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At least 793 records · Page 44Linked to original sources
PubMed1991

Thieno-triazolo-1,4-diazepines as antagonists of platelet-activating factor: present status.

The platelet-activating factor, 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine, (PAF) antagonistic activity of thienotriazolodiazepines has recently been described. The lead compound in this series was brotizolam, which also exhibits sedative and hypnotic effects. By combination of brotizolam with the benzodiazepine receptor antagonist RO 15-1788, PAF antagonistic and central nervous system (CNS) activities could be segregated. Systematic structure variation has led to potent and selective PAF antagonists without CNS effects. WEB 2086 and its analogues WEB 2170 and STY 2108 are representative examples of this structural type and have shown a high potency and selectivity in PAF-induced and PAF-dependent in vitro tests and in experimental models. Studies in healthy volunteers have demonstrated potent pharmacological activity and good safety and tolerance of oral, intravenous or inhaled WEB 2086 in man. These agents should therefore prove useful for the further elucidation of the pathophysiological role of PAF and provide an opportunity for therapeutic applications in diseases in which the involvement of PAF has been implicated.

Animals↗
PubMed1987

Functional polymorphisms among HLA-DR4+ DR beta chains associated with limited peptide diversity.

Tryptic peptide map analysis by high-pressure liquid chromatography of DR4- associated DR beta chains revealed limited structural variation within DR beta polypeptides. Comparison of 3H-leucine-labelled tryptic peptide maps of Dw4 and Dw14 homozygous cells identified distinct peaks corresponding to Dw4 and Dw14-associated DR beta polypeptides. HPLC analysis of cell line 256, heterozygous for two DR4-related specificities, Dw4 and Dw14, displayed both peptides, corresponding to the variable Dw4 and Dw14 chromatograms. This observation was confirmed using a deletion mutant cell line derived from 256 lacking Dw4-associated class II genes. The observed peptide variation correlated precisely with predicted nucleotide-derived amino acid sequences implicating amino acids 66-71 of the DR beta chain as contributing to HLA-D structural and functional polymorphisms.

Amino Acid Sequence↗
PubMed2006

Rational design of polymerase inhibitors as antiviral drugs.

Almost all viruses have polymerases which are suitable targets for antiviral drugs. The development of selective polymerase inhibitors started with screening of compounds in virus-infected cell cultures and the mechanism of action was investigated once an inhibitor had been found. Especially nucleoside analogs were screened as their triphosphates were potential substrates for polymerases. However, the stepwise phosphorylation by cellular, and sometimes viral, kinases to the active triphosphate prevented a truly rational design of polymerase inhibitors. Nucleotide analogs offers a type of compounds which could be designed in a more rational way than nucleoside analogs since the first, most selective, phosphorylation step is eliminated in the path to the active inhibitor. The development of pyrophosphate analogs made rational design possible since these compounds act directly on the viral enzyme, but the room for structural variation was limited. The non-nucleoside HIV reverse transcriptase inhibitors are direct inhibitors and can thus be designed in a truly rational way by use of structure information on the enzyme-inhibitor complex by use of X-ray and NMR. This rational design of allosteric inhibitors is also being used in the development of inhibitors to other viral polymerases.

Antiviral Agents↗
PubMed2002

Effects of strand and directional asymmetry on base-base coupling and charge transfer in double-helical DNA.

Mechanistic models of charge transfer (CT) in macromolecules often focus on CT energetics and distance as the chief parameters governing CT rates and efficiencies. However, in DNA, features unique to the DNA molecule, in particular, the structure and dynamics of the DNA base stack, also have a dramatic impact on CT. Here we probe the influence of subtle structural variations on base-base CT within a DNA duplex by examining photoinduced quenching of 2-aminopurine (Ap) as a result of hole transfer (HT) to guanine (G). Photoexcited Ap is used as a dual reporter of variations in base stacking and CT efficiency. Significantly, the unique features of DNA, including the strandedness and directional asymmetry of the double helix, play a defining role in CT efficiency. For an (AT)n bridge, the orientation of the base pairs is critical; the yield of intrastrand HT is markedly higher through (A)n compared with (T)n bridges, whereas HT via intrastrand pathways is more efficient than through interstrand pathways. Remarkably, for reactions through the same DNA bridge, over the same distance, and with the same driving force, HT from photoexcited Ap to G in the 5' to 3' direction is more efficient and less dependent on distance than HT from 3' to 5'. We attribute these differences in HT efficiency to variations in base-base coupling within the DNA assemblies. Thus base-base coupling is a critical parameter in DNA CT and strongly depends on subtle structural nuances of duplex DNA.

