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At least 955 records · Page 53Linked to original sources
PubMed1991

Human leucocyte aspartylglucosaminidase. Evidence for two different subunits in a more complex native structure.

Human leucocyte aspartylglucosaminidase (AGA: 1-aspartamido-beta-N-acetylglucosamine amidohydrolase, EC 3.5.1.26) was purified to homogeneity by using affinity chromatography, gel filtration, chromatofocusing and reverse-phase h.p.l.c. As shown by SDS/PAGE, the homogeneous purified enzyme preparation consists of four polypeptide chains with molecular masses of 25, 24, 18 and 17 kDa. In the native polyacrylamide gel these polypeptides migrate as one active enzyme complex, and by gel filtration the peak of enzyme activity can be detected in a position of about 65 kDa. Digestion with endoproteinase Lys-C or endoproteinase Asp-N, followed by peptide analysis with reverse-phase h.p.l.c., reveals an identical peptide pattern for the 24 and 25 kDa bands as well as for the 17 and 18 kDa bands. This treatment further demonstrated a totally different peptide pattern for the 24/25 kDa versus the 17/18 kDa subunit. The N-terminal sequences of the 17 kDa and the 18 kDa peptides were identical, as determined by Edman degradation. The N-termini of the 24 kDa and the 25 kDa peptides were blocked. The enzyme was partly resistant to endoglycosidases H and F, but N-glycosidase F transformed the 24/25 kDa band into one 23 kDa band and the 17/18 kDa band into one 16 kDa band. Also, immunological data obtained with antisera produced against these subunits showed that AGA consists of two non-identical polypeptides.

Amino Acid Sequence↗
PubMed1996

Formation and maturation of the calcium release apparatus in developing and adult avian myocardium.

Muscle fibers release large amounts of calcium from an internal compartment, the sarcoplasmic reticulum (SR), during activation. Two proteins are involved in this process and its control: plasma membrane calcium channels, or dihydropyridine receptors (DHPRs), and SR calcium release channels, or ryanodine receptors (RyRs). The two proteins form part of a structural complex, perhaps unique to muscle cells, which allows an interaction between plasma membrane and SR, resulting in calcium release from the latter. The surface-SR interaction is a step in the coupling between electrical events in the plasma membrane and contraction (excitation-contraction coupling). The structural complexes have been called calcium release units. One key to further understanding the control of calcium homeostasis in muscle is knowledge of how DHPRs and RyRs assemble into calcium release units. We have studied the development of avian myocardium, using immunocytochemistry to locate DHPRs and RyRs and electron microscopy to follow the formation of calcium release units containing feet (RyRs) and large membrane particles (presumably DHPRs). We find that the initial step is a docking of SR vesicles to the plasma membrane, followed by the appearance of feet in the junctional gap between SR and plasma membrane. Feet aggregate in ordered arrays, and the arrays increase in size until they fill the entire junctional gap. Clustering of membrane particles, presumably DHPRs, is apparently coupled to clustering of feet, since the two junction components assemble within patches of membrane of approximately equal size and containing an approximately constant ratio of particles to feet. Thus, despite the fact that no evidence exists for a direct interaction between DHPRs and RyRs in cardiac muscle, some mechanism exists to ensure that the two molecules are clustered in proximity to each other and in the appropriate proportion.

Animals↗
PubMed2003

Automated generation of MCSS-derived pharmacophoric DOCK site points for searching multiconformation databases.

All docking methods employ some sort of heuristic to orient the ligand molecules into the binding site of the target structure. An automated method, MCSS2SPTS, for generating chemically labeled site points for docking is presented. MCSS2SPTS employs the program Multiple Copy Simultaneous Search (MCSS) to determine target-based theoretical pharmacophores. More specifically, chemically labeled site points are automatically extracted from selected low-energy functional-group minima and clustered together. These pharmacophoric site points can then be directly matched to the pharmacophoric features of database molecules with the use of either DOCK or PhDOCK to place the small molecules into the binding site. Several examples of the ability of MCSS2SPTS to reproduce the three-dimensional pharmacophoric features of ligands from known ligand-protein complex structures are discussed. In addition, a site-point set calculated for one human immunodeficiency virus 1 (HIV1) protease structure is used with PhDOCK to dock a set of HIV1 protease ligands; the docked poses are compared to the corresponding complex structures of the ligands. Finally, the use of an MCSS2SPTS-derived site-point set for acyl carrier protein synthase is compared to the use of atomic positions from a bound ligand as site points for a large-scale DOCK search. In general, MCSS2SPTS-generated site points focus the search on the more relevant areas and thereby allow for more effective sampling of the target site.

