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PubMed1991

Structural features of the cell-wall polysaccharides of Asparagus officinalis seeds.

The fine structure of a beta-)1----4)-linked glucomannan from Asparagus officinalis has been determined by n.m.r. analysis of the oligosaccharides obtained by acidic and enzymic hydrolyses. Cleavage of the glucomannan with beta-D-mannase from Aspergillus niger and purification by h.p.l.c. gave oligosaccharide fractions that contained Man (mannose), GlcMan (beta-glucopyranosylmannose), Man2, Glc2Man, and Glc3Man as the major components. Simulated digestion of a polymer composed of randomly distributed monomers with the same Glc:Man ratio as glucomannan from A. officinalis led to the same polysaccharides. The random distribution of the monomers of glucomannan from A. officinalis was corroborated by the diffraction diagram of the raw flour, which indicated that the "in situ" glucomannan was amorphous, whereas both cellulose and mannans are crystalline.

Acids↗

PubMed1987

Structural features of antigenic determinants on variant surface glycoproteins from Trypanosoma brucei.

The immunochemical structure of two variant surface glycoproteins (VSGs) from Trypanosoma brucei has been studied using monoclonal and polyclonal antibodies. These two VSGs, WaTat 1.1 and WaTat 1.12 have been shown to possess cross-reactive surface-exposed antigenic determinants [Barbet et al., Nature 300, 53-57 (1982)] and similar N-terminal amino acid sequences [Olafson et al., Molec. Biochem. Parasit. 12, 287-298 (1984)]. Monoclonal and polyclonal antibodies were raised against the soluble forms of the two VSGs and against their reduced, alkylated and cyanogen bromide (CNBr) cleaved forms. None of the monoclonal antibodies which bound to the surface of living trypanosomes bound to CNBr fragments of the VSGs nor to denatured VSGs. Polyclonal antibodies raised against denatured and cleaved VSG did not bind to the surface of the living trypanosomes. These results suggest that the variable surface exposed antigenic determinants of VSG are topographically assembled structures. It was also shown that the conserved amino terminal peptides of WaTat 1.1 and WaTat 1.12 do not contain antigenic determinants.

Animals↗

PubMed2002

Structural features of non-granular spherulitic maize starch.

Complementary analyses of the internal structure of spherulites crystallized from high-amylose maize starch were obtained using light, electron and atomic force microscopy. Radially oriented crystalline lamellae were observed in transmission and scanning electron microscopy, as well as AFM. Internal structures consistent with the central hilum region of starch granules were observed. Spherulites were composed largely of linear or lightly branched starch polymers. Degradation of amylopectin at gelatinization temperatures of 180 degrees C was evident, but iodine binding suggested a high molecular weight (>100 DP) for the spherulitic polymers.

Calorimetry, Differential Scanning↗

PubMed2005

Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3.

Despite its importance for group II intron catalytic activity, structural information on conserved domain 3 (D3) is extremely limited. This domain is known to specifically stimulate the chemical rate of catalysis and to function as a 'catalytic effector'. Of all the long-range tertiary contacts that have been identified within group II introns, none has included D3 residues. Furthermore, little is known about the atoms and functional groups in D3 that contribute to catalysis. Using a nucleotide analog interference mapping assay with an extended repertoire of nucleotide analogs, we have identified functional groups in D3 that are critical for ribozyme activity. These data, together with mutational analysis, suggest the formation of noncanonical base pairs within the phylogenetically conserved internal loop at the base of D3. Finally, a related nucleotide analog interference suppression study resulted in the identification of a direct tertiary interaction between D3 and catalytic domain 5, which sheds new light on D3 function in the group II intron structure and mechanism.

Catalytic Domain↗

PubMed1999

Structural features of autoreactive TCR that determine the degree of degeneracy in peptide recognition.

