SEARCH · Search PubMed

Results for “Structure variation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,261 records · Page 70Linked to original sources

PubMed1985

Simultaneous liquid chromatographic determination of glutaric acid, phenylephrine, and benzyl alcohol in a prototype nasal spray with application to di- and tricarboxylic acids.

A rapid reversed-phase high-performance liquid chromatographic method for the simultaneous determination of glutaric acid, phenylephrine, and benzyl alcohol in nasal spray has been developed. UV detection was utilized at 210 nm for the assay of glutaric acid and phenylephrine with an adjustment to 254 nm for the measurement of benzyl alcohol. Linearity and recovery data were obtained for each component in spiked placebo studies. An investigation of the retention mechanisms of the three components showed that phenylephrine was retained by ion-pairing with octanesulfonate anion while glutaric acid and benzyl alcohol partitioned as a suppressed ion and a neutral molecule, respectively. The method has been further extended to the reversed-phase separation of di- and tricarboxylic acids using a totally aqueous 0.0074 M phosphoric acid mobile phase. The retention of these acids was related to their octanol-water partition coefficients and structural variation.

Aerosols↗

PubMed1984

The binding of peroxidase-labelled lectins to human breast epithelium. III--Altered fucose-binding patterns of breast carcinomas and their significance.

Tissue sections from 80 human breast carcinomas have been examined for evidence of binding of the two fucose-specific lectins, Lotus tetragonolobus and Ulex europeus I, with enzymes utilized as an indicator system. Both single-staining and double-staining methods (Lotus tetragonolobus-peroxidase and Ulex europeus I-alkaline phosphatase) have been employed. In contrast to normal breast in which there is consistent reactivity of all epithelium with Lotus tetragonologus a variable loss of binding has been found within carcinomas. Surprisingly, this bears no relationship to tumour differentiation; nor does it correlate with local lymph node metastasis. Ulex europeus I has a variable reactivity with carcinomas, as it does with normal breast epithelium, and this likewise has no correlation with differentiation. However, a relationship has been found between specific patterns of binding and axillary lymph node status. The value of using two lectins with the same major sugar specificity but having different binding affinities is illustrated in this study, in which differences in behavioural characteristics have been identified between fucose-containing glyco-conjugates having minor structural variations.

Breast↗

PubMed2005

Mass spectrometry-based analytical tools for the molecular protein characterization of human plasma lipoproteins.

Lipoproteins are a heterogeneous population of blood plasma particles composed of apolipoproteins and lipids. Lipoproteins transport exogenous and endogenous triglycerides and cholesterol from sites of absorption and formation to sites of storage and usage. Three major classes of lipoproteins are distinguished according to their density: high-density (HDL), low-density (LDL) and very low-density lipoproteins (VLDL). While HDLs contain mainly apolipoproteins of lower molecular weight, the two other classes contain apolipoprotein B and apolipoprotein (a) together with triglycerides and cholesterol. HDL concentrations were found to be inversely related to coronary heart disease and LDL/VLDL concentrations directly related. Although many studies have been published in this area, few have concentrated on the exact protein composition of lipoprotein particles. Lipoproteins were separated by density gradient ultracentrifugation into different subclasses. Native gel electrophoresis revealed different gel migration behaviour of the particles, with less dense particles having higher apparent hydrodynamic radii than denser particles. Apolipoprotein composition profiles were measured by matrix-assisted laser desorption/ionization-mass spectrometry on a macromizer instrument, equipped with the recently introduced cryodetector technology, and revealed differences in apolipoprotein composition between HDL subclasses. By combining these profiles with protein identifications from native and denaturing polyacrylamide gels by liquid chromatography-tandem mass spectrometry, we characterized comprehensively the exact protein composition of different lipoprotein particles. We concluded that the differential display of protein weight information acquired by macromizer mass spectrometry is an excellent tool for revealing structural variations of different lipoprotein particles, and hence the foundation is laid for the screening of cardiovascular disease risk factors associated with lipoproteins.

