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At least 253 records · Page 14Linked to original sources

PubMed1999

Structural analysis at 2.2 A of orthorhombic crystals presents the asymmetry of the allophycocyanin-linker complex, AP.LC7.8, from phycobilisomes of Mastigocladus laminosus.

An electrophoretically purified allophycocyanin-linker complex, AP. LC7.8, from phycobilisomes of Mastigocladus laminosus has been crystallized in the orthorhombic space group P212121. Cryocrystallographic x-ray measurements enabled the structural analysis of the complex at a resolution of 2.2 A. The asymmetric unit contains two side-to-side associated "trimeric" (alphabeta)3 allophycocyanin complexes comprising the linker polypeptide in a defined orientation inside the trimer. The linker representing a protein fold related to the prosegment of procarboxypeptidase A is in contact with only two of the three beta-subunits and directly interacts with the corresponding chromophores of these proteins. In addition to a modulation of the chromophores' spectral properties, the linker polypeptide attracts the alphabeta-subcomplexes, thereby bringing the beta-chromophores closer together. These results will enable interpretations of energy-transfer mechanisms within phycobiliproteins.

Amino Acid Sequence↗

PubMed1991

Evaluating measurement models in clinical research: covariance structure analysis of latent variable models of self-conception.

Indirect measures of psychological constructs are vital to clinical research. On occasion, however, the meaning of indirect measures of psychological constructs is obfuscated by statistical procedures that do not account for the complex relations between items and latent variables and among latent variables. Covariance structure analysis (CSA) is a statistical procedure for testing hypotheses about the relations among items that indirectly measure a psychological construct and relations among psychological constructs. This article introduces clinical researchers to the strengths and limitations of CSA as a statistical procedure for conceiving and testing structural hypotheses that are not tested adequately with other statistical procedures. The article is organized around two empirical examples that illustrate the use of CSA for evaluating measurement models with correlated error terms, higher-order factors, and measured and latent variables.

Analysis of Variance↗

PubMed2000

Structural analysis of (methyl-esterified) oligogalacturonides using post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

The use of post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the structural analysis of ((partly) methyl-esterified) oligogalacturonides (oligoGalA) is described. The fragmentation behavior of purified (un)saturated oligoGalA (degree of polymerization 3-6), methyl-esterified and methyl-glycosydated oligoGalA was studied. General fragmentation patterns are described and used for the elucidation of the positions of methyl esters on partly methyl-esterified oligoGalA. This technique now permits the determination of the position of methyl esters or other substituents on pectic fragments, helping in understanding the mode of action of pectinolytic enzymes.

Carbohydrate Conformation↗

PubMed1986

Nucleotide sequence of the yeast cell division cycle start genes CDC28, CDC36, CDC37, and CDC39, and a structural analysis of the predicted products.

The nucleotide sequences of the yeast cell division cycle start genes CDC36, CDC37, and CDC39 are presented. An open reading frame corresponding in size and mapped position to the mRNA for each gene was revealed. These sequences, as well as that of the CDC28 gene, were analyzed for the presence of consensus sequences postulated to be transcriptional or translational signals, or to be involved in mRNA processing. In addition, the predicted protein products of the four genes were subjected to a number of structural and statistical analyses including codon usage bias analysis, secondary structure analysis and hydropathicity analysis.

Amino Acid Sequence↗

PubMed1985

Fine structural analysis of the human pro-alpha 1 (I) collagen gene. Promoter structure, AluI repeats, and polymorphic transcripts.

