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PubMed2000

Molecular organization, structural features, and ligand binding characteristics of CD44, a highly variable cell surface glycoprotein with multiple functions.

CD44 is a type I transmembrane protein and member of the cartilage link protein family. It is involved in cell-cell and cell-matrix interactions and signal transduction. Several CD44 ligands have been identified. CD44 is a major cell surface receptor for hyaluronan, a component of the extracellular matrix. It is implicated in diseases such as cancer and inflammation and therefore intensely studied. A characteristic feature of CD44 is the occurrence of many isoforms that are expressed in a cell-specific manner and differentially glycosylated. Although a number of CD44 isoforms have been characterized, the structural diversity of CD44 makes it often challenging to study (isoform-specific) CD44-ligand interactions at the molecular level of detail. The structural organization and ligand binding characteristics of CD44 are focal points of this review. On the basis of recent structural and mutagenesis studies, details of the CD44-hyaluronan interaction are beginning to be understood. Proteins 2000;39:103-111.

Humans↗
PubMed2003

Contemporary seasonal and altitudinal variations of leaf structural features in oregano (Origanum vulgare L.).

The effects of elevation (200, 950 and 1760 m) and season (April-October) on leaf morphological, anatomical, ultrastructural, morphometrical and photosynthetic parameters were studied in Origanum vulgare plants. Observations aimed at the determination of the alterations in leaf structure and function associated with differential growth and adaptation of plants. Raising elevation results in a progressive decrease of plant height. During the growing period, summer plants are taller than spring and autumn plants at all elevations examined. In high-altitude populations (O. vulgare ssp. vulgare), the blade size becomes reduced in June leaves as compared with October leaves, while it does not change remarkably in low-altitude populations (O. vulgare ssp. hirtum). Leaf thickness remains more or less stable during the growing period. Expanded leaves in June and October at 200 m elevation contain dark phenolics only in their epidermis, whereas leaves of August are densely filled with phenolics in all of their tissues. In June at 1760 m elevation, leaves are devoid of phenolics, which, however, occur in the epidermis of the leaves in August and October. At higher altitudes, larger mesophyll chloroplasts with more starch grains are present in June leaves, whereas in August and October leaves chloroplasts are smaller with fewer starch grains. Leaf stomata and non-glandular hairs increase in number from the lowland to the upland habitats, whereas glandular hairs decrease in number. During the growing season, the density of stomata and of glandular and non-glandular hairs progressively increases. In the low- and mid-altitude oregano populations, leaf chlorophyll a content and PSII activity significantly increase in October, whereas they simultaneously decrease in the high-altitude population, suggesting a phenomenon of chilling-induced photoinhibition. The highest photochemical efficiency of PSII appears in the mid-altitude population (having characteristics intermediate between those of O. vulgare ssp. hirtum and ssp. vulgare) where environmental conditions are more favourable. This conclusion is also confirmed by the observation that the 950 m O. vulgare population has larger and thicker leaves with highly developed palisade and spongy parenchymas.

Altitude↗
PubMed1994

Structural features in heparin which modulate specific biological activities mediated by basic fibroblast growth factor.

The biological activity of basic fibroblast growth factor (bFGF) is influenced greatly by direct binding to heparin and heparan sulphate (HS). Heparin-derived oligosaccharides have been utilized to determine the structural requirements present in the polymer that account for binding to bFGF. We had previously demonstrated that fragments > 6 mer can inhibit the interaction between cell surface heparan sulphate proteoglycan (HSPG) and bFGF, and bFGF-induced proliferation of adrenocortical endothelial (ACE) cells. In contrast, oligosaccharides > 10 mer can enhance the binding of bFGF to its high-affinity receptor or support bFGF-induced mitogenesis in ACE cells (Ishihara et al., J. Biol. Chem., 268, 4675-4683, 1993). We have extended these studies to size- and structure-defined oligosaccharides from heparin, 2-O-desulphated (2-O-DS-) heparin, 6-O-desulphated (6-O-DS-) heparin, carboxy-reduced (CR-) heparin and carboxy-amidomethylsulphonated (AMS-) heparin. Oligosaccharides from these polymers were fractionated on a bFGF-affinity column and were assessed as inhibitors or enhancers of specific bFGF-derived biological activities. The results of these studies indicate that both 2-O-sulphate and the negative charge of the carboxy group [L-iduronic acid (IdoA) residues] are required for specific interactions of heparin-derived oligosaccharides with bFGF and for modulation of bFGF mitogenic activity. In addition, the charge of the carboxy groups in uronic acids can be replaced by other functional groups with a negative charge, such as the amidomethyl sulphonate moiety described here.

