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At least 163 records · Page 9Linked to original sources
PubMed1984

The molecular biology of rotaviruses. VII. Detailed structural analysis of gene 10 of bovine rotavirus.

cDNA cloning and nucleotide sequence analysis have allowed detailed structural studies on RNA segment 10 of the U.K. bovine rotavirus to be undertaken. The complete sequence of 751 nucleotides was determined and found to contain only a single long open reading frame capable of coding for a protein of 175 amino acids. The gene has an unusually long 3' untranslated region of 184 nucleotides or some 24.5% of the total sequence, whose start was confirmed by analysing the carboxyterminal amino acid of the gene 10 product, the glycoprotein VP10c. Analysis of purified virions radio-labelled with [3H]glucosamine and [3H]mannose showed that VP10c is not a detectable component of the virus particle. The two potential glycosylation sites were found to be very close to the amino terminus of the putative translation product, strongly suggesting that the glycoprotein VP10c does not contain a cleavable signal sequence.

Base Sequence↗
PubMed1992

Structural analysis of the carbohydrate chains isolated from mistletoe (Viscum album) lectin I.

Two glycopeptide fractions prepared from mistletoe (Viscum album) lectin I by Pronase digestion were fractioned by affinity chromatography on a concanavalin A-Sepharose column. With 400-MHz 1H NMR spectroscopy, in conjunction with sugar analysis, the following oligosaccharide structures could be determined: two oligomannose-type glycans in the ratio 4:1, one containing six mannose and the other containing five mannose units, both with two 2-acetamido-2-deoxyglucose units. In addition, a mannotriosyl-->N,N'-diacetylchitobiose glycan containing a xylosyl group and an alpha-fucosyl group (1-->3)-linked to the 2-acetamido-2-deoxyglycosyl-1 residue, a common core element of many plant glycoproteins, was also observed.

Carbohydrate Sequence↗
PubMed1986

Structure and assembly of turnip crinkle virus. I. X-ray crystallographic structure analysis at 3.2 A resolution.

The structure of turnip crinkle virus has been determined at 3.2 A resolution, using the electron density of tomato bushy stunt virus as a starting point for phase refinement by non-crystallographic symmetry. The structures are very closely related, especially in the subunit arm and S domain, where only small insertions and deletions and small co-ordinate shifts relate one chain to another. The P domains, although quite similar in fold, are oriented somewhat differently with respect to the S domains. Understanding of the structure of turnip crinkle virus has been important for analyzing its assembly, as described in an accompanying paper.

Capsid↗
PubMed1979

Proposed replicative role of the NS polypeptide of vesicular stomatitis virus: structural analysis of an electrophoretic variant.

The structural lesion in the temperature-sensitive mutant E1 of the New Jersey serotype of vesicular stomatitis virus has been assigned to the NS protein. Although the packaged wild-type and mutant NS proteins were similarly phosphorylated, the mutant NS protein migrated faster than the wild-type NS protein in polyacrylamide slab gels electrophoresed in the presence of sodium dodecyl sulfate. The resolution appears to be the result of conformational rather than size differences since the two proteins comigrated in polyacrylamide gels which contained 4 M urea in addition to sodium dodecyl sulfate. Peptide maps, obtained by limited proteolysis of 32P-labeled wild-type and mutant NS proteins with Staphylococcus aureus V8 protease and papain, revealed striking differences which suggested that the mutant alteration could involve an aspartic or glutamic acid residue. Since NS proteins obtained from naturally occurring revertants of E1 were indistinguishable from the wild-type protein in all of these analyses, the structural alteration in the mutant NS protein correlates with the functional lesion. Because E1 is defective in the RNA replication pathway at the restrictive temperature, a replicative role is proposed for the NS protein.

Electrophoresis, Polyacrylamide Gel↗
PubMed1992

A structural analysis of the genotoxic and carcinogenic potentials of cyclosporin A.

The structural determinants identified by CASE, a knowledge-based structure--activity relational expert system, as contributing to toxicological effects have been distilled from the informational content of over 2000 molecules that have been adequately tested. This methodology has been applied to an analysis of the potential structural determinants of the mutagenicity, clastogenicity and carcinogenicity of cyclosporin A. The analysis predicts that cyclosporin A is devoid of mutagenicity, clastogenicity and DNA-modifying activity. There is however, a structural basis for its carcinogenicity in rodents, i.e. it appears to be a 'non-genotoxic' carcinogen. As a group, 'non-genotoxic' carcinogens are considered by some to pose a far lesser risk to humans than 'genotoxic' ones. The analysis is consistent with the interpretation that the carcinogenicity and immunosuppressive properties of cyclosporin A derive from different mechanisms and are, therefore, separable.