The human pro-alpha 1(I) collagen gene is 18 kilobases long, and its coding information is subdivided in 51 exons. We have recently reported a detailed analysis of this elaborate structure. Here we describe the exact termini of the gene as well as its 5' flanking sequences (promoter region). Sequence comparison between the human and mouse pro-alpha 1(I) gene showed an unusual highly conserved region 5' to the initiation site of transcription, which may be important for pro-alpha 1(I) collagen expression. Sequence comparison between the pro-alpha 1(I) and other collagen genes revealed the presence of a conserved secondary structure possibly implicated in the regulation of collagen mRNA translation and/or collagen secretion. Two short repetitive sequences closely associated with the pro-alpha 1(I) gene have been identified to be different members of the AluI family of repeats. Like the independently co-expressed pro-alpha 2(I) collagen gene, the analysis of the last exon has revealed that the pro-alpha 1(I) gene transcribes two different mRNAs in cultured fibroblasts. The colinearity and exact location of the termini of these transcripts, as well as their monogenic nature, have been conclusively determined.

Base Sequence↗

PubMed1990

Structural analysis of the specific capsular polysaccharide of Rhodococcus equi serotype 1.

The specific capsular polysaccharide produced by Rhodococcus equi serotype 1 was found to be a high molecular weight acidic polymer composed of D-glucose, D-mannose, and D-glucuronic acid. Structural analysis of the polysaccharide employed a combination of chemical and nuclear magnetic resonance techniques, from which it was determined that the polysaccharide possessed a linear repeating tetrasaccharide unit containing a single O-acetyl substituent and and acetal-linked pyruvic acid moiety: [formula: see text] The 1H and 13C nuclear magnetic resonances of O-deacetylated and pyruvic-free serotype 1 polysaccharides were fully assigned by homo- and hetero-nuclear chemical shift correlation methods.

Acetylation↗

PubMed1987

Isolation and structure analysis of bee venom mast cell degranulating peptide.

The venom of Apis mellifera was processed by gel permeation chromatography on Sephadex G-50 and by reversed-phase HPLC. The initial gel permeation step was carried out in the presence of phosphate ions (0.5 M). Ion pair reagents were required to resolve the strongly basic peptides, secapin, mast cell degranulating (MCD-) peptide and apamin, by reversed-phase (RP) HPLC. Using this relatively simple procedure it is possible to isolate these peptides essentially free of melittin (less than 1 in 10(7)) and phospholipase (less than 1 in 10(5] in high yield. The CD spectrum and secondary structure analysis are reported for MCD-peptide and on this basis a solution structure is proposed for this toxin.

Animals↗

PubMed1994

Native-like in vivo folding of a circularly permuted jellyroll protein shown by crystal structure analysis.

A jellyroll beta-sandwich protein, the Bacillus beta-glucanase H(A16-M), is used to probe the role of N-terminal peptide regions in protein folding in vivo. A gene encoding H(A16-M) is rearranged to place residues 1-58 of the protein behind a signal peptide and residues 59-214. The rearranged gene is expressed in Escherichia coli. The resultant circularly permuted protein, cpA16M-59, is secreted into the periplasm, correctly processed, and folded into a stable and active enzyme. Crystal structure analysis at 2.0-A resolution, R = 15.3%, shows cpA16M-59 to have a three-dimensional structure nearly identical with that of the parent beta-glucanase. An analogous experiment based on the wild-type Bacillus macerans beta-glucanase, giving rise to the circularly permuted variant cpMAC-57, yields the same results. Folding of these proteins, therefore, is not a vectorial process depending on the conformation adopted by their native N-terminal oligopeptides after ribosomal synthesis and translocation through the cytoplasmic membrane.

Amino Acid Sequence↗

PubMed1992

Peptide/protein structure analysis using the chemical shift index method: upfield alpha-CH values reveal dynamic helices and alpha L sites.

The alpha-CH shifts observed by 1H NMR for medium-sized peptides and for an unusual small protein, herein, which has a high density of alpha L conformations within its 43 residue length, reveal that the recently introduced chemical shift index (CSI) analysis places short dynamic helices (alpha R) and alpha L residues in the same category as stable helices. The method appears to be a promising addition to the arsenal of methods for peptide structure analysis and is clearly not limited to rigid protein systems.

