscopy to study the structure of frozen, unstained filaments. Analyses of such images provides information on the mass per unit length and on the distribution of mass within the filament. These data impose rigorous constraints on possible models for the packing of protofilaments within the filament. Epidermal keratin filaments assembled in vitro are polymorphic; however, the majority of bovine filaments weigh about 37 kD/nm, but most human filaments have masses of only about 27 kD/nm. The filament width is at least 15 nm, substantially more than the generally accepted value of 8 to 10 nm, owing to the existence of low-density mass at the periphery that has not been visualized by conventional microscopic methods. We currently postulate that the alpha-helical regions of the subunits comprise the structural core or backbone of the filament from which at least some of the glycine-rich sequences protrude.

Amino Acid Sequence↗

PubMed2000

Structural features of an anti-diabetic polysaccharide (TAP) from Tremella aurantia.

The structure of an anti-diabetic polysaccharide (TAP) obtained from the fruiting bodies of Tremella aurantia was investigated by methylation analysis, Smith degradation, partial acid hydrolysis, 13C-NMR spectrometry, and enzymatic digestion. The results suggested that TAP was composed of (1-->3)-linked alpha-D-mannopyranosyl residues as a backbone, some of which were substituted at position 2 with (1-->3)-linked beta-D-xylopyranose side chains and with beta-D-glucopyransyluronic acid at position 4 linked to terminal alpha-D-mannopyranose.

Acetylation↗

PubMed1997

Importance of structural features for tRNA(Met) identity.

We showed previously that the tRNA tertiary structure makes an important contribution to the identity of yeast tRNA(Met) (Senger B, Aphasizhev R, Walter P, Fasiolo F, 1995, J Mol Biol 249:45-58). To learn more about the role played by the tRNA framework, we analyzed the effect of some phosphodiester cleavages and 2'OH groups in tRNA binding and aminoacylation. The tRNA is inactivated provided the break occurs in the central core region responsible for the tertiary fold or in the anticodon stem/loop region. We also show that, for tRNA(Met) to bind, the anticodon loop, but not the anticodon stem, requires a ribosephosphate backbone. A tertiary mutant of yeast tRNA(Met) involving interactions from the D- and T-loop unique to the initiator species fails to be aminoacylated, but still binds to yeast methionyl-tRNA synthetase. In the presence of 10 mM MgCl2, the mutant transcript has a 3D fold significantly stabilized by about 30 degrees C over a wild-type transcript as deduced from the measure of their T(m) values. The k(cat) defect of the tRNA(Met) mutant may arise from a failure to overcome an increase of the free energetic cost of distorting the more stable tRNA structure and/or a tRNA based MetRS conformational change required for formation of transition state of aminoacylation.

Anticodon↗

PubMed2003

Finding discriminating structural features by reassembling common building blocks.

We present a new method for constructing discriminating substructures by reassembling common medicinal chemistry building blocks. The algorithm can be parametrized to meet differing objectives: (1) to build features that discriminate for biological activity in a local structural neighborhood, (2) to build scaffolds for R-group analysis, (3) to construct cluster signatures that discriminate for membership in the cluster and provide a graphical representation for its members, and (4) to identify substructures that characterize major classes in a heterogeneous compound set. We illustrated the results of the algorithm on a literature dataset is of 118 compounds with in vitro inhibition data against recombinant human protein tyrosine phosphatase 1B (PTP-1B).

Algorithms↗