Base Pairing↗
PubMed2006

Structural changes of Escherichia coli ferric uptake regulator during metal-dependent dimerization and activation explored by NMR and X-ray crystallography.

Ferric uptake regulator (Fur) is a global bacterial regulator that uses iron as a cofactor to bind to specific DNA sequences. Escherichia coli Fur is usually isolated as a homodimer with two metal sites per subunit. Metal binding to the iron site induces protein activation; however the exact role of the structural zinc site is still unknown. Structural studies of three different forms of the Escherichia coli Fur protein (nonactivated dimer, monomer, and truncated Fur-(1-82)) were performed. Dimerization of the oxidized monomer was followed by NMR in the presence of a reductant (dithiothreitol) and Zn(II). Reduction of the disulfide bridges causes only local structure variations, whereas zinc addition to reduced Fur induces protein dimerization. This demonstrates for the first time the essential role of zinc in the stabilization of the quaternary structure. The secondary structures of the mono- and dimeric forms are almost conserved in the N-terminal DNA-binding domain, except for the first helix, which is not present in the nonactivated dimer. In contrast, the C-terminal dimerization domain is well structured in the dimer but appears flexible in the monomer. This is also confirmed by heteronuclear Overhauser effect data. The crystal structure at 1.8A resolution of a truncated protein (Fur-(1-82)) is described and found to be identical to the N-terminal domain in the monomeric and in the metal-activated state. Altogether, these data allow us to propose an activation mechanism for E. coli Fur involving the folding/unfolding of the N-terminal helix.

Amino Acid Sequence↗
PubMed2000

In vitro characterization of anti-glucosylceramide rabbit antisera.

Glucosylceramides (GlcCer) are biosynthetic precursors of glycosphingolipids. They are widely distributed in biological systems where they exhibit numerous biological functions. Studies on the localization of glucosylceramides in different tissues have used biochemical methods only since specific antibodies against GlcCer were not previously available. We have characterized two commercially available rabbit antisera which were prepared against GlcCer of plant origin (1-O-(beta-D-glucopyranosyl)-N-acyl-4-hydroxysphinganine; GlcCer-3) or human origin (1-O-(beta-D-glucopyranosyl)-N-acyl-sphingosine; GlcCer-2) and claimed to be specific for GlcCer. The antisera were also able to detect specifically GlcCer species in crude lipid extracts from human epidermis after separation by thin-layer chromatography. The reagents are sensitive since both antisera reacted at dilutions higher than 1:500 with their homologous antigen in the nanogram range in thin layer immunostaining or dot-blot assays. The antisera are specific for GlcCer although they did not differentiate between GlcCer-2 and GlcCer-3 containing sphingosine or 4-hydroxysphinganine. The antisera also reacted with N-stearoyl-DL-dihydroglucocere-broside indicating that the naturally occurring structural variations in the amino alcohol moiety are not determining the specificity. No crossreactivity was observed with other mono- or diglycosylceramides (galactosylceramides, lactosyl-ceramide), free ceramides or structurally unrelated lipids (cholesterol, sphingomyelin, or phospholipids). Therefore, the glycosylmoiety seems to represent the major antigenic determinant. Finally, the antisera also proved to be useful for the immunohistochemical localization of GlcCer in human epidermis by which earlier biochemical data on the distribution of GlcCer in the various epidermal layers were confirmed.

Animals↗
PubMed1982

Kinetic investigation of the alpha-chymotrypsin-catalyzed hydrolysis of peptide substrates. The relationship between the peptide structure C-terminal to the cleaved bond and reactivity.

Peptide substrates of the general structure Ac-Tyr-Ly1-Ly2-..-Lym-NH2 and Ac-Phe-Ly1-NH2 have been synthesized and subjected to alpha-chymotrypsin-catalyzed hydrolysis to collect information on the interactions between the enzyme active site and the amino-acid residues Ly1, Ly2, etc., C-terminal to the susceptible bond of the peptide. For this purpose changes in the dissociation constants of the enzyme-substrate complexes and in the rate constants of acylation have been related to the structural variations of the substrates. The results indicate that interactions occur with the two residues next to the scissible bond, Ly1 and Ly2, but not with residue Ly3. Structural description of individual interactions was carried out with the aid of skeletal models of the active site. From such combination of kinetic and structural data a plausible interaction scheme for the substrate side C-terminal to the scissible bond has been deduced. This interaction scheme, which defines conformation and orientation of this part of the substrate within the active site, is characterized by the presence of a single hydrogen bond occurring between NH(Ly2) and O(Phe-41). No donor interacting with the back-bone carbonyl groups of residues Ly1 and Ly2 could be detected in the model of alpha-chymotrypsin. The effect of modification of the side chains of residues Ly1 and Ly2 on the kinetic constants was shown to be consistent with the interactions assumed to occur between the side chains of these residues and the active site. The interpretation of the results obtained from these specificity studies have led to refined concepts concerning the relative importance of different sets of enzyme-substrate interactions in determining reactivity.