Animals↗
PubMed1998

Structural features of the minimal DNA binding domain (M98-F219) of human nucleotide excision repair protein XPA.

XPA, an essential protein in nucleotide excision repair (NER), interacts with damaged DNA and other proteins (RPA, ERCC1 and TFIIH) to remove a wide variety of chemically and structurally distinct DNA lesions from the eukaryotic genome. To understand the structural basis for the role of XPA in the repair process, the structure of the minimal DNA binding domain of human XPA [XPA-MBD (M98-F219)] was studied by NMR spectroscopy. A three-dimensional structure for XPA-MBD was generated using distance geometry and simulated annealing methods from NOE-based distance restraints, hydrogen bond and Zn-S distance restraints, and dihedral restraints. The structure calculations indicate that XPA-MBD contains elements of well-defined secondary structure interspaced with disordered loops organized into two non-interactive sub-domains: a zinc-binding core (D101-K137) and a loop-rich domain (L138-F219). The zinc-associated core contains an antiparallel beta-sheet (Y102-C105 and K110-M113) and an alpha-helix (C126-K137) separated by a poorly defined turn, reminiscent of the structure of the zinc-binding domain of the chicken erythroid transcription factor GATA-1 when bound to its cognate DNA sequence. The loop-rich domain contains a triple-strand antiparallel beta-sheet (L138-T140, L182-M178 and K163-K167), three loops (K151-L162, N169-D177 and Q208-F219) and three alpha-helices (K141-L150, K183-W194 and Q197-R207). The XPA-MBD structure is discussed in terms of known functions: binding single- and double-stranded DNA and binding RPA.

Amino Acid Sequence↗
PubMed1994

Comparative analysis of functional and structural features in the primase-dependent priming signals, G sites, from phages and plasmids.

The primase-dependent priming signals, G sites, are directly recognized by the Escherichia coli primase (dnaG gene product) and conduct the synthesis of primer RNAs. In nucleotide sequence and secondary structure, there is no striking resemblance between the phage- and plasmid-derived G sites, except for the limited sequence homology near the start position of primer RNA synthesis. In this study, we analyzed the structure and function of a G site of plasmid R100, G site (R100), and discovered the necessity of the coexistence of two domains (domains I and III), which contains blocks A, B, and C, which are nucleotide sequences highly conserved among the plasmid-derived G sites. However, neither the internal region, domain II, between domains I and III nor the potential secondary structure proposed by Bahk et al. (J. D. Bahk, N. Kioka, H. Sakai, and T. Komano, Plasmid 20:266-270, 1988) is essential for single-stranded DNA initiation activity. Furthermore, chimeric G sites constructed between a G site of phage G4, G site(G4), and G site(R100) maintained significant single-stranded DNA initiation activities. These results strongly suggest that phage- and plasmid-derived G sites have functionally equivalent domains. The primase-dependent priming mechanisms of phage- and plasmid-derived G sites are discussed.

Base Sequence↗
PubMed1998

Conserved structural features between HLA-DO beta and -DR beta.

HLA-DO is a non-classical MHC class II molecule presumed to play a specialized role in the antigen processing pathway. We have modeled the HLA-DO beta-chain and found its overall structure compatible with the one of DR beta. Functional studies further highlighted the similarity between these beta-chains of the class II family of proteins. Indeed, a mixed heterodimer composed of the DR alpha and a chimeric DO beta-chains presented bacterial superantigens to T cells and was shown to interact with CD4. The implications of such structural conservation for the in vivo functions of HLA-DO are discussed.

Amino Acid Sequence↗
PubMed1996

Structural features of mammalian gonadotropins.