Amino Acid Sequence↗

PubMed1992

Cloning and primary structural analysis of the bullous pemphigoid autoantigen BP180.

Bullous pemphigoid (BP) is an autoimmune skin disease that is characterized by the presence of subepidermal blisters resulting from a disruption of the adhesive interactions between basal keratinocytes and the cutaneous basement membrane. Autoantibodies from patients suffering from this disorder recognize two epidermal antigens, BP180 and BP230, both of which have been localized to the hemidesmosome, a transmembrane structure of stratified, squamous epithelia that functions in cell-matrix adhesion. In the present study we report the primary structural analysis of BP180 based on the sequence of a series of overlapping cDNA clones encompassing 4,669 bases of the BP180 transcript. A polymerase chain reaction-based protocol was used to confirm the contiguity of the cDNA segments. This cloned portion of the BP180 transcript was found to contain one long open reading frame (ORF) 4.596 bases in length. This ORF encodes a polypeptide of 155,000 Daltons with an isoelectric point of 9.7. The carboxy-terminal half of BP180, a stretch of 916 amino acids, consists of 15 collagen domains of variable length (15 to 242 amino acids) that are separated from one another by short stretches of non-collagen sequences. Located 76 amino acids upstream of the collagenous region is a putative transmembrane domain, a structural feature that distinguishes BP180 from all of the well-characterized members of the collagen family. This membrane-spanning domain is predicted to function as a signal-anchor sequence, directing the C-terminal collagenous segment of this protein to the exterior of the cell. The putative intracellular domain is highly basic with an isoelectric point of 10.37. This molecular analysis predicts that the BP180 antigen is an integral membrane protein of the hemidesmosome that contains a long extracellular collagenous tail. This combination of structural features suggests that BP180 may function as a cell-matrix adhesion molecule, with the collagenous region acting as a potential site of interaction with basement membrane components. Autoantibody-mediated disruption of such an adhesive interaction may play a critical role in the development of sub-epidermal blisters in BP patients.

Amino Acid Sequence↗

PubMed1984

[Quantitative and qualitative structure analysis of cell exfoliated from the normal vulva and from benign, precancerous and malignant vulvar lesions].

The value of cytological smears for screening for cancer of the external female genital organs has been stressed recently on repeated occasions. The evaluation of the cornified cells obtained from different vulvar diseases has however only been undertaken by subjective criteria. The qualitative structural analysis and the planimetric evaluation of 3,260 cornified cells from 123 patients with vulvar lesions of different types showed fundamental and essential differences in the criteria of malignancy compared to cytology of the uterine cervix. Whereas the nuclear plasmatic ratio and the chromatine structure are of secondary importance, the absolute size of the nucleus and the cell and especially the degree of cytoplasmatic polymorphy have a high degree of cytoplasmatic polymorphy have a high degree of importance. The special cytomorphological criteria described permit the differentiation of benign and malignant lesions of the vulva from the cytology of the cornified cells.

Biopsy↗

PubMed1991

Purification of an endogenous digitalislike factor from human plasma for structural analysis.

In previous reports, we described the isolation and characterization of an endogenous digitalislike factor (EDLF). In this report, we describe a unique combination of bioassay and large-scale purification methodology that made possible the purification of sufficient quantities of this inhibitor of Na+,K(+)-ATPase for structural analysis. Using an initial XAD-2 extraction and preparative high-performance liquid chromatography followed by a batch enzyme affinity extraction and two subsequent semipreparative chromatographic steps, 300 l of human plasma was processed, yielding 31 micrograms (53 nmol) of pure EDLF and representing purification on a dry weight basis in excess of 0.6 billionfold. Four divergent pieces of evidence, including chromatographic, mass spectrometric, immunoreactive, and binding characteristics, suggested that the EDLF purified in the present study was either ouabain or an isomer of ouabain. This material may represent a plasma-borne, naturally occurring, selective, high-affinity ligand for the digitalis binding site that may play a significant role in the modulation of the sodium pump and thereby cellular electrolyte homeostasis in humans.