Binding Sites↗
PubMed2005

Rational design of potent mimic peptide derived from monoclonal antibody: antibody mimic design.

The variable regions of antibody molecules bind antigens with high affinity and specificity. The binding sites are imparted largely to the hypervariable portions (i.e. CDRs) of the variable region. Peptides derived from antibody CDRs can bind antigen with similar specificity acted as mimic of antibody and become drug-designing core, although with markedly lower affinity. In this study, the 3D complex structure of tumor necrosis factor-alpha (TNFalpha) and its neutralizing monoclonal antibody Z12 was modeled using molecular docking method and optimized with molecular mechanism and dynamics method. The binding domains between TNFalpha and Z12 were determined theoretically and functional antigen epitopes were predicted. According to the 3D complex structure of TNFalpha and Z12, a novel antagonist peptide, named PT1, was designed theoretically. The experimental result showed that PT1 possessed significantly binding inhibition of TNFalpha to Z12 and protected L929 cells from the cytotoxic effect of TNFalpha. The designed mimic peptide was more amenable to synthetic chemistry and thus might be useful starting points for the design of smaller organic mimics.

Amino Acid Sequence↗
PubMed2001

Tissue engineering: complete autologous valve conduit--a new moulding technique.

OBJECTIVE: The use of fibrin gel, which can be produced from patients' blood, was investigated as an autologous, biodegradable scaffold. A new moulding technique was developed to create a complete aortic root. METHODS: A new moulding technique was generated for the creation of complete valve conduit. On the basis of biomechanical valve design studies, a tricuspid "ventricular" and "aortic" stamp were developed. A silicone-coated aluminum cylinder was used to circumferentially limit the mould. The cell/gel suspension was filled into the mould and polymerization was started. RESULTS: The creation of complex structures such as complete valve conduits is possible with the moulding technique described. With a layer thickness of up to 2 mm, histological investigations showed excellent tissue development with viable fibroblasts surrounded by collagen bundles. CONCLUSION: Fibrin gel unifies many properties of an ideal scaffold: The formation of complex structures is possible, the degradation and polymerization is controllable and the formation of the extracellular matrix is excellent.

Aortic Valve↗
PubMed2004

Cytological indications of the complex subtelomeric structure.

Research on the subtelomeric region has considerably increased because this chromosome segment (1) keeps the chromosome number constant, (2) intervenes in cancer and cell senescence processes, (3) presents more crossovers than other regions of the genome and, (4) is the site of cryptic chromosome aberrations associated with mental retardation and congenital malformations. Quantitative microphotometrical scanning and computer graphic image analysis enables the detection of differentially distributed Giemsa-stained structures in T-banded subtelomeric segments of human and Chinese hamster ovary (CHO) chromosomes. The presence of high density stain patterns in the subtelomeric region was confirmed using endoreduplicated chromosomes as a model. Besides, prolonging the incubation in the T-buffer, specific holes were induced in subtelomeric segments. Hole specificity was confirmed inducing them in complex CHO chromosome aberrations obtained by AluI. The method was also used to detect minute sister chromatid exchanges in the T-banded subtelomeric area (t-SCEs). The presence of t-SCEs was suspected to reflect, at the microscope level, the high crossover activity prevailing in the region. Due to the fact that the fluorescent signals obtained with subtelomeric probes seem to be colocalized with subtelomeric high density areas, measurements on the position of both structures with respect to the diffraction and chromosome edges were carried out. Data obtained showed comparable values suggesting that the high density segments were located where telomeric probes usually fluoresce. The possible relationship of the high density patterns, the production of specific holes, the localization of fluorescent areas and the detection of minute SCEs in the subtelomeric segment observed in T-banded CHO and human chromosomes is briefly reviewed.

Animals↗
PubMed2005

Modulation of MPP+ uptake by procyanidins in Caco-2 cells: involvement of oxidation/reduction reactions.