Structural aspects of human TCRs that allow the activation of autoreactive T cells by diverse microbial peptides were examined using two human myelin basic protein (MBP)-specific T cell clones. The TCR sequences of these clones differed only in the N region of TCR-alpha and -beta since the clones had the same Valpha-Jalpha and Vbeta-Jbeta rearrangements. The two clones had a similar fine specificity for the MBP peptide, except for the P5 position of the peptide (lysine). In the crystal structure of the HLA-DR2/MBP peptide complex, P5 lysine is a prominent, solvent-exposed residue in the center of the DR2/MBP peptide surface. Five microbial peptides with conservative or nonconservative changes at the P5 position (lysine to arginine, serine, or proline) activated one of these clones. In contrast, the other clone was activated only by three of these peptides which had a conservative lysine to arginine change at P5. The degree of specificity/degeneracy in recognition of the P5 side chain was the key difference between these TCRs since the Escherichia coli/Haemophilus influenzae peptide stimulated both clones when the P5 position was substituted from serine to arginine. These results demonstrate that the complementarity-determining region 3 loops contribute to the degree of degeneracy in peptide recognition by human MBP-specific TCRs.

Amino Acid Sequence↗

PubMed1996

Structural features of latex gloves in dental practice.

The aim of this study was to define from a morpho-structural point of view, using scanning electron microscopy, the features of various types of disposable latex gloves commonly used in Italian dental practice (Biogel D, Trend, Pagni, J&J, Latechnics, Pehasoft, Bantex). None of the brands examined was free from morphological flaws; however, while in some of these only slight depressions were found (Biogel D, Trend), in others (Latechnics, Bantex) there was a marked lack of homogeneity in the latex structure or real holes (Pehasoft). This study emphasizes the current difficulties faced by dentists in the search for safe working conditions.

Biocompatible Materials↗

PubMed1993

Conserved structural features in glycoprotein processing glucosidase I from several tissues and species.

Glucosidase I initiates the processing of the oligosaccharide, Glc3Man9GlcNAc2, in newly assembled glycoproteins by excising the distal alpha 1,2-linked glucosyl residue in the oligosaccharide. Earlier, the enzyme purified from the ER of rat and bovine mammary gland has been found to have M(r) of 85 kDa, as examined by SDS-PAGE along with a domain structure in which a 39 kDa lumenally-oriented region is anchored to the ER through a transmembrane segment and a short cytoplasmic tail. These studies were further extended to include the enzyme from several different tissues of the rat, mouse, guinea pig and bovine mammary glands, sheep liver and pig kidney. Using anti-rat glucosidase I antibody as a probe and several biochemical parameters such as SDS-PAGE analysis, trypsin-catalyzed digestion, ConA-binding, endo H susceptibility and peptide mapping analysis by cleavage of the tryptophanyl peptide linkages within the enzyme, it was found that glucosidase I in all of the tissue sources examined has an M(r) of 85 kDa and is cross-reactive to anti-rat glucosidase antibody. The enzyme is a high mannose glycoprotein, and has domain features in its structure; the enzyme from mouse, rat, guinea pig and bovine mammary glands and sheep liver is sequentially cleaved by trypsin to generate fragments of 69, 55 and 39 kDa. The rate of release of the different fragments differs for different sources, indicating some evolutionary changes in its primary structure. The trypsin-released fragments from pig kidney enzyme are 69, 45 and 29 kDa in size, identical to the same observed earlier for pig liver.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2004

Identification of common structural features of binding sites in galactose-specific proteins.

