[Structural variations of heptacaine. 2. Preparation and antiarrhythmic activity of N-2-(2-heptyloxyphenylcarbamoyloxy)ethyl-n-benzylpiperidiniu+ ++ m chloride].
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Animals↗
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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↗
Peptide aldehyde inhibitors of the kallikreins: an investigation of subsite interactions with tripeptides containing structural variations at the amino terminus.
A series of tripeptide aldehyde derivatives containing variations at the P3 subsite and the amino terminus has been prepared and evaluated for trypsin-like serine protease inhibition. These compounds exhibit strong in vitro inhibition of human plasma kallikrein (HPK), porcine pancreatic kallikrein (PPK) and human plasmin (HP). As suspected from an examination of a related crystal structure, the presence of a hydrophobic residue (adamantyl) at the amino terminus dramatically improves the binding to PPK. The adamantyl group, however, represents a peak in binding; larger residues cause the binding to be reduced, and thus are less well accommodated in this subsite. Although both HP and HPK also can accept large molecular volume at the amino terminus, they do not exhibit the same preference for large residues at this subsite that is demonstrated by PPK. Selectivity differences also are observed with P3 subsite substitution; with PPK preferring a bulky, but compact side-chain (t-butyl) and HP and HPK preferring a more extended (e.g. benzyl) group.
Aldehydes↗
Structural variations of collagen in normal and pathological tissues: role of electron microscopy.
The spectrum of ultrastructural appearances assumed by collagen in normal and pathological tissues is illustrated using techniques of thin section transmission electron microscopy and computer-assisted analysis. The normal fibrillar collagen types are described in order to provide a basis for comparing other normal and abnormal forms. In normal tissues, the anchoring fibril and basal lamina (basement membrane) represent tissue structures largely containing collagen but differing significantly in organisation from normal types I to III fibrillar collagen. In pathological tissue, deviations from normal fine structure are reflected in abnormal aggregates of collagen fibrils (amianthoid and skeinoid fibres) and abnormalities in fibril diameter and cross-sectional profile. Fibrous and segment long-spacing collagen represent two further organisational variants of collagen, the former found widely in pathological tissues, the latter very rarely. Much remains to be discovered about these abnormal collagen variants-their mode of formation, the cells that produce them, and their roles. They also present a challenge for the collagen biologist formulating hypotheses of collagen fibril assembly and molecular organisation.
Animals↗
Toxoplasma gondii-structure variations of the antigen P30.
The major surface immunodominant antigen (P30) of Toxoplasma gondii was purified by two methods (i) SDS-PAGE and (ii) immunoaffinity chromatography. The secondary elements within this protein were assessed by circular dichroism and spectra obtained were compared to those proposed by Manavalan & Johnson (1983). The results allowed us to determine an all beta protein status for this antigen. This experimental result was in agreement with the predicted secondary structures deduced from the P30 primary sequence. Modifications in conformation according to pH and temperature were recorded without any change in immunoactivity. The epitope, which was always recognized by a monoclonal antibody against P30, could be a linear epitope.
Amino Acid Sequence↗
cycloSal-d4TMP pronucleotides structural variations, mechanistic insights and antiviral activity.
Pronucleotides represent a promising alternative to improve the biological activity of nucleoside analogues against different viral diseases. The basic idea is to achieve nucleotide delivery into cells, bypassing limitations with intracellular formation of nucleotides from their nucleoside precursors. The cycloSal-concept is one of several pronucleotide systems reported so far. For the nucleoside analogue d4T, the cycloSal-approach improved antiviral potency. The basic idea, chemistry, different structural modifications and their effects on the antiviral potency of the cycloSal-d4TMP triesters have been discussed in this review.
Antiviral Agents↗
Investigation of mechanistic consequences of natural structural variation within the cysteine proteinases by knowledge-based modelling and kinetic methods.
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Amino Acid Sequence↗
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↗
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↗
Motor proteins of the kinesin family. Structures, variations, and nucleotide binding sites.
Microtubule-dependent motors of the kinesin family convert the energy from ATP hydrolysis into mechanical work in order to transport vesicles and organelles along microtubules. The motor domains of several kinesins have been solved by X-ray diffraction, but the conformational changes associated with force development remain unknown. Here we describe conformational properties of kinesin that might be related to the mechanism of action. First, we have evaluated the conformational variability among all known kinesin structures and find they are concentrated in six areas, most of which are functionally important either in microtubule binding or in linking the core motor to the stalk. Secondly, we show that there is an important difference between kinesins when compared with myosins or GTPases (with which kinesin motor domains bear structural and catalytic similarities); in the diphosphate-state (with bound ADP), all kinesins show a 'tight' nucleotide-binding pocket, comparable with myosin or GTPases in the triphosphate state, whose nucleotide-binding pockets become open, or 'loose', following nucleotide hydrolysis. Thus, kinesin-ADP appears to be in a tense state, resembling that observed in myosin-ATP or p21ras-GTP.