Apolipoproteins↗

PubMed1993

Substrate specificities of catalytic fragments of protein tyrosine phosphatases (HPTP beta, LAR, and CD45) toward phosphotyrosylpeptide substrates and thiophosphotyrosylated peptides as inhibitors.

The transmembrane PTPase HPTP beta differs from its related family members in having a single rather than a tandemly duplicated cytosolic catalytic domain. We have expressed the 354-amino acid, 41-kDa human PTP beta catalytic fragment in Escherichia coli, purified it, and assessed catalytic specificity with a series of pY peptides. HPTP beta shows distinctions from the related LAR PTPase and T cell CD45 PTPase domains: it recognizes phosphotyrosyl peptides of 9-11 residues from lck, src, and PLC gamma with Km values of 2, 4, and 1 microM, some 40-200-fold lower than the other two PTPases. With kcat values of 30-205 s-1, the catalytic efficiency, kcat/Km, of the HPTP beta 41-kDa catalytic domain is very high, up to 5.7 x 10(7) M-1 s-1. The peptides corresponding to PLC gamma (766-776) and EGFR (1,167-1,177) phosphorylation sites were used for structural variation to assess pY sequence context recognition by HPTP beta catalytic domain. While exchange of the alanine residue at the +2 position of the PLC gamma (Km of 1 microM) peptide to lysine or aspartic acid showed little or no effect on substrate affinity, replacement by arginine increased the Km 35-fold. Similarly, the high Km value of the EGFR pY peptide (Km of 104 microM) derives largely from the arginine residue at the +2 position of the peptide, since arginine to alanine single mutation at the -2 position of the EGFR peptide decreased the Km value 34-fold to 3 microM. Three thiophosphotyrosyl peptides have been prepared and act as substrates and competitive inhibitors of these PTPase catalytic domains.

Amino Acid Sequence↗

PubMed1997

Limited proteolysis of ribonuclease A with thermolysin in trifluoroethanol.

We have examined the proteolysis of bovine pancreatic ribonuclease A (RNase) by thermolysin when dissolved in aqueous buffer, pH 7.0, in the presence of 50% (v/v) trifluoroethanol (TFE). Under these solvent conditions, RNase acquires a conformational state characterized by an enhanced content of secondary structure (helix) and reduced tertiary structure, as given by CD measurements. It was found that the TFE-resistant thermolysin, despite its broad substrate specificity, selectively cleaves the 124-residue chain of RNase in its TFE state (20-42 degrees C, 6-24 h) at peptide bond Asn 34-Leu 35, followed by a slower cleavage at peptide bond Thr 45-Phe 46. In the absence of TFE, native RNase is resistant to proteolysis by thermolysin. Two nicked RNase species, resulting from cleavages at one or two peptide bonds and thus constituted by two (1-34 and 35-124) (RNase Th1) or three (1-34, 35-45 and 46-124) (RNase Th2) fragments linked covalently by the four disulfide bonds of the protein, were isolated to homogeneity by chromatography and characterized. CD measurements provided evidence that RNase Th1 maintains the overall conformational features of the native protein, but shows a reduced thermal stability with respect to that of the intact species (-delta Tm 16 degrees C); RNase Th2 instead is fully unfolded at room temperature. That the structure of RNase Th1 is closely similar to that of the intact protein was confirmed unambiguously by two-dimensional NMR measurements. Structural differences between the two protein species are located only at the level of the chain segment 30-41, i.e., at residues nearby the cleaved Asn 34-Leu 35 peptide bond. RNase Th1 retained about 20% of the catalytic activity of the native enzyme, whereas RNase Th2 was inactive. The 31-39 segment of the polypeptide chain in native RNase forms an exposed and highly flexible loop, whereas the 41-48 region forms a beta-strand secondary structure containing active site residues. Thus, the conformational, stability, and functional properties of nicked RNase Th1 and Th2 are in line with the concept that proteins appear to tolerate extensive structural variations only at their flexible or loose parts exposed to solvent. We discuss the conformational features of RNase in its TFE-state that likely dictate the selective proteolysis phenomenon by thermolysin.