Galactose-binding proteins characterize an important subgroup of sugar-binding proteins that are involved in a variety of biological processes. Structural studies have shown that the Gal-specific proteins encompass a diverse range of primary and tertiary structures. The binding sites for galactose also seem to vary in different protein-galactose complexes. No common binding site features that are shared by the Gal-specific proteins to achieve ligand specificity are so far known. With the assumption that common recognition principles will exist for common substrate recognition, the present study was undertaken to identify and characterize any unique galactose-binding site signature by analyzing the three-dimensional (3D) structures of 18 protein-galactose complexes. These proteins belong to 7 nonhomologous families; thus, there is no sequence or structural similarity across the families. Within each family, the binding site residues and their relative distances were well conserved, but there were no similarities across families. A novel, yet simple, approach was adopted to characterize the binding site residues by representing their relative spatial dispositions in polar coordinates. A combination of the deduced geometrical features with the structural characteristics, such as solvent accessibility and secondary structure type, furnished a potential galactose-binding site signature. The signature was evaluated by incorporation into the program COTRAN to search for potential galactose-binding sites in proteins that share the same fold as the known galactose-binding proteins. COTRAN is able to detect galactose-binding sites with a very high specificity and sensitivity. The deduced galactose-binding site signature is strongly validated and can be used to search for galactose-binding sites in proteins. PROSITE-type signature sequences have also been inferred for galectin and C-type animal lectin-like fold families of Gal-binding proteins.

Amino Acid Sequence↗

PubMed1986

Morphological and fine structural features of the basilar papilla in ambystomatid salamanders (Amphibia; Caudata).

The morphology and fine structure of the basilar recess and basilar papilla were investigated in four species of salamanders from the family Ambystomatidae. The otic relationships of the recess and papilla to the proximal part of the lagena and saccule are described, and new terminology is suggested for the periotic relationships of the basilar recess to a diverticulum of an intracapsular periotic sac. The basilar papilla consists of supporting cells united laterally by gap junctions, capped by microvilli uniformly arranged around a short, central cilium, and hair cells that typically show several synapses with a single afferent nerve fiber, each marked by a rounded synaptic body surrounded by vesicles. In contrast to anuran basilar papillae, efferent nerve terminals were observed in synapse with hair cells and, rarely, upon afferent fibers. The distal half of the ambystomatid papilla contained hair cells capped by tall ciliary bundles, with kinocilia that show swellings near their tips with delicate attachments to adjacent tall stereocilia. A tectorial body covers only this region of the papilla. Hair cells with shorter stereocilia, situated in the proximal half and at the papillar margins, are related only to filamentous extensions of the tectorial body. The ambystomatid basilar recess and papilla are compared to auditory end-organs in other vertebrates, and it is suggested that a basic distinction can be made between aural neuroepithelia in amniotes versus that in nonamniotic vertebrate ears.

Ambystomatidae↗

PubMed2000

Review: chromatin structural features and targets that regulate transcription.

The nucleosome and chromatin fiber provide the common structural framework for transcriptional control in eukaryotes. The folding of DNA within these structures can both promote and impede transcription dependent on structural context. Importantly, neither the nucleosome nor the chromatin fiber is a static structure. Histone dissociation, histone modification, nucleosome mobility, and assorted allosteric transitions contribute to transcriptional control. Chromatin remodeling is associated with gene activation and repression. Energy-dependent processes mediate the assembly of both activating and repressive proteins into the nucleosomal infrastructure. Recent progress allows the structural consequences of these processes to be visualized at the chromosomal level. DNA and RNA polymerase, SWI/SNF complexes, histone deacetylases, and acetyltransferases are targeted by gene-specific regulators to mediate these structural transitions. The mistargeting of these enzymes contributes to human developmental abnormalities and tumorigenesis. These observations illuminate the roles of chromatin and chromosomal structural biology in human disease.

Animals↗

PubMed1997

Protein chains in hair and epidermal keratin IF: structural features and spatial arrangements.

Over the past decade the progress made in characterising the structural hierarchy of both the hard and the epidermal keratin intermediate filaments has exceeded all expectations. The origin of much of this progress can be traced back to the quantity of amino acid sequence data that became available in the early/mid 1980s, and their interpretation in terms of a heterodimeric molecular structure. Subdomains were subsequently identified in both the rod and terminal domains, and now the roles of most of these have been determined in principle, if not yet fully in detail. TEM and STEM, together with very revealing crosslinking analyses have also allowed details to be determined of the mechanism by which molecules assemble into oligomers and oligomers into IF. It remains for the three-dimensional packing of keratin molecules in the IF to be elucidated, but even here progress is being made. A particularly exciting development over the last two or three years has been the establishment of the link between keratinopathies and single point nucleotide mutations in keratin genes. Furthermore, the clustering of mutation sites in regions involved in a key structural mode of molecular aggregation has provided, for the first time, an understanding of keratin diseases at the molecular level.