Animals↗
PubMed1988

Structural analysis of polymers of sickle cell hemoglobin. I. Sickle hemoglobin fibers.

The structure of fibers of deoxyhemoglobin S has been under investigation for several years and a number of different models have been proposed for the arrangement of molecules within the particles. We have used reconstruction and modeling techniques in our analysis of these structures. Several new approaches have been employed in this analysis in order to provide improved estimates of the co-ordinates, pairing, and polarity of the hemoglobin S molecules. Fibers have a variable pitch and, in order to minimize distortions in the reconstructed density maps associated with these variations in pitch, we have developed an iterative procedure to measure the instantaneous pitch and have modified the reconstruction algorithm to incorporate the measured values. This procedure improves the accuracy with which the hemoglobin S molecules can be located in the density maps. Furthermore, the determination of the instantaneous pitch allows us to measure directly the rotation of the individual hemoglobin molecules. These measurements are in excellent agreement with the values predicted using a random angular walk model (as originally proposed for F-actin) to describe the variable pitch. The reconstructions confirm that the fiber consists of 14 strands of hemoglobin S arranged in a hexagonally shaped cross-section. We have determined the pairing of the molecules to form double strands directly from the density maps by identifying the molecules that have intermolecular distances that conform to those of double strands in the Wishner-Love crystal. The seven double strands identified in this manner are consistent with the strand pairings proposed by Dykes et al. (1979) rather than the alternate pairings proposed by Rosen & Magdoff-Fairchild (1985). In addition, we have for the first time determined the polarity of the double strands directly from the reconstruction data. This was achieved using a procedure that amounts to essentially "dissecting" individual double strands from the reconstructed density maps so that their density distribution could be examined independently of the neighboring double strands. Knowledge of the relative polarities of the double strands is essential for determining the intermolecular interactions that stabilize the fiber.

Crystallography↗
PubMed1986

Larval salivary gland secretion proteins in Drosophila structural analysis of the Sgs-5 gene.

The structure of the Drosophila melanogaster salivary gland secretion gene Sgs-5 has been determined by DNA sequence analysis of cloned genomic DNA. This developmentally and tissue-specific gene is a member of the third instar intermolt gene set and is under control of the insect molting hormone ecdysterone. RNA protection experiments show that the RNA coding region of Sgs-5 contains 769 nucleotides and is divided into three exons by two small introns. The protein-coding region appears to begin after a short untranslated RNA leader (33 nucleotides) and to result in a protein of 163 amino acids. The first 18 amino acids give the amino-terminal end the highly hydrophobic nature characteristic of a signal peptide.

Amino Acid Sequence↗
PubMed1991

Escherichia coli aspartate carbamoyltransferase: the probing of crystal structure analysis via site-specific mutagenesis.

Crystal structures are known for aspartate carbamoyltransferase (ATCase) in the T and R states, with and without the allosteric activator adenosine triphosphate (ATP) or inhibitor cytidine triphosphate (CTP). Visual inspection of X-ray crystal structures does not provide all of the information necessary for the determination of structure--function relationships in protein molecules. This problem is compounded because the crystalline states of the molecule may introduce effects due to crystal packing, restricted flexibility and less than optimum enzymatic conditions. Therefore, alternative techniques are required to test mechanisms conjectured from three-dimensional crystal structures of proteins. The technique of site-specific mutagenesis allows the researcher to test structure--function models based on three-dimensional structures and to obtain further insight into characteristics of the enzyme. Site-specific mutagenesis has been used to probe residues believed to be critical in the structure and function of ATCase. Selection of residues to be mutated has depended extensively on three-dimensional crystal structures of the enzyme. To date, 48 site-specific mutations at 37 different amino acid sites have been published. Although a total of 118 mutants at 58 different sites has been communicated to our laboratory, only published mutants will be considered in this review. In this paper, we compile for the first time, review, and analyze the site-specific mutants of ATCase. Site-specific mutagenesis of proteins has become a powerful technique in modern-day molecular biology, especially in studying a molecule as large as aspartate carbamoyltransferase. In this review, the role of site-specific mutagenesis of ATCase is discussed and improvements in the analysis are suggested.

Amino Acid Sequence↗
PubMed1987

Fluorescence method for the structural analysis of oligomannose-type sugar chains by partial acetolysis.