Animals↗

PubMedDate not supplied

Quantitative analysis of EcoR1 methylase-DNA complex by atomic force microscopy.

The EcoR1 methylase specifically recognize 5'-GA* ATTC-3' in DNA duplex. We directly applied atomic force microscopy (AFM) to investigate linear pBR322-EcoR1 methylase complexes and quantitatively analyzed the bend angles of linear pBR322-EcoR1 methylase complexes and the bound protein widths. In this study, we made a novel observation that DNA-EcoR1 methylase complexes exhibited two populations of conformation at recognition site: DNA bent an acute angle at the recognition site in the presence of one EcoR1 methylase monomeric molecule, while DNA bent an unacute angle at the recognition site and the complementary site on duplex DNAs in the presence of EcoR1 methylase dimer. The data indicated that the unacute angle state was the result of unique interactions between EcoR1 methylase and the recognition site and the complementary site on duplex DNAs, and suggested that the acute angle conformation could be an intermediate in the formation of the unacute angle state. Our works provide a detail insight into the DNA structural variations involved in EcoR1 methylase-binding processes and demonstrate further the versatility of AFM as an imaging technique for studying the interaction between large DNA fragment and protein.

Binding Sites↗

PubMed1998

Cloning and tissue distribution of novel splice variants of the rat GABAB receptor.

We have identified two novel splice variants of the metabotropic gamma-aminobutyric acid receptor (GABABR1), designated GABABR1c and GABABR1d, when screening a rat cerebellum cDNA library. GABABR1c has an amino acid sequence identical to GABABR1b, a member of GABABR1 isoforms, and an additional 93-bp insertion that generates an additional 31-amino-acid sequence in the fifth transmembrane region of GABABR1b. Thus, GABABR1c may have a structural variation in the second extracellular loop and fifth transmembrane region. GABABR1d also has an amino acid sequence identical to GABABR1b and an additional insertion of 566 bp that generates a divergent amino acid sequence in the carboxylterminal end. Reverse-transcription polymerase chain reaction analysis showed that in various rat tissues GABABR1c mRNA was ubiquitously expressed and GABABR1d mRNA in forebrain, cerebellum, eye, kidney, and urinary bladder. GABABR1 isoforms may function not only in the central nervous system but also in various peripheral tissues.

Alternative Splicing↗

PubMed2000

A novel FUS/CHOP chimera in myxoid liposarcoma.

The cytogenetic hallmark of myxoid liposarcoma is the chromosomal aberration t(12;16)(q13;p11), which is pathognomonic for this tumor type. The translocation results in the hybrid gene FUS/CHOP, where the central and C-terminal parts of FUS, coding for the RNA binding domain and the RGG triplet motif, are replaced by the full length CHOP protein. Thus, CHOP is under the control of the FUS promoter and the FUS/CHOP chimera contains the 5'-terminal part of FUS which provides a transcriptional activation function. Although different structural variations of the FUS/CHOP chimeric transcript have been reported, none of them contains the parts of FUS encoding the RNA binding properties. An explanation is the location of the genomic breakpoint in FUS, which frequently occurs in the region spanning exon 5 to intron 8. We describe here a case of myxoid liposarcoma containing two novel FUS/CHOP chimeric transcripts and with the breakpoint occurring in intron 14 of FUS. Reverse transcription-polymerase chain reaction, using FUS forward and CHOP reverse primers, amplified strongly a 2.1-kbp DNA fragment and weakly a 0.9-kbp DNA fragment. Direct sequencing showed that in the 2.1-kbp transcript nt 1474, which corresponds to the third nucleotide of exon 14 of FUS, was in-frame fused to exon 2 of CHOP. In the 0.9-kbp DNA fragment, exon 3 of FUS was in-frame fused to exon 2 of CHOP. Genomic analyses revealed that the breaks were located at the end of exon 14/beginning of intron 14 of FUS and in intron 1 of CHOP and that microdeletions had occurred in the close vicinity of the breakpoints.