Antibodies↗

PubMed1975

Structural analysis of compartmental models for the hepatic kinetics of drugs.

The structure of some compartmental models for the analysis of the hepatobiliary kinetics of bromosulphalein (BSP) was studied in order to evaluate their adequacy in the estimation of the processes involved in the hepatic metabolism of drugs, namely uptake, conugation, and biliary excretion. Biological measurements were obtained from 4 cholecystectomized patients with a biliary T-tube. Blood and bile specimens were taken at various intervals after the administration of a single intravenous dose of BSP and analyzed for both direct BSP quantitation and chromatographic separation and estimation of BSP metabolic fractions. The structural analysis was carried out by using a mathematical model that described the kinetics of BSP. By means of computer simulations different measurement situations were analyzed, showing for each experimental condition the available information and the degree of accuracy of each estimated parameter. The obtained results show that the use of compartmental models can provide a useful theoretical framework by which the experimental data can be interpreted for the evaluation of the hepatobiliary metabolism and for a discriminant analysis between different physiopathological conditions.

Bile↗

PubMed1979

Structural analysis of four strains of Paracoccus denitrificans.

Two out of eleven newly isolated strains of Paracoccus denitrificans were investigated by light and electron microscopic methods and compared with two strains of P. denitrificans already kept in culture collections. Samples were taken from different growth phases revealing short rods and nearly spherical cells in the exponential growth phase, and an increasing ratio of nearly spherical cells in the stationary growth phase. Cell division followed the binary fission mode; higher cell aggregates were not observed. Fine structural analysis revealed extracellular surface material stainable with Ruthenium red, a gram-negative cell wall and different storage material inclusions. Structural properties and variations within the four strains under investigation are discussed and compared with those of related bacteria.

Cell Division↗

PubMed1997

Molecular cloning and chromatin structure analysis of the murine alpha1(I) collagen gene domain.

We have isolated molecular clones of genomic mouse DNA spanning 55 kb, including the entire coding region of the murine alpha1(I) collagen (Col1a1) gene and 24 kb of 5' and 13 kb of 3'-flanking sequences, and have performed a detailed chromatin structure analysis of these sequences. Several new DNase-I-hypersensitive sites were identified. The distal 5'-flanking region contains two clusters of DNase-I-hypersensitive sites located between 7 and 8 kb and between 15 and 20 kb upstream of the start site of transcription, respectively. Several of these sites were shown to be present in collagen-producing, but not in non-producing cells, indicating that they are associated with transcription of the gene and may function in its regulation. One strong constitutive DNase-I-hypersensitive site at -18.5 kb was also cleaved by endogenous nucleases. The 3'-flanking region of the gene contains a DNase-I-hypersensitive site located 6 kb downstream of the end of the gene, as well as sequences that can induce a non-B DNA structure. Because these latter sequences coincide with DNase-I-hypersensitive sites in the homologous human gene, our results suggest that some regulatory elements may play a role in gene regulation, not by specific protein-DNA interactions but by virtue of their ability to induce a non-B DNA structure and/or an alternate chromatin conformation. A comparison of the murine and human Col1a1 domains shows a similar, although not identical, distribution of DNase-I-hypersensitive sites, indicating a conserved arrangement of regulatory elements. Our results strongly suggest that these new sites constitute regulatory elements which are involved in the transcriptional regulation and/or chromatin loop organization of the Col1a1 gene, and they are now amenable for functional analyses.

3T3 Cells↗

PubMed1991

Structural analysis of the Neurospora mitochondrial large rRNA intron and construction of a mini-intron that shows protein-dependent splicing.