It is becoming increasingly evident that the absorption of certain nutrients and drugs and their effects are largely influenced by the concomitant ingestion of other substances. As various xeno- and endobiotics belong to the class of organic cations, the aim of this work was to study the modulation of the intestinal apical uptake of organic cations by diet procyanidins. Five procyanidin fractions with different structural complexity were obtained after fractionation of a grape seed extract. The effect of these compounds on 1-methyl-4-phenylpyridinium (MPP+) uptake was evaluated in Caco-2 cells. Apical uptake of 3H-MPP+ by Caco-2 cells was increased by a 60 min exposure to 600 microg ml(-1) of procyanidin fractions, that increase being positively related with procyanidins structural complexity. It was verified that 3H-MPP+ uptake increased with preincubation time. It was speculated that procyanidins were oxidized during preincubation, this change could interfered with transport activity. Tested oxidizing agents showed that the redox state of the transporter could affect its activity. Additionally, trans-stimulation experiments showed that catechin and fraction I (the simpler fraction) can use the same transporter as MPP+. The results are compatible with the hypothesis of these compounds being competitive inhibitors of MPP+ transport. In conclusion, procyanidins are capable to modulate MPP+ apical uptake in Caco-2 cells, this transport being most probably modulated through oxidation-reduction phenomena. Interactions between these compounds and drugs present in the diet may affect their absorption and bioavailability. Both the concentration and complexity of the procyanidin compounds should be taken into account in medical practice.

1-Methyl-4-phenylpyridinium↗
PubMed2001

The 1997/1998 mass mortality of corals: effects on fish communities on a Tanzanian coral reef.

The abnormally high surface temperatures in the world's oceans during 1997/1998 resulted in widespread coral bleaching and subsequent coral mortality. An experiment was performed to study the effects of this coral mortality as well as the influence of the structural complexity on fish communities on a Tanzanian coral reef. Changes in fish communities were investigated on plots of transplanted corals after 88% of these corals had died. A distinct shift in fish community composition was found, although diversity was not affected. Fish abundance rose by 39% mostly due to an increase in herbivores, which seemed to benefit from enhanced algal growth on the dead corals. Fish abundance, species diversity and community composition were also strongly influenced by the structural complexity provided by the live and dead corals. This suggests that a coral reef can support abundant and diverse fish populations also after the corals have died as long as the reef structure is sustained.

Animals↗
PubMed1989

A complex nucleoprotein structure involved in activation of transcription of two divergent Escherichia coli promoters.

Initiation of transcription at malEp and malKp, two divergent Escherichia coli promoters, depends on the presence of both CRP, a pleiotropic activator, and MalT, the maltose regulon activator. We carried out in vivo genetic and functional analysis of these promoters and characterized their interaction with MalT and CRP using DNase I footprinting. The functional limits of the promoters are located about 240 base-pairs (bp) upstream of their transcription start sites, which are 271 bp apart. These promoters therefore overlap by about 210 bp. The overlapping region encompasses four CRP-binding sites and at least four MalT-binding sites. Insertions in the centre of this region are tolerated provided that they correspond to an integral number of DNA helix turns. In DNase I footprinting experiments performed on the complex formed by MalT with malEp-malKp, the DNA appears to be wrapped around the protein. We propose a model for the nucleoprotein structure that might be involved in transcription activation at these divergent promoters.

Bacterial Proteins↗
PubMed2001

De novo formation of focal complex-like structures in host cells by invading Streptococci.

Group A streptococcus (GAS) induces its own entry into eukaryotic cells in vitro and in vivo. Fibronectin (Fn) bound to protein F1, a GAS surface protein, acts as a bridge connecting the bacterium to host cell integrins. This triggers clustering of integrins, which acquire a polar pattern of distribution similar to that of protein F1 on the GAS surface. A unique and transient adhesion complex is formed at the site of GAS entry, which does not contain alpha-actinin. Vinculin is recruited to the site of GAS entry but is not required for uptake. The invading GAS recruits focal adhesion kinase (FAK), which is required for uptake and is tyrosine phosphorylated. The Src kinases, Src, Yes and Fyn, enhance the efficiency of GAS uptake but are not absolutely required for GAS entry. In addition, Rac and Cdc42, but not Rho, are required for the entry process. We suggest a model in which integrin engagement by Fn-occupied protein F1 triggers two independent signalling pathways. One is initiated by FAK recruitment and tyrosine phosphorylation, whereas the other is initiated by the recruitment and activation of Rac. The two pathways subsequently converge to trigger actin rearrangement leading to bacterial uptake.