Amino Acid Sequence↗

PubMed1997

Confocal analysis of primary cilia structure and colocalization with the Golgi apparatus in chondrocytes and aortic smooth muscle cells.

Detyrosinated and acetylated alpha-tubulins represent a stable pool of tubulin typically associated with microtubules of the centrosome and primary cilium of eukaryotic cells. Although primary cilium-centrosome and centrosome-Golgi relationships have been identified independently, the precise structural relationship between the primary cilium and Golgi has yet to be specifically defined. Confocal immunohistochemistry was used to localize detyrosinated (ID5) and acetylated (6-11B-1) tubulin antibodies in primary cilia of chondrocytes and smooth muscle cells, and to demonstrate their relationship to the Golgi complex identified by complementary lectin staining with wheat germ agglutinin. The results demonstrate the distribution and inherent structural variation of primary cilia tubulins, and the anatomical interrelationship between the primary cilium, the Golgi apparatus and the nucleus. We suggest that these interrelationships may form part of a functional feedback mechanism which could facilitate the directed secretion of newly synthesized connective tissue macromolecules.

Acetylation↗

PubMed1997

Heterogeneity in rates of recombination in the 6-Mb region telomeric to the human major histocompatibility complex.

Analysis of 784 informative meioses in the CEPH pedigrees revealed a total of 22 recombination events having occurred in the 6-Mb region between D6S265 (70 kb centromeric of HLA-A) and D6S276. These 22 breakpoints were localized with respect to anonymous polymorphic markers, leading to a detailed genetic map of the region telomeric to the human major histocompatibility complex. A nonrandom pattern of recombination was observed throughout this region: the low recombination rate of 0.19% within the 4-Mb interval centromeric to the HLA class I-like candidate gene for hemochromatosis indeed contrasts with the approximate 1% rate observed within the most telomeric two megabases. This reduced rate of recombination may be due to selective constraints depending on environmental factors related to immunity and iron status or to structural variations hampering proper meiotic pairing of homologous sequences. Population data from other human genome segments are now needed to determine whether linkage disequilibrium extending over 4 Mb is unique to this region.

Chromosome Mapping↗

PubMed1998

Folding intermediates of wild-type and mutants of barnase. I. Use of phi-value analysis and m-values to probe the cooperative nature of the folding pre-equilibrium.

It is difficult to determine whether transient folding intermediates have a cooperative (or first-order) folding transition without measuring their rates of formation directly. An intermediate I could be formed by a second-order transition from a denatured state D that is progressively changed into I as conditions are changed. We have not been able to monitor the rate of formation of the folding intermediate of barnase directly, but have analysed its reactivity and the equilibrium constant for its formation over a combination of wide ranges of temperature, concentration of denaturant and structural variation. Phase diagrams have been constructed for wild-type and 16 mutant proteins to map out the nature of the energy landscape of the denatured state. The free energy of unfolding of I, delta GD-I, changes with [urea] according to a highly cooperative transition. Further, mD-I (= delta delta GD-I/delta [urea]) for wild-type and several mutants is relatively insensitive to temperature, as would be expected for an intermediate that is formed cooperatively, rather than one that melts out according to a second-order transition. The phi-values for the formation of I change abruptly through the folding transitions rather than have the smooth changes expected for a second-order transition. There is a subset of mutants for which both mD-I and phi-value analysis indicate that a second intermediate becomes populated close to the melting temperatures of the native proteins. The folding intermediate of barnase is, thus, a relatively discrete and compact entity which is formed cooperatively.