Amino Acid Sequence↗
PubMed1988

Genotyping and sequence analysis of apolipoprotein E isoforms.

Apolipoprotein E (apoE), a polymorphic plasma protein, is essential for catabolism of lipoproteins by receptor-mediated endocytosis. One of the apoE isoforms (E2) differs in its binding affinity to specific receptors and contributes to variations in lipoprotein metabolism. Diagnosis of apoE isoforms is done by isoelectric focusing, but it is hindered by various degrees of post-translational sialylation of the apoE protein. Electrophoretically silent structural variations may also escape detection by this technique. We describe a method for genotyping apoE based on hybridization of allele-specific oligonucleotides with enzymatically amplified genomic DNA, which permits unambiguous diagnosis of six common apoE phenotypes within 24 h. Among 100 E2 alleles present in 81 unrelated individuals genotyped by this technique, we found two rare structural mutants of apoE in addition to the common E2 form, E2(158Arg----Cys). Automated sequencing of amplified DNA identified the rare mutants as E2(136Arg----Ser) and E2(145Arg----Cys). The genotypic method may complement or even replace isoelectric focusing for routine determination of apoE phenotypes and for identification of rare structural variants.

Alleles↗
PubMed1986

Bimodal variations in subcellular structures of rat thyroid follicular cells during 24 hours: fine structural and morphometric studies.

To clarify 24-hr variations in rat thyroid follicular cells under physiological conditions, their subcellular structures were examined at six evenly spaced times during 24 hr by using a morphometric technique. The volume, surface, and numerical densities of subcellular structures varied distinctly over each 24-hr period, with a bimodal pattern. The cellular and nuclear volumes varied also bimodally over 24 hr. A decrease in the surface density of the apical plasmalemma at 1200 and 0000 hr coincided with an increase in volume density of cytoplasmic granules representing colloid droplets and dense bodies. Most granules (colloid droplets) appearing at these times were reduced in electron density. At other times, especially at 1600 and 0400 hr, morphometric parameters of rough endoplasmic reticulum (rER), Golgi complex, and subapical vesicles were prominently increased, although values for rER did not peak at 1600 hr. At these times, the volume densities of cytoplasmic granules, most of which were heterogeneous and of homogeneous electron density, were decreased. These findings coincided with immediate and subsequent reactions of follicular cells after injection of thyroid-stimulating hormone (TSH). From the evidence, it seems likely that variations in follicular cells over a 24-hr period reflect variations in blood TSH concentration. The total membrane areas of membrane components in follicular cells were calculated from the morphometric measurements. These areas fluctuated unimodally during 24 hr over a 65% range. This suggests that the membranes in follicular cells are subjected to cyclic degradation and regeneration during each 24-hr period.

Animals↗
PubMedDate not supplied

Genetic studies of low-abundance human plasma proteins. VII. Heterogeneity of the C1S subcomponent of the first complement component.

Charge-based structural variation has been observed in the C1s subcomponent of the first complement component C1 after isoelectric focusing and immunoblotting. One common and two uncommon autosomal co-dominantly expressed alleles, designated C1S*1, C1S*2 and C1S*3, have been recognized at the C1S structural locus. The frequency of these alleles was 0.979, 0.016 and 0.005, respectively, in a U.S. white population. No variation at the C1S locus was observed in a U.S. black sample (n = 95).

Alleles↗
PubMed2007

Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons.

The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome.

Animals↗
PubMed1989

Generalizability of WAIS-R factor structure within and between populations.

We investigated the reliability of the factor structure of the Wechsler Adult Intelligence Scale-Revised (WAIS-R). The WAIS-R subtests, as administered to 146 head-injured males, were factor analyzed. Two- and three-factor solutions were extracted that were consistent with past findings. Congruence coefficients were computed to determine degree of association between factor structures from all samples reported in the literature. All coefficients were impressive. Also, congruence coefficients based on factor structures derived from different samples within the same population were compared to coefficients based on different samples from different populations. No significant discrepancies emerged. Apparently, the slight factor structure variation that does exist is due to chance data fluctuation rather than to systematic population bias. This reflects well on the robustness of the WAIS-R factor structure.