Fluorescence labeling was used in the analysis of partial acetolysis products of oligomannose-type sugar chains with five to nine mannose residues. The principle of the method was the pyridylamination of fragments obtained by the partial acetolysis of pyridylamino sugar chains and the identification of the fragments with an HPLC apparatus equipped with a fluorescence spectrophotometer. The method was tested by analysis of eight oligomannose-type sugar chains with known chemical structures and was found to be effective for analysis of branching structures with samples of 0.5 nmol.

Carbohydrate Sequence↗
PubMed1986

The complete sequence and structural analysis of human apolipoprotein B-100: relationship between apoB-100 and apoB-48 forms.

We have isolated and sequenced overlapping cDNA clones covering the entire sequence of human apolipoprotein B-100 (apoB-100). DNA sequence analysis and determination of the mRNA transcription initiation site by S1 nuclease mapping showed that the apoB mRNA consists of 14,112 nucleotides including the 5' and 3' untranslated regions which are 128 and 301 nucleotides respectively. The DNA-derived protein sequence shows that apoB-100 is 513,000 daltons and contains 4560 amino acids including a 24-amino-acid-long signal peptide. The mol. wt of apoB-100 implies that there is one apoB molecule per LDL particle. Computer analysis of the predicted secondary structure of the protein showed that some of the potential alpha helical and beta sheet structures are amphipathic, whereas others have non-amphipathic neutral to apolar character. These latter regions may contribute to the formation of the lipid-binding domains of apoB-100. The protein contains 25 cysteines and 20 potential N-glycosylation sites. The majority of cysteines are distributed in the amino terminal portion of the protein. Four of the potential glycosylation sites are in predicted beta turn structures and may represent true glycosylation positions. ApoB lacks the tandem repeats which are characteristic of other apolipoproteins. The mean hydrophobicity the mean value of H1 and helical hydrophobic moment the mean value of microH profiles of apoB showed the presence of several potential helical regions with strong polar character and high hydrophobic moment. The region with the highest hydrophobic moment, between amino acid residues 3352 and 3369, contains five closely spaced, positively charged residues, and has sequence homology to the LDL receptor binding site of apoE. This region is flanked by three neighbouring regions with positively charged amino acids and high hydrophobic moment that are located between residues 3174 and 3681. One or more of these closely spaced apoB sequences may be involved in the formation of the LDL receptor-binding domain of apoB-100. Blotting analysis of intestinal RNA and hybridization of the blots with carboxy apoB cDNA probes produced a single 15-kb hybridization band whereas hybridization with amino terminal probes produced two hybridization bands of 15 and 8 kb. Our data indicate that both forms of apoB mRNA contain common sequences which extend from the amino terminal of apoB-100 to the vicinity of nucleotide residue 6300. These two messages may have resulted from differential splicing of the same primary apoB mRNA transcript.

Adult↗
PubMed1989

Age-related changes in the cholinergic components within the central nervous system of CW1 female mice. I. Structural analysis.

Histomorphometric analysis of age-related structural changes in the brain was performed in CW1 female mice, 3, 9, 24 and 32 months of age. Cholinergic regions, such as the hippocampus, NBM and the medial habenula (MH) were investigated in more detail focusing on morphological parameters. The thickness of the frontoparietal cortex (FPC), and the surface area of the dorsal hippocampus and the MH were found to decrease significantly from 9 to 24 months of age. Except for the unique appearance of pseudo-cysts within the FPC, the structural changes culminated by 24 months. Cells' degeneration, in the CA3 hippocampal subfield, was noted already by 9 months of age whereas in other regions the cells' surface area decreased only between 9 and 24 months. Lipofuscin accumulation was most pronounced in the large neurons of the cortex, hippocampus and NBM at 24 months of age.

Aging↗
PubMed1989

[Antipeptide antibodies to the porcine lactate dehydrogenase isoenzyme M4 active center fragment as a probe for the structural analysis of active centers of human lactate dehydrogenase isoforms].

Antipeptide antibodies (AB) to the fragment of the active center of porcine lactate dehydrogenase M4 isoform were used for the analysis of antigenic properties and structural comparison of active centers of human lactate dehydrogenase isoforms. Selective precipitation of the M-subunit-containing isoforms using an immunoadsorbent based on antipeptide AB as well as selective inhibition of the enzymic activity of the M4 isoform by antipeptide AB testify to the specific binding of isoforms to antipeptide AB. The experimental results confirm the literary data on conformational changes in the structure of the active centers of corresponding human lactate dehydrogenase isoforms. The specific interaction of antipeptide AB with human lactate dehydrogenase isoforms suggests that the site of the amino acid sequence (residues 180-214) in both human and porcine M4 isoenzymes is immunochemically identical. The data obtained suggest that antipeptide AB are convenient probes for detecting differences (including minor ones) in the primary and spatial structure of enzymes.