Amino Acid Sequence↗

PubMed2002

Characterization of phi 12, a bacteriophage related to phi 6: nucleotide sequence of the small and middle double-stranded RNA.

The isolation of additional bacteriophages containing segmented double-stranded RNA genomes has expanded the Cystoviridae family to nine members. Comparing the genomic sequences of these viruses has allowed evaluation of important genetic as well as structural motifs. These comparative studies are resulting in greater understanding of viral evolution and the role played by genetic and structural variation in the assembly mechanisms of the cystoviruses. In this regard, the small and middle double-stranded RNA genomic segments of bacteriophage phi 12 were copied as cDNA and their nucleotide sequences determined. This genome's organization is similar to that of the small and middle segments of bacteriophages phi 6, phi 8, and phi 13. Although there is little similarity in the nucleotide sequences, similarity exists in the amino acid sequence of the lysis cassette proteins to those of phi 6. The host cell attachment proteins are found to have marked similarity to the phi 13 attachment proteins.

Bacteriophage phi 6↗

PubMed2002

Characterization of phi12, a bacteriophage related to phi6: nucleotide sequence of the large double-stranded RNA.

The isolation of additional bacteriophages besides phi6 containing segmented double-stranded RNA genomes (dsRNA) has expanded the Cystoviridae family to nine members. Comparing the genomic sequences of these viruses has allowed evaluation of important genetic as well as structural motifs. These comparative studies are resulting in greater understanding of viral evolution and the role played by genetic and structural variation in the assembly mechanisms of the cystoviruses. In this regard, the large double-stranded RNA genomic segment of bacteriophage phi12 was copied as cDNA and its nucleotide sequence determined. This genome's organization is similar to that of the large segment of bacteriophages phi6, phi8, and phi13. In the amino acid sequence of the viral RNA-dependent RNA polymerase (P2), similarity was found to the comparable proteins of phi6, phi8, and phi13. Amino acid sequence similarity was also noted in the nucleotide triphosphate phosphorylase (P4) to the comparable proteins of phi8 and phi13.

Amino Acid Sequence↗

PubMed1996

The linear organization of cell columns in human and nonhuman anthropoid Tpt cortex.

Neurons in the cerebral cortex are organized horizontally into laminae and vertically into columns and modules. Little is known about the structural variation of neuronal organization in the vertical (pia to white matter) dimension. We describe here a new computer-assisted methodology that quantifies the linear arrangement of cells and shows how cortical columns in a homologous region differ by species and age. Perikarya in eulaminate temporal cortex, Tpt, were segmented from the background on the basis of their optical densities and sizes in human, rhesus (Macaca mulatta), and chimpanzee (Pantroglodytes) brains. Within each lamina, the two-dimensional arrays of neurons were divided into repetitive, objectively defined vertical clusters. Following this, ratios and indices quantified the displacement of perikaryal centroids from the central axis and from the center point in each cell cluster. The extremely linear and vertical arrangement of cells in the prelaminated fetal cortical plate served as the template to which the other arrays were compared. In all species, the linear arrangements of perikarya in lamina III, and to a lesser extent, in lamina V, closely resemble that of the early fetal template, whereas perikaryal arrangements in layers II and IV diverge from the template formation. Corroborating subjective visualization, each lamina had its own 'fingerprint'. As expected, cell density is less in the species with larger brains, with most of the differences in density coming from increased spacing between cellular columns rather than among the cells within columns. Not all aspects of perik-aryal organization alter when bigger brains are compared with smaller ones. Although chimpanzee brains are about four times bigger than those of rhesus monkeys and human brains are about three times larger than chimpanzee brains, absolute measures of cellular linearity in chimpanzees and rhesus monkeys resemble each other more closely than the same measures do in humans and chimpanzees. After accounting for differences in interval widths, the parameters of linearity sorted on the basis of brain weight in pyramidal cell layers III and V, but not in the stellate cell layers II and IV. Human perikarya have the widest horizontal dispersion and this displacement is most pronounced in layer II, least in layer III.