Adult↗
PubMed2001

Finding and using local symmetry in identifying lower domain movements in hexon subunits of the herpes simplex virus type 1 B capsid.

A characteristic of virus assembly is the use of symmetry to construct a complex capsid from a limited number of different proteins. Many spherical viruses display not only icosahedral symmetry, but also local symmetries, which further increase the redundancy of their structural proteins. We have developed a computational procedure for evaluating the quality of these local symmetries that allows us to probe the extent of local structural variations among subunits. This type of analysis can also provide orientation parameters for carrying out non-icosahedral averaging of quasi-equivalent subunits during three-dimensional structural determination. We have used this procedure to analyze the three types of hexon (P, E and C) in the 8.5 A resolution map of the herpes simplex virus type 1 (HSV-1) B capsid, determined by electron cryomicroscopy. The comparison of the three hexons showed that they have good overall 6-fold symmetry and are almost identical throughout most of their lengths. The largest difference among the three lies near the inner surface in a region of about 34 A in thickness. In this region, the P hexon displays slightly lower 6-fold symmetry than the C and E hexons. More detailed analysis showed that parts of two of the P hexon subunits are displaced counterclockwise with respect to their expected 6-fold positions. The most highly displaced subunit interacts with a subunit from an adjacent P hexon (P'). Using the local 6-fold symmetry axis of the P hexon as a rotation axis, we examined the geometrical relationships among the local symmetry axes of the surrounding capsomeres. Deviations from exact symmetry are also found among these local symmetry axes. The relevance of these findings to the process of capsid assembly is considered.

Capsid↗
PubMed1996

The structure of a highly virulent Theiler's murine encephalomyelitis virus (GDVII) and implications for determinants of viral persistence.

GDVII is a highly virulent Theiler's murine encephalomyelitis virus (TMEV) which causes acute encephalitis in mice, while the BeAn and DA strains are the less virulent TMEV which cause chronic demyelinating disease in the central nervous system as a result of persistent infection. Purified GDVII virus isolated from infected BHK-21 cells was crystallized and its structure was determined to 3.5-A resolution by X-ray crystallography. In contrast to other TMEV structures, the VP1 C-terminus of GDVII virus has an ordered conformation that forms a hook over the VP3 knob near the threefold axis. Comparisons with the atomic structures of the less virulent BeAn and DA viruses revealed significant structural variations in a major site (cluster B) on the protruding surface loop puff B of VP2. Puff B is located near the VP3 GH loop region which is structurally analogous to the host receptor attachment site of the major serogroup of human rhinoviruses. Mutations at residue 1101 in VP1 and residue 2141 in VP2, which are also near the VP3 GH loop and adjacent to cluster B, were previously shown to influence persistence of DA virus. These observations indicate that the characteristic interaction with the host receptor through these sites may potentially alter TMEV persistence.

Amino Acid Sequence↗
PubMed1983

Isolation of a rabbit IgG fraction with cytophilic properties.

About 15% of rabbit IgG loaded on a column of Con A-Sepharose 4B was found to be specifically bound to the column due to a structural variation in its carbohydrate moiety. The Con A-retained rabbit IgG contained a higher amount of neutral hexoses than the initial IgG but its molecular weight, antigenic structure and half-life were identical or similar. The Con A-retained rabbit IgG has an affinity for the Fc receptor-bearing homologous macrophages which is 10 times higher than that of the initial IgG. The IgG fraction not retained on Con A-Sepharose is practically devoid of binding ability. These results suggest that the Con A-bound IgG may represent the cytophilic fraction of monomeric IgG responsible for the binding of IgG to Fc receptor-bearing cells.

Animals↗
PubMed1986

Substrate and inhibitor studies of thermolysin-like neutral metalloendopeptidase from kidney membrane fractions. Comparison with bacterial thermolysin.

The inhibitory constants of a series of synthetic N-carboxymethyl peptide inhibitors and the kinetic parameters (Km, kcat, and kcat/Km) of a series of model synthetic substrates were determined for the membrane-bound kidney metalloendopeptidase isolated from rabbit kidney and compared with those of bacterial thermolysin. The two enzymes show striking similarities with respect to structural requirements for substrate binding to the hydrophobic pocket at the S1' subsite of the active site. Both enzymes showed the highest reaction rates with substrates having leucine residues in this position while phenylalanine residues gave the lowest Km. The two enzymes were also inhibited by the same N-carboxymethyl peptide inhibitors. Although the mammalian enzyme was more susceptible to inhibition than its bacterial counterpart, structural variations in the inhibitor molecules affected the inhibitory constants for both enzymes in a similar manner. The two enzymes differed significantly, however, with respect to the effect of structural changes in the P1 and P2' positions of the substrate on the kinetic parameters of the reaction. The mammalian enzyme showed the highest reaction rates and specificity constants with substrates having the sequence -Phe-Gly-Phe- or -Phe-Ala-Phe- in positions P2, P1, and P1', respectively, while the sequence -Ala-Phe-Phe- was the most favored by the bacterial enzyme. The sequence -Gly-Gly-Phe- as found in enkephalins was not favored by either of the enzymes. Of the substrates having an aminobenzoate group in the P2' position, the mammalian enzyme favored those with the carboxyl group in the meta position while the bacterial enzyme favored those with the carboxyl group in the para position.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2003