There are two species for which both pituitary and placental gonadotropins are readily available, humans and horses. The human gonadotropins are better characterized than equine gonadotropins. Nevertheless, the latter are very interesting because they provide exceptions to some of the general structure-function principles derived from studies on human and other mammalian gonadotropins. For example, separate genes encode the hLH beta and hCG beta subunits while a single gene encodes eLH beta and eCG beta. Thus, eCG and eLH differ only in their oligosaccharide moieties and eLH is the only LH that possesses the O-glycosylated C-terminal extension previously believed to be restricted to chorionic gonadotropins. Truncation experiments involving eLH beta and hCG beta have suggested the C-terminal extension has no effect on receptor binding. However, the largest of three eCG forms which differ only in the extent of O-glycosylation possessed reduced affinity for LH and FSH receptors. This result suggested that effects of O-glycosylation need to be considered when examining the glycosylation differences between eLH and eCG responsible for the 10-fold lower eCG receptor binding affinity compared with that of eLH. Contribution of alpha Asn56 N-linked oligosaccharides to the different biological activities of eLH and eCG has been evaluated following selective removal using peptide-N-glycanase digestion of native equine alpha-subunit preparations. Hormones-specific patterns of glycosylation were observed on alpha Asn56 of eLH, eFSH, and eCG. Removal of alpha Asn56 oligosaccharides increased the rate of subunit association, the extent of association, and receptor binding activity. Some unassociated alpha-subunit oligosaccharides were identified which may interfere with subunit association because they were more abundant in unassociated subunit oligosaccharide maps than in a total oligosaccharide map. This was most striking in the case of eCG alpha in which two minor peaks became the major oligosaccharide peaks detectable in the unassociated eCG alpha fraction following association with eLH beta and eFSH beta. The biological activities exhibited by hybrid hormones, eLH alpha reassociated with oLH beta and pLH beta, found to be greater than those of oLH and pLH provided an interesting exception to the general rule that the beta-subunit determines the potency of the heterodimer. LH receptor binding activities of eLH beta-chimeric ovine/equine alpha-subunits suggested that the equine alpha-subunit N-terminal domain may be responsible for this effect. Equine FSH has higher FSH receptor binding activity than human, ovine, and porcine FSH preparations. This probably results from two factors. First, the presence of the equine alpha-subunit promotes receptor binding as noted above. Second, the overall -2 charge of the eFSH beta determinant loop, which is less negative that the -3 observed in other species, results from the presence of an Asn residue at position 88 instead of Asp. This apparently facilitates binding to the FSH receptor.

Amino Acid Sequence↗
PubMed2002

Structural features of bovine caseinomacropeptide A and B by 1H nuclear magnetic resonance spectroscopy.

Samples of bovine caseinomacropeptide (CMP) were isolated from kappa-casein A and kappa-casein B and fractionated to give aglycosylated CMP A and CMP B and monoglycosylated CMP A. The secondary structures of these three peptides were compared under neutral and acidic (pH 4.2) conditions, using two-dimensional (2D) 1H nuclear magnetic resonance (NMR) spectroscopy. The differences between the spectra at pH 4.2 and 7.0 and the spectra of the aglycosylated and glycosylated CMP A were subtle, indicating little change in backbone conformation with these changes. These results Suggest that differences in the coagulation properties of milks containing either kappa-casein A or kappa-casein B are more likely to be related to factors, such as micelle size or charge, than to structural differences arising from altered backbone conformation of the macropeptide segments of the kappa-caseins.

Algorithms↗
PubMed2005

Adsorption of Wells-Dawson tungsten heteropolyacid on sol-gel alumina: structural features and thermal stability.

The Wells-Dawson tungsten heteropolyacid, H6P2W18O62 supported on sol-gel and non-sol-gel alumina has been investigated by infrared spectroscopy (IR), thermal analysis (TGA/DSC), and X-ray diffraction (XRD). X-ray diffraction indicates that the heteropolyacid primary structure in bulk form holds up to 350 degrees C and by supporting it on the sol-gel alumina the thermal stability rose to 650 degrees C. UV-vis spectroscopy showed that the sol-gel alumina has a higher tendency to adsorb Wells-Dawson tungsten heteropolyacid than the non-sol-gel alumina. The heteropolyacid showed higher interaction with the sol-gel alumina than with the non-sol-gel. Esterification of propanoic acid with hexanol in the presence of alumina-supported heteropolyacid revealed that the acidic character of the heteropolyacid remains active to some extent.

Journal Article↗
PubMed2000

The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence.