Adult↗

PubMed1977

Ultrastructure of lymphatic capillaries in the human dental pulp.

Occlusal intradentinal cavities, prepared in normal human premolars and third molars to be extracted for orthodontic reasons, were filled for 7 to 11 days with gutta percha. A superficial pulpitis with localized small abscesses developed in the pulp chamber. Under local anesthesia, 0.2 to 0.3 cc of sterile colloidal carbon was injected in the pulp horn and the teeth were extracted 1 to 3 h later. Lymphatic capillaries could thus be identified in the pulpal tissues. They were characterized by a thin endothelium with occasional large intercellular clefts, absence or incompleteness of basement membrane, absence of pericytes, absence of luminal red blood cells, and presence of a filamentous material between the endothelium and the surrounding collagen fibrils. Moreover, some structural variations were observed.

Adolescent↗

PubMed1986

Structure and distribution of gap junctions in lens epithelium and fiber cells.

We report a comparative study of gap junctions in lens epithelia of frog, rabbit, rat and human, using a "double mounting" method for freeze-fracture electron microscopy. The gap junctions on the narrow sides of hexagonal cortical fiber cells of various species were also studied with the same technique. Gap junctions were commonly present between epithelial cells of the entire undifferentiated epithelium, between fiber cells on both wide and narrow sides, and between epithelial cells and fiber cells. Structural diversity of gap junctions, based on connexon arrangements, was evident in lens epithelia among the four species studied. Gap junctions with random arrays of connexons were found predominantly in frog lens epithelium, while the crystalline and striated configurations were mainly observed in the epithelia of human and rat, and of rabbit, respectively. On the other hand, there was no structural variation of gap junctions observed on either wide or narrow sides of lens fiber cells from any species studied. Only the random-type gap junction was found. However, the distribution of gap junctions was unique on the narrow sides. There was a single row of junctional plaques along the middle of the narrow sides, whereas the wide sides showed an uneven distribution pattern. The gap junctions between epithelial cells and fiber cells had a random packing of connexons.

Adolescent↗

PubMedDate not supplied

The adenylyl cyclase family.

Hormone-sensitive adenylyl cyclase is a model system for the study of receptor-mediated signal transduction. It is comprised of three types of components: 1) receptors for hormones that regulate cyclic AMP (cAMP) synthesis, 2) regulatory GTP binding proteins (G proteins), and 3) the family of enzymes, the adenylyl cyclases. Concentrations of cAMP are altered by at least 35 different stimulatory or inhibitory hormones and neurotransmitters. Other signalling pathways may also influence cAMP production through regulation of particular adenylyl cyclase subtypes. The second messenger, cAMP propagates the hormone signal through the effects of cAMP-dependent protein kinase. While structural information on the adenylyl cyclases is limited, a cDNA clone for a calmodulin-sensitive form of bovine brain adenylyl cyclase has been isolated. The amino acid sequence encoded by the Type I cDNA is approximately 40% identical to those specified by three other adenylyl cyclase cDNAs that have been cloned subsequently. This degree of structural variation implies that there must be functional differences between the adenylyl cyclases.

Adenylyl Cyclases↗

PubMed1984

Population and formal genetics of the human C81(alpha-gamma) polymorphism.

One hundred and ninety-six unrelated healthy individuals and 30 families with 75 offspring have been studied for the C81(alpha-gamma) polymorphism. The following allele frequencies were calculated: C81*A = 0.5536; C81*B = 0.4286; C81*A1 = 0.0178. Observed and expected phenotype frequencies were in a good agreement according to the Hardy Weinberg law. No exceptions from the mode of inheritance were found. In family W the segregation of the rare allele C81*A1 could be followed. Comparing the results of this study with previous data from Boston and Oslo, a combined technology including C8-dependent lysis and C8 structural variation is suggested for future investigations.

Alleles↗