N-(omega-(4-(2-methoxyphenyl)piperazin-1-yl)alkyl)carboxamides as dopamine D2 and D3 receptor ligands.

The dopamine D(3) receptor is recognized as a potential therapeutic target for the treatment of various neurological and psychiatric disorders. Targetting high affinity and D(3) versus D(2) receptor-preferring ligands, the partial agonist BP 897 was taken as a lead structure. Variations in the spacer and the aryl moiety led to N-alkylated 1-(2-methyoxyphenyl)piperazines with markedly improved affinity and selectivity. Molecular modeling studies supported the structural development. Pharmacophore models for dopamine D(2) and D(3) receptor ligands were developed from their potentially bioactive conformation and were compared in order to get insight into molecular properties of importance for D(2)/D(3) receptor selectivity. For the 72 compounds presented here, an extended and more linear conformation in the aliphatic or aryl spacers turned out to be crucial for dopamine D(3) receptor selectivity. Structural diversity in the aryl moiety (benzamides, heteroarylamides, arylimides) had a major influence on (sub)nanomolar D(3) receptor affinity, which was optimized with more rigid aryl acrylamide derivatives. Compound 38 (ST 280, (E)-4-iodo-N-(4-(4-(2-methoxyphenyl)piperazin-1-yl)butyl)cinnamoylamide) displayed a most promising pharmacological profile (K(i) (hD(3)) = 0.5 nM; K(i) (hD(2L)) = 76.4 nM; selectivity ratio of 153), and above that, compound 38 offered the prospect of a novel radioligand as a pharmacological tool for various D(3) receptor-related in vitro and in vivo investigation.

Animals↗
PubMed2005

Cluster size selectivity in the product distribution of ethene dehydrogenation on niobium clusters.

Ethene reactions with niobium atoms and clusters containing up to 25 constituent atoms have been studied in a fast-flow metal cluster reactor. The clusters react with ethene at about the gas-kinetic collision rate, indicating a barrierless association process as the cluster removal step. Exceptions are Nb8 and Nb10, for which a significantly diminished rate is observed, reflecting some cluster size selectivity. Analysis of the experimental primary product masses indicates dehydrogenation of ethene for all clusters save Nb10, yielding either Nb(n)C2H2 or Nb(n)C2. Over the range Nb-Nb6, the extent of dehydrogenation increases with cluster size, then decreases for larger clusters. For many clusters, secondary and tertiary product masses are also observed, showing varying degrees of dehydrogenation corresponding to net addition of C2H4, C2H2, or C2. With Nb atoms and several small clusters, formal addition of at least six ethene molecules is observed, suggesting a polymerization process may be active. Kinetic analysis of the Nb atom and several Nb(n) cluster reactions with ethene shows that the process is consistent with sequential addition of ethene units at rates corresponding approximately to the gas-kinetic collision frequency for several consecutive reacting ethene molecules. Some variation in the rate of ethene pick up is found, which likely reflects small energy barriers or steric constraints associated with individual mechanistic steps. Density functional calculations of structures of Nb clusters up to Nb(6), and the reaction products Nb(n)C2H2 and Nb(n)C2 (n = 1...6) are presented. Investigation of the thermochemistry for the dehydrogenation of ethene to form molecular hydrogen, for the Nb atom and clusters up to Nb6, demonstrates that the exergonicity of the formation of Nb(n)C2 species increases with cluster size over this range, which supports the proposal that the extent of dehydrogenation is determined primarily by thermodynamic constraints. Analysis of the structural variations present in the cluster species studied shows an increase in C-H bond lengths with cluster size that closely correlates with the increased thermodynamic drive to full dehydrogenation. This correlation strongly suggests that all steps in the reaction are barrierless, and that weakening of the C-H bonds is directly reflected in the thermodynamics of the overall dehydrogenation process. It is also demonstrated that reaction exergonicity in the initial partial dehydrogenation step must be carried through as excess internal energy into the second dehydrogenation step.

Journal Article↗