Actinin↗
PubMed1991

Argument structure frames: a lexical complexity metric?

The number of semantic argument structure frames associated with a verb has been reported to influence ease of processing during language comprehension. The present experiments tested the generality of the argument structure complexity effect with three dependent measures: eye-fixation times, naming latencies, and lexical decision latencies. Two eye-movement experiments and two experiments using cross-modal tasks failed to provide evidence supporting the argument structure complexity effect. The present experiments indicated that results reflecting verbs' argument structure complexity are not generalizable.

Attention↗
PubMed2000

Preparation and characterisation of quillaja saponin with less heterogeneity than Quil-A.

Immunisation against pathogens remains one of the most effective ways of preventing or reducing losses due to infectious diseases in animal husbandry. When inactivated vaccines are used, adjuvants are most often required to obtain satisfactory immune responses. One such type of adjuvant is saponin derived from the bark of Quillaja saponaria Molina, a tree of the rose family. A few different commercial sources exist, but due to the structural complexity and heterogeneity of these saponin preparations, it has been difficult to establish exactly which components are responsible for the adjuvant activity. By carefully selecting the bark source, we have succeeded in preparing a much less heterogeneous preparation of quillaja saponin. In this report we describe the preparation, in terms of structural complexity, hemolytic activity, adjuvant activity, and its ability to form ISCOM matrix. This new preparation could have implications for use per se, or as starting material for more effective preparation of pure substances.

Adjuvants, Immunologic↗
PubMed2005

Community assembly at the patch scale in a species rich tropical river.

In tropical floodplain rivers, communities associated with structurally complex habitats are disassembled and reassembled as aquatic organisms repeatedly colonize new areas in response to gradual but continuous changes in water level. Thus, a neutral model reflecting random colonization and extinction dynamics may be sufficient to predict assemblage patterns at the scale of local habitat patches. If water level fluctuations and associated patch dynamics are sufficiently predictable, however, community assembly on habitat patches also may be influenced by species-specific responses to habitat features and/or species interactions. We experimentally manipulated structural complexity and proximity to source habitat (which influences colonization rate) of simulated rocky patches in the littoral zone of a tropical lowland river and demonstrate significant effects of both factors on species density of fishes and macroinvertebrates. Interspecific variation in vagility significantly affected assemblage response to habitat complexity. In a second experiment, created habitat patches were sampled over time intervals ranging from 1 day to 36 days to examine temporal dynamics of community assembly. A null-model test revealed that assemblage structure became increasingly non-random, concomitant with increasing species density, over time. Community dynamics in newly formed habitat patches appeared to be dominated by dispersal, whereas in older patches, abundances of individual species increasingly were influenced by habitat characteristics. These data suggest that species-specific responses to environmental variation resulted, in part, because of species interactions. We conclude that community assembly in shallow habitats of this tropical lowland river is influenced by physical habitat characteristics, the spatial distribution of habitat patches, and species interactions as habitats are saturated with individuals.

Analysis of Variance↗
PubMed1996

DNA binding mechanism of O6-alkylguanine-DNA alkyltransferase: stoichiometry and effects of DNA base composition and secondary structure on complex stability.

O6-Alkylguanine-DNA alkyltransferase (AGT) is an important cellular defense against the mutagenic effects of DNA alkylating agents. In humans this defense can contribute to the ability of some tumors to resist the effects of chemotherapeutic agents that act through DNA alkylation. We report here studies that characterize the interaction of AGT with DNA. We show that although AGT sediments as a monomer in the absence of DNA, it binds cooperatively to single stranded deoxyribonucleotides. The stoichiometries of complexes formed with 16-, 30-, and 80-base oligodeoxyribonucleotides are 3.8 +/- 0.3, 5.3 +/- 0.2, and 8.9 +/- 0.2, respectively; the binding density decreasing from approximately 4 nt/monomer to approximately 9 nt/monomer as DNA length increases over this range. Binding competition assays show that DNA affinities depend only weakly on base composition or secondary structure, although in general G + C-rich sequences are bound with greater affinity than are A + T-rich ones and single-stranded DNA is bound with greater affinity than duplex forms. These results suggest mechanisms by which AGT may search for alkylated sites and interact with them to effect DNA repair.