Animals↗
Constituents of Mammea americana L. 8. Novel structural variations on the mammein theme and antitumor activity of mammein and related coumarin and phloroglucinol derivatives.
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Alkenes↗
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↗
[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↗
Structural variations across the lanthanide series of macrocyclic DOTA complexes: insights into the design of contrast agents for magnetic resonance imaging.
It was early shown that the macrocyclic Ln(DOTA) complexes (DOTA = 1,4,7,10-tetra-azacyclododecane-N,N',N' ',N' "-tetraacetic acid) exists in solution as a mixture of two enantiomeric pairs of diastereoisomers differing in the ligand conformation, namely, square antiprismatic (SA) and twisted square antiprismatic (TSA) geometries, respectively. Later, extensive (1)H NMR investigations suggested that a coordination change may be superimposed on this conformational equilibrium involving two additional structures in which the metal ion possesses a coordination number of eight (CN 8). It was predicted that these two species, lacking the apical coordinated water molecule, would maintain the SA and TSA coordination geometries, and therefore, they have been labeled as SA' and TSA', respectively. In this work we report the X-ray solid-state crystal structure determination of six Ln(DOTA) complexes representative of all four coordination geometry typologies deduced from NMR solution studies. A distinctive structural feature that discriminates SA (and SA') and TSA (and TSA') structures is represented by the twist angle between the two square planes of the antiprism, the basal four nitrogen, and the apical four oxygen planes. [Ce(DOTA)(H(2)O)](-) displays a TSA structural typology with a twist angle of 25 degrees and a Ce-O(water) distance of 2.59 A. The SA-type structure has been found in the case of complexes with Pr(III), Nd(III), and Dy(III), where the twist angle is 39, 39, and 38 degrees, respectively, and the metal-water oxygen distance varies significantly (Pr-O(w) 2.529 A; Nd-O(w) 2.508 A; and Dy-O(w) 2.474 A). [Tm(DOTA)](-) displays a TSA'-type structure with a twist angle of 24 degrees. As compared with the TSA structure of the corresponding Ce(III) complex, the Tm(III) complex shows an overall marked shrinkage of all metal-nitrogen and metal-oxygen distances (ca. 0.2 A), which reflects the contraction of the metal ionic radius across the series but also the effect associated with the decrease of the CN from 9 to 8. In [Sc(DOTA)](-), the even smaller ionic radius of Sc(III) shifts the geometry of the coordination cage to the more compact SA' typology with a twist angle of 41 degrees, a value very similar to that found in the SA structures of lanthanide(III) ions with CN 9. Finally, an investigation was made into the hydration spheres of the complexes with SA and TSA geometries to account for the experimental evidence of a markedly different rate of water exchange for the two isomeric structures. This is of fundamental importance to the understanding of the corresponding Gd(III) complexes as MRI contrast agents.
Journal Article↗
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↗
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↗
Conformational structure variations in DNA: a PCILO study.
Perturbative configuration interaction using localized orbital (PCILO) computations have been carried out on conformational preference of d(GpC) and d(CpG) units of Z-II DNA. By keeping the sugar pucker fixed in the crystallographic conformation, PCILO energies have been calculated as a function of torsion angles alpha and zeta around two P-O ester bonds with preselected values of beta, gamma and epsilon. The results indicate that the d(GpC) unit is energetically more stable than the d(CpG) unit and prefers a g+ t conformation in (alpha-zeta) hyper-space observed in the crystal structure. The d(CpG) unit, on the other hand, shows intrinsic preference for g-g- conformation with other torsion angles close to DNA-B structure. The possibility of d(GpC) unit responsible for the stability of Z-helix has been discussed.
Base Sequence↗
Structural variation in the 16S-23S rRNA intergenic spacers of Vibrio parahaemolyticus.
The 16S-23S rRNA intergenic spacers (IGS) of Vibrio parahaemolyticus were PCR-amplified and cloned with pT7Blue T vector. A total of six clones were isolated dependent on size difference. The clones were different with respect to both the number and the composition of the tRNA genes included, and were designated IGS-0, IGS-E, IGS-IA, IGS-AE, IGS-EKV and IGS-EKAV. IGS-EKAV included the cluster of tRNA(Glu)-tRNA(Lys)-tRNA(Ala)-tRNA(Val); IGS-EKV, tRNA(Glu)-tRNA(Lys)-tRNA(Val); IGS-AE, tRNA(Ala)-tRNA(Glu); IGS-IA, tRNA(Ile)-tRNA(Ala); and IGS-E, tRNA(Glu). IGS-0 had no tRNA gene. Some similarities were found in the nucleotide sequence of the non-coding regions flanked by the tRNA genes. The structure difference found in the spacers is meaningful for elucidating the evolutionary line of each ribosomal RNA operon and the profile is applicable as a molecular marker of the bacterium.
Cloning, Molecular↗