Animals↗
PubMed1990

Negative ion fast atom bombardment-tandem mass spectrometry for structural analysis of isoprenoid diphosphates.

Applicability of negative ion fast atom bombardment (FAB)-tandem mass spectrometry (MS/MS) was examined in trace mixture analyses and structural assignments of some isoprenoid diphosphates. Negative ion FAB-MS spectra using a glycerol matrix of these isoprenoid diphosphates showed predominantly molecular ions (M-H)- together with fragment ions at m/z 177 (H3P2O7)-, 176 (H2P2O7)-, 159 (HP2O6)-, and 79 (PO3)- which were characteristic of the diphosphate ester moiety. The molecular ions did not overlap with peaks arising from any impurities even when crude sample such as butanol extracts from enzymatic reaction mixtures were directly analyzed without any purification. Moreover, collisionally activated dissociation spectra of the molecular ion showed many structurally significant fragment ions which enabled us to elucidate the structures of such irregular alkyl chain moieties as those having a homoisoprenoid skeleton or substituted structures. These studies indicate that negative ion FAB-MS/MS is a simple and useful technique for trace mixture analysis and structure elucidation of isoprenoid diphosphates.

Esters↗
PubMed1987

Structural analysis of an HLA-B27 functional variant, B27d, detected in American blacks.

The structure of a new functional variant B27d has been established by comparative peptide mapping and radiochemical sequencing. This analysis completes the structural characterization of the six known histocompatibility leukocyte antigen (HLA)-B27 subtypes. The only detected amino acid change between the main HLA-B27.1 subtype and B27d is that of Tyr59 to His59. Position 59 has not been previously found to vary among class I HLA or H-2 antigens. Such substitution accounts for the reported isoelectric focusing pattern of this variant. HLA-B27d is the only B27 variant found to differ from other subtypes by a single amino acid replacement. The nature of the change is compatible with its origin by a point mutation from HLA-B27.1. Because B27d was found only in American blacks and in no other ethnic groups, it is suggested that this variant originated as a result of a mutation of the B27.1 gene that occurred within the black population.

Amino Acid Sequence↗
PubMed1990

[Structural analysis of melanocytic pigment nevi using epiluminescence microscopy. Review and personal experiences].

Epiluminescent microscopy is now used frequently for the differential diagnosis of pigmented skin lesions. In order to improve the distinction between benign and malignant melanocytic tumours it seemed advisable to develop a standardized pathway of epiluminescent microscopical analysis and to determine the frequency of structures recognizable with the microscope. A total of 600 melanocytic lesions were examined by epiluminescent microscopy, photographed and classified histologically after excision, revealing 426 naevocellular naevi and 174 melanoma. The experience achieved during the course of the investigation was used as the basis of a procedure for stepwise analysis of keratin layer, pigment structures and blood vessels. The most important findings are described and referred to malignancy. The photographs were analysed for the frequency of occurrence of various pigment structures in different types of lesions. The results differ in several aspects from previous findings.

Diagnosis, Differential↗
PubMed1992

Immunochemical and structural analysis of the O polysaccharides of Salmonella zuerich [1,9,27,(46)].

Salmonella zuerich [1,9,27,(46)] has been shown to exhibit two levels of structural heterogeneity. The bacterium carries two distinct O-polysaccharide molecules with and without O:factor 1. Both sets of molecules (1+ and 1-) carry the two O:factors 27 and 46 on the same O chain, but they are expressed unevenly; in contrast to factor 27, O:factor 46 is always weakly expressed. Part of this weak expression was thought to be due to strong inhibition of factor 46 by factor 1. In this study, serological analysis gave more detailed information on the sizes of the different O:factor epitopes. Structural analysis of S. zuerich O polysaccharides showed that they are constructed of the expected chemical sequences characteristic of factors 1, 9, 27, and 46. No modification in the sugar sequence could account for the weak expression of O:factor 46. Factors 27 and 46 are present on oligosaccharides carrying either an alpha-Man (factor 27) or a beta-Man (factor 46) residue. In S. zuerich, the alpha-Man configuration is predominant, corroborating the expression of strong factor 27 and weak factor 46 on the bacteria. Questions raised by the existence of such heterogeneous O polysaccharides on the specificity of the O chain polymerase, as well as the place of S. zuerich in Salmonella evolution, are dicussed in this paper.

Carbohydrate Sequence↗