Base Composition↗
PubMed2001

Pectin: cell biology and prospects for functional analysis.

Pectin is a major component of primary cell walls of all land plants and encompasses a range of galacturonic acid-rich polysaccharides. Three major pectic polysaccharides (homogalacturonan, rhamnogalacturonan-I and rhamnogalacturonan-II) are thought to occur in all primary cell walls. This review surveys what is known about the structure and function of these pectin domains. The high degree of structural complexity and heterogeneity of the pectic matrix is produced both during biosynthesis in the endomembrane system and as a result of the action of an array of wall-based pectin-modifying enzymes. Recent developments in analytical techniques and in the generation of anti-pectin probes have begun to place the structural complexity of pectin in cell biological and developmental contexts. The in muro de-methyl-esterification of homogalacturonan by pectin methyl esterases is emerging as a key process for the local modulation of matrix properties. Rhamnogalacturonan-I comprises a highly diverse population of spatially and developmentally regulated polymers, whereas rhamnogalacturonan-II appears to be a highly conserved and stable pectic domain. Current knowledge of biosynthetic enzymes, plant and microbial pectinases and the interactions of pectin with other cell wall components and the impact of molecular genetic approaches are reviewed in terms of the functional analysis of pectic polysaccharides in plant growth and development.

Cell Wall↗
PubMed1988

Structure of helical RecA-DNA complexes. III. The structural polarity of RecA filaments and functional polarity in the RecA-mediated strand exchange reaction.

The RecA protein of Escherichia coli has been used in vitro to mediate a strand-exchange reaction between homologous DNA molecules. A three-dimensional reconstruction of a RecA filament on double-stranded DNA has been previously determined from electron micrographs, and the reconstruction displays a clear axial polarity. The RecA-mediated strand-exchange reaction between a double-stranded DNA and a homologous single-stranded DNA that is complexed with a RecA helical polymer proceeds with a known polarity. Using image analysis of electron micrographs, we have determined the relation between the structural polarity of RecA filaments and the 3' and 5' polarity of single-stranded DNA. Thus, the structural polarity of RecA filaments can now be related to the direction in which the RecA-mediated strand-exchange reaction advances along the complexed single-stranded DNA.

DNA, Bacterial↗
PubMed1992

Information tradeoffs in complex stimulus structure: local and global levels in naturalistic scenes.

An information tradeoff is an increased processing or utilization of information from one stimulus source at the expense of processing or utilization of information from a different source. An experiment was conducted to determine whether information tradeoffs occurred when subjects attended selectively to one of two different structural levels of naturalistic scenes. The subjects' attentional focus was directed to either the global or local structure of a scene (i.e., the scene or an object in the scene, respectively) either before or after presentation of a scene. They then had to use the information obtained from a 100-msec exposure of the scene to choose between two forced-choice alternatives that described one of the levels. The nature of the alternatives was such that both alternatives adequately characterized one of the structural levels on the basis of physical and semantic relations within the scene. Results showed that the subjects were significantly slower and less accurate when their attentional focus and the forced-choice alternatives were at different levels of stimulus structure than when they were at the same level, providing evidence of an information tradeoff when different types of information from a scene were used. When processing information from a particular structural level, information from the other level either was less available or was not used efficiently. Furthermore, the information tradeoffs were more severe in the precue than in the postcue condition, indicating differences in the efficiency of the selectivity process. The results are interpreted with respect to the role of selective attention in processing complex stimuli such as naturalistic scenes.

Adult↗
PubMed2001

Syntheses, reactivity, and pi-donating ligand metathesis reaction of five-coordinate sixteen-electron manganese(I) complexes: crystal structures of [Mn(CO(3)(-TeC(6)H(4)-o-NH-)](-), [(Mn(CO)(3))2(mu-SC(6)H(4)-o-S--S--C(6)H(4)-o-mu-S--)], [(CO)(3)Mn(mu-SC(6)H(4)-o-NH(2)-)]2, and [(CO)(3)Mn(mu-SC(8)N(2)H(4)-o-S-)](2)(2-).