The performances of five global multiple-sequence alignment programs (CLUSTAL W, Divide and Conquer, Malign, PileUp, and TreeAlign) were evaluated using part of the animal mitochondrial small subunit (12S) rRNA molecule. Conserved sequence motifs derived from an alignment based on secondary structural information were used to score how well each program aligned a data set of five vertebrate and five invertebrate taxa over a range of parameter values. All of the programs could align the motifs with reasonable accuracy for at least one set of parameter conditions, although if the whole sequence was considered, similarity to the structural alignment was only 25%-34%. Use of small gap costs generally gave more accurate results, although Malign and TreeAlign generated longer alignments when gap costs were low. The programs differed in the consistency of the alignments when gap cost was varied; CLUSTAL W, Divide and Conquer, and TreeAlign were the most accurate and robust, while PileUp performed poorly as gap cost values increased, and the accuracy of Malign fluctuated. Default settings for the programs did not give the best results, and attempting to select similar parameter values in different programs did not always result in more similar alignments. Poor alignment of even well-conserved motifs can occur if these are near sites with insertions or deletions. Since there is no a priori way to determine gap costs and because such costs can vary over the gene, alignment of rRNA sequences, particularly the less well conserved regions, should be treated carefully and aided by secondary structure and conserved motifs. Some motifs are single bases and so are often invisible to alignment programs. Our tests involved the most conserved regions of the 12S rRNA gene, and alignment of less well conserved regions will be more problematical. None of the alignments we examined produced a fully resolved phylogeny for the data set, indicating that this portion of 12S rRNA is insufficient for resolution of distant evolutionary relationships.

Algorithms↗
PubMed2005

Structural features of the focal adhesion kinase-paxillin complex give insight into the dynamics of focal adhesion assembly.

The C-terminal region of focal adhesion kinase (FAK) consists of a right-turn, elongated, four-helix bundle termed the focal adhesion targeting (FAT) domain. The structure of this domain is maintained by hydrophobic interactions, and this domain is also the proposed binding site for the focal adhesion protein paxillin. Paxillin contains five well-conserved LD motifs, which have been implicated in the binding of many focal adhesion proteins. In this study we determined that LD4 binds specifically to only a single site between the H2 and H3 helices of the FAT domain and that the C-terminal end of LD4 is oriented toward the H2-H3 loop. Comparisons of chemical-shift perturbations in NMR spectra of the FAT domain in complex with the binding region of paxillin and the FAT domain bound to both the LD2 and LD4 motifs allowed us to construct a model of FAK-paxillin binding and suggest a possible mechanism of focal adhesion disassembly.

Amino Acid Motifs↗
PubMed1978

[Structural features of varicose dilatations of vasomotor nerves (according to data from a three dimensional reconstruction)].

Ultrastructure of varicous dilatation of the axons composing small neuronal fasciculi in the sympathetic plexus of the rabbit coronary artery has been studied. According to the data of three dimensional reconstruction, space structure of three neuronal fasciculi has been restorted. Axons of every fasciculus form varicous dilatation at the same area along their course. A lemmocytic process, accompanying the axon as a thin cylinder at the intervaricous part flattens, in the area of varicous dilatations. and embraces all the axons, thus forming a peculiar functional unit of the neuronal fasciculus. From the data obtained and those of literature, it is possible to suggest that not only single axons situating in the nearest approximation to smooth muscle cells, but also single neuronal fasciculi having in their composition axons with varicous dilatation might effectively influence the smooth musculature of the vascular wall.

Animals↗
PubMed1998

Comparative analysis of the noncollagenous NC1 domain of type IV collagen: identification of structural features important for assembly, function, and pathogenesis.

Type IV collagen alpha1-alpha6 chains have important roles in the assembly of basement membranes and are implicated in the pathogenesis of Goodpasture syndrome, an autoimmune disorder, and Alport syndrome, a hereditary renal disease. We report comparative sequence analyses and structural predictions of the noncollagenous C-terminal globular NC1 domain (28 sequences). The inferred tree verified that type IV collagen sequences fall into two groups, alpha1-like and alpha2-like, and suggested that vertebrate alpha3/alpha4 sequences evolved before alpha1/alpha2 and alpha5/alpha6. About one fifth of NC1 residues were identified to confer either the alpha1 or alpha2 group-specificity. These residues accumulate opposite charge in subdomain B of alpha1 (positive) and alpha2 (negative) sequences and may play a role in the stoichiometric chain selection upon type IV collagen assembly. Neural network secondary structure prediction on multiple aligned sequences revealed a subdomain core structure consisting of six hydrophobic beta-strands and one short alpha-helix with a significant hydrophobic moment. The existence of opposite charges in the alpha-helices may carry implications for intersubdomain interactions. The results provide a rationale for defining the epitope that binds Goodpasture autoantibodies and a framework for understanding how certain NC1 mutations may lead to Alport syndrome. A search algorithm, based entirely on amino acid properties, yielded a possible similarity of NC1 to tissue inhibitor of metalloproteinases (TIMP) and prompted an investigation of a possible functional relationship. The results indicate that NC1 preparations decrease the activity of matrix metalloproteinases 2 and 3 (MMP-2, MMP-3) toward a peptide substrate, though not to [14C]-gelatin. We suggest that an ancestral NC1 may have been incorporated into type IV collagen as an evolutionarily mobile domain carrying proteinase inhibitor function.