Amino Acid Sequence↗

PubMed1988

Analysis of structural features responsible for the sweetness of the sesquiterpene, hernandulcin.

The relationship between sweetness and structure was studied for several analogues of the intensely sweet sesquiterpene, hernandulcin. These derivatives were prepared synthetically, and were spectroscopic and conformational analysis. With the exception of the parent substance, none of the derivatives tested proved to be sweet. Evidence gathered in this study suggests that hernandulcin binds to its putative receptor through a three-point interaction, involving the C-1 carbonyl and C-1' hydroxyl groups, and the double bond between C-4' and C-5'. In the course of a preliminary safety assessment, the 3-desmethyl derivative of hernandulcin was found to be mutagenic toward Salmonella typhimurium strain TM677.

Chemical Phenomena↗

PubMed1991

Structural features of an exocyclic adduct positioned opposite an abasic site in a DNA duplex.

Structural studies have been extended to dual lesions where an exocyclic adduct is positioned opposite an abasic site in the center of a DNA oligomer duplex. NMR and energy minimization studies were performed on the 1,N2-propanodeoxyguanosine exocyclic adduct (X) positioned opposite a tetrahydrofuran abasic site (F) with the dual lesions located in the center of the (C1-A2-T3-G4-X5-G6-T7-A8-C9).(G10-T11-A12-C-13-F14-C15 -A16-T17-G-18) X.F 9-mer duplex. Two-dimensional NMR experiments establish that the X.F 9-mer helix is right-handed with Watson-Crick A.T and G.C base pairing on either side of the lesion site. NOEs are detected from the methylene protons of the exocyclic ring of X5 to the imino protons of G4.C15 and G6.C13 which flank the lesion site, as well as to the H1' and H1" protons of the cross strand F14 tetrahydrofuran moiety. These NMR results establish that the exocyclic adduct X5 is positioned between flanking G4.C15 and G6.C13 base pairs and directed toward the abasic lesion F14 on the partner strand. These studies establish that the exocyclic ring of the 1,N2-propanodeoxyguanosine adduct fits into the cavity generated by the abasic site.

Base Composition↗

PubMed1997

The structure of the isolated, central hairpin of the HDV antigenomic ribozyme: novel structural features and similarity of the loop in the ribozyme and free in solution.

The structure of an RNA hairpin containing a seven-nucleotide loop that is present in the self-cleaving sequence of hepatitis delta virus antigenomic RNA was determined by high resolution NMR spectroscopy. The loop, which is composed of only one purine and six pyrimidines, has a suprisingly stable structure, mainly supported by sugar hydroxyl hydrogen bonds and base-base and base-phosphate stacking interactions. Compared with the structurally well-determined, seven-membered anticodon loop in tRNA, the sharp turn which affects the required 180 degrees change in direction of the sugar-phosphate backbone in the loop is shifted one nucleotide in the 3' direction. This change in direction can be characterized as a reversed U-turn. It is expected that the reversed U-turn may be found frequently in other molecules as well. There is evidence for a new non-Watson-Crick UC base pair formed between the first and the last residue in the loop, while most of the other bases in the loop are pointing outwards making them accessible to solvent. From chemical modification, mutational and photocrosslinking studies, a similar picture develops for the structure of the hairpin in the active ribozyme indicating that the loop structure in the isolated hairpin and in the ribozyme is very similar.

Base Sequence↗

PubMed2003

A non-intuitive design of a cyclic decapeptide library with unique backbone structural features.