The preparation of the varieties of five-coordinate sixteen-electron manganese(I) complexes [Mn(CO)(3)(-EC(6)H(4)-o-E'-)](-) (E = Te, Se, S, O; E' = NH, S, O) by (a) oxidative addition of 2-aminophenyl dichalcogenides to anionic manganese(0)-carbonyl, (b) pi-donating ligand metathesis reaction of complex [Mn(CO)(3)(-TeC(6)H(4)-o-NH-)](-), and (c) reduction /deprotonation of the neutral dimetallic [(Mn(CO)(3))(2)(mu-SC(6)H(4)-o-S-S-C(6)H(4)-o-mu-S-)]/[(CO)(3)Mn(mu-SC(6)H(4)-o-NH(2)-)](2) proved successful approaches in this direction. The IR nu(CO) data of the coordinatively and electronically unsaturated [Mn(CO)(3)(-EC(6)H(4)-o-E'-)](-) (E = Te, Se, S, O; E' = NH, S, O) complexes suggest the relative order of pi-donating ability of the series of bidentate ligands being [TeC(6)H(4)-o-NH](2)(-) > [SeC(6)H(4)-o-NH](2)(-) > [SC(6)H(4)-o-NH](2)(-) > [SC(6)H(4)-o-S](2)(-) > [SC(6)H(4)-o-O](2)(-) > [OC(6)H(4)-o-O](2)(-). Proton NMR spectra of the [Mn(CO)(3)(-EC(6)H(4)-o-NH-)](-) (E = Te, Se, S) derivatives show the low-field shift of the amide proton ((1)H NMR (C(4)D(8)O): delta 9.66 (br) ppm (E = Te), 9.32 (br) ppm (E = Se), 8.98 (br) ppm (E = S)). The formation of the dimetallic [(CO)(3)Mn(mu-SC(8)N(2)H(4)-o-S-)](2)(2-) can be interpreted as coordinative association of two units of unstable mononuclear [(CO)(3)Mn(-SC(8)N(2)H(4)-o-S-)](-) and reflects the pi-donating ability of the bidentate ligand is responsible for the formation of pentacoordinate, sixteen-electron manganese(I) carbonyl complexes. The neutral bimetallic manganese(I)-bismercaptophenyl disulfide complex [(Mn(CO)(3))(2)(mu-SC(6)H(4)-o-S-S-C(6)H(4)-o-mu-S-)] with internal S-S bond length of 2.222(1) A and the five-coordinate sixteen-electron complex [Mn(CO)(3)(-SC(6)H(4)-o-S-)](-) are chemically interconvertible. In a similar fashion, treatment of complex [Mn(CO)(3)(-SC(6)H(4)-o-NH-)](-) with HBF(4) yielded neutral dinuclear complex [(CO)(3)Mn(mu-SC(6)H(4)-o-NH(2)-)](2) and showed that the amine deprotonation is reversible. Investigations of pi-donating ligand metathesis reactions of complex [Mn(CO)(3)(-TeC(6)H(4)-o-NH-)](-) revealed that the stable intermediate, not the pi-donating ability of bidentate ligands, is responsible for the final protonation/oxidation product. This argument is demonstrated by reaction of [Mn(CO)(3)(-TeC(6)H(4)-o-NH-)](-) with 1,2-benzenedithiol, hydroxythiophenol, and catechol, respectively leading to the formation of [Mn(CO)(3)(-EC(6)H(4)-o-E'-)](-) (E = S, O; E' = S, O), although any pi-donor containing the amido group is a more effective donor than any other pi-donor lacking an amido group. Also, the reactions of [Mn(CO)(3)(-TeC(6)H(4)-o-NH-)](-) with electrophiles occurring at the more electron-rich amide site support that the more electron-rich amide donor of the chelating 2-tellurolatophenylamido occupies an equatorial site as indicated by a shorter Mn(I)-N bond length of the distorted trigonal bipyramidal [Mn(CO)(3)(-TeC(6)H(4)-o-NH-)](-).

Journal Article↗