The gene encoding the Neurospora mitochondrial large rRNA contains a single group I intron of 2.3 kilobases that is not self-splicing in vitro. We showed previously that the splicing of this intron in vivo and in vitro is dependent on the Neurospora cyt-18 protein, mitochondrial tyrosyl-tRNA synthetase. In the present work, we carried out further structural analysis of the intron and constructed mutant derivatives of it in order to identify features that are either required for splicing or prevent it from self-splicing. Previous studies showed that the intron contains a large hairpin structure near the 5' splice site. By mapping RNase III cleavage sites, we identified this hairpin structure as an extended P2 stem. We construct a mini-intron of 388 nucleotides by deleting the 426-amino acid intron open reading frame, most of the 5' intron hairpin, and all of L8. This mini-intron shows the same protein-dependent splicing as the full length intron, but is still not self-splicing. Further deletions, which remove all of P2 or all or part of P4, P6, P7, or P9, inactivate splicing, suggesting that an intact group I intron core structure is required. Strengthening the P1, P10, or P9.0 pairings did not enable the mini-intron to self-splice. Our findings indicate that the inability of the mitochondrial large rRNA intron to self-splice reflects deficiency of a structure or activity required for cleavage at the 5' splice site, either in the intron core itself or in the interaction between the core and the P1 stem.

Base Sequence↗

PubMed1990

Structural analysis of the specific capsular polysaccharide of Rhodococcus equi serotype 2.

The specific capsular polysaccharide produced by Rhodococcus equi serotype 2 is a high-molecular-weight acidic polymer composed of D-glucose, D-mannose, D-glucuronic acid and 3-O-[(S)-1-carboxyethyl]-L-rhamnose in equimolar proportions. Structural analysis, employing a combination of chemical and n.m.r. techniques, established that the polysaccharide is composed of linear repeating tetrasaccharide units. (formula; see text) in which the beta-D-mannose residues carry O-acetyl groups at O-2 and O-3 to the extent of 1.7 mol equivalents. Unequivocal determination of the absolute chirality of the 3-O-[(S)-1-carboxyethyl]-alpha-L-rhamnose residues was achieved by chemical correlation with an authentic synthetic sample. The 1H and 13C-n.m.r. resonances of the native and O-deacetylated serotype 2 polysaccharides were fully assigned by homo- and heteronuclear chemical-shift correlation methods.

Carbohydrate Conformation↗

PubMed2000

Structural analysis of the transcriptional activation region on Fis: crystal structures of six Fis mutants with different activation properties.

The Fis protein regulates gene expression in Escherichia coli by activating or repressing transcription of a variety of genes. Fis can activate transcription when bound to DNA upstream of the RNA-polymerase-binding site, such as in the rrnB P1 promoter, or when bound to a site overlapping the -35 RNA polymerase binding site, such as in the proP P2 promoter. It has been suggested that transcriptional activation in both promoters results from interactions between specific amino acids within a turn connecting the B and C helices (the BC turn) in Fis and the C-terminal domain of the alpha-subunit of RNA polymerase (alphaCTD of RNAP). Here, crystal structures of six Fis BC turn mutants with different transcriptional activation properties, Q68A, R71Y, R71L, G72A, G72D and Q74A, were determined at 1.9 to 2.8 A resolution. Two of these mutants, R71Y and R71L, crystallized in unit cells which are different from that of wild-type Fis, and the structure of R71L offers the most complete Fis model to date in that the extended structure of the N-terminal region is revealed. The BC turn in all of these mutant structures remains in a nearly identical gamma gamma beta-turn conformation as present in wild-type Fis. Analyses of the molecular surfaces of the transactivation region of the mutants suggest that several residues in or near the BC turn, including Gln68, Arg71, Gly72 and Gln74, form a ridge that could contact the alphaCTD of RNAP on one side. The structures and biochemical properties of the mutants suggest that Arg71 is the most critical residue for contacting RNAP within this ridge and that the glycine at position 72 helps to stabilize the structure.

Amino Acid Substitution↗