An analysis of hydrogen bonding patterns of cyclic decapeptide (CDP) beta-sheet structures has resulted in a 'non-intuitive' design of cyclic decapeptides wherein their beta-turns and residue positions can be fixed by choosing 2 of the 10 residues, i.e. positions i and i+4, to be Prolines or N-substituted residues. This sequence relationship between the two Pro or N-substituted residues is shown to uniquely define the conformation of the CDP. Furthermore, this design of the 2 beta-turn, beta-sheet CDP structure is expected to be characterised by residues disposed in an exclusive fashion in which four residues are on one side of the ring, two on the other and the four corner residues in the beta-turn are in the plane of the ring. This opens up the possibility of fine-tuning the four residues facing one way and /or the two residues facing the other way such that a library containing a myriad of chemically diverse systems could be obtained. The design process along with the molecular modelling of specific CDP-s and the building of a CDP library are discussed in detail.

Amino Acids↗

PubMedDate not supplied

[Structural features of the integration site of foreign DNA in the transgenic mouse genome].

The structure of the transgenic mouse DNA region containing an integrated transgene (fragment of pBR322 sequence) was analysed. In one of the sequences flanking the transgene, short direct and inverted overlapping repeats were revealed at a distance of 60 bp from the integration site. In the same flanking sequence, there is an extended sequence (3.5 kbp) 0.3-1 kbp away from the transgene. It repeats 100-300 times in the mouse genome and is highly conservative (the homologs of the repeat have been revealed in other mammalian, bird, fish and insect genomes). This up-to-date unknown family of highly-conserved dispersed repeats has been denoted by T1. We believe that both the revealed short inverted repeats capable of forming hairpins with loops and the T1 repeat are structures involved in the process of non-homologous insertion of foreign DNA into the region of the transgenic mouse genome.

Animals↗

PubMed2005

Crystal structure of the human vascular adhesion protein-1: unique structural features with functional implications.

The expression of human vascular adhesion protein-1 (hVAP-1) is induced at sites of inflammation where extravasation of lymphocytes from blood to the peripheral tissue occurs. We have solved the X-ray structure of hVAP-1, a human copper amine oxidase (CAO), which is distinguished from other CAOs in being membrane-bound. The dimer structure reveals some intriguing features that may have fundamental roles in the adhesive and enzymatic functions of hVAP-1, especially regarding the role of hVAP-1 in inflammation, lymphocyte attachment, and signaling. Firstly, Leu469 at the substrate channel may play a key role in controlling the substrate entry; depending on its conformation, it either blocks or gives access to the active site. Secondly, sugar units are clearly observed at two of the six predicted N-glycosylation sites. Moreover, mutagenesis analysis showed that all of the predicted sites were glycosylated in the protein used for crystallization. Thirdly, the existence of a solvent-exposed RGD motif at the entrance to each active site in hVAP-1 suggests that it may have a functional role.

Amine Oxidase (Copper-Containing)↗

PubMed1995

Deduced amino acid sequence of 2S storage protein from Brassica species and their conserved structural features.

2S seed storage albumin coding regions from five Brassica species, namely Brassica campestris, B. oleracea, B. nigra, B. juncea, and B. carinata have been cloned by PCR amplification of genomic DNA using oligonucleotide primers and their nucleotide sequences have been determined. These sequences showed more than 85% homology amongst themselves and considerable homology with some other crucifer 2S protein coding sequences. The deduced amino acid sequences showed more homology due to some inconsequential mutations in codons without changing the amino acids. Computer analysis of the protein sequences for possible secondary structure revealed a high degree of conservation of hydrophilic and hydrophobic domains and the invariant positions of cysteine residues. Unrooted phylogenic tree based on the coding region of 2S albumin from different Brassica species cloned by us and published sequences from other Cruciferae indicated that these genes originated before the evolutionary divergence of different Brassica species and were conserved due to some stringent structural and functional features required for seed metabolism.

Amino Acid Sequence↗