Algorithms↗
PubMed2006

Identification of separate structural features that affect rate and cation concentration dependence of self-cleavage by the Neurospora VS ribozyme.

The cleavage site of the Neurospora VS ribozyme is located in an internal loop in a hairpin called stem-loop I. Stem-loop I undergoes a cation-dependent structural change to adopt a conformation, termed shifted, that is required for activity. Using site-directed mutagenesis and kinetic analyses, we show here that the insertion of a single-stranded linker between stem-loop I and the rest of the ribozyme increases the observed self-cleavage rate constant by 2 orders of magnitude without affecting the Mg(2+) requirement of the reaction. A distinct set of mutations that favors the formation of the shifted conformation of stem-loop I decreases the Mg(2+) requirement by an order of magnitude with little or no effect on the observed cleavage rate under standard reaction conditions. Similar trends were seen in reactions that contained Li(+) instead of Mg(2+). Mutants with lower ionic requirements also exhibited increased thermostability, providing evidence that the shifted conformation of stem-loop I favors the formation of the active conformation of the RNA. In natural, multimeric VS RNA, where a given ribozyme core is flanked by one copy of stem-loop I immediately upstream and another copy 0.7 kb downstream, cleavage at the downstream site is strongly preferred, providing evidence that separation of stem-loop I from the ribozyme core reflects the naturally evolved organization of the RNA.

Base Sequence↗
PubMedDate not supplied

[The effect of alpha-tocopherol in a wide range of concentrations on the structural features of the lipid bilayer regions of endoplasmic reticulum membranes in the mouse liver cells in vitro].

The aim of the present work was to study by ESR-spin-probe technique the effect of the natural antioxidant alpha-tocopherol (alpha-tp) in vitro on the structural parameters (microviscosity, order parameter) of endoplasmic reticulum membranes of the mice liver cells starting from the concentration of 10(-3) mol/l and down to the dilution of 10(-25) mol/l. The stable nitroxyl radicals 16-doxylstearic acid (with the deep localization depth of 20 A) and 5-doxylstearic acid (with the surface localization depth of 8 A) were used as spin probes. It has been shown that alpha-tp causes the increase in microviscosity of the deep lipid bilayer regions and in rigidity of the surface ones at the certain concentrations. The concentration curves obtained have the polymodal shapes being typical of the effects of substances at ultra low doses. Using 16-doxylstearic acid it is detected the increase in the number of thermoinduced structural transitions and appearance of much more high-cooperative ones, as well as the increase in their effective activation energy with the rise of temperature at the supplement of different alpha-tp doses.

Animals↗
PubMed1985

[Structural features of the brains of rats selected for their thresholds of neuromuscular excitability].

As a result of selection of rats possessing a high threshold of neuro-muscular exitability in comparison with rats possessing a low threshold of neuro-muscular exitability, certain changes take place in the structures that are connected with the learning process: the visual cortex is wider, volumes of the pyramidal cells in the fields CA1 and CA3 of the hippocampus are increased, density of the glial elements in the fornix is essentially increased and that of neurons in the septal nucleus is decreased.

Animals↗
PubMed1985

[Structural features of the intrinsic venous bed of the human urinary bladder].

The intraorganic veins of the human urinary bladder have been studied in a vast sectional material. The veins within the organ make an enormous multilayered plexus which is differently organized in various layers of its wall. Abundant anastomoses, multiplicated ways for outflow from every layer, manifested interactions between the venous plexuses are specific for the intraorganic venous bed of the urinary bladder. The structures for an active regulating the hemomicrocirculatory blood stream are widely presented in the urinary bladder. In its every tunic certain specific morpho-functional features for organization and adaptation of the intraorganic venous bed are revealed.

Adolescent↗