Novel common structural feature among several classes of antimalarial agents.
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Acridines↗
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Results for “structural features”
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Correlation of biological activities with structural features of transfer RNA.
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Base Sequence↗
A bZIP protein from halophilic archaea: structural features and dimer formation of cGvpE from Halobacterium salinarum.
The cGvpE protein of Halobacterium salinarum PHH4 has been identified as transcriptional activator for the promoter of the c-gvpA gene encoding the major gas vesicle structural protein cGvpA. Molecular modelling of the carboxy-terminal region of cGvpE suggests that this protein resembles a basic leucine-zipper protein, and mutations in the putative DNA binding domain DNAB completely abolish the activator function in Haloferax volcanii transformants. Mutations in the key residues of the putative leucine-zipper region AH6 of cGvpE confirmed that the three residues V159, L166 and L173 were essential for the activator function of cGvpE at the c-gvpA promoter, whereas the cysteine residue C180 could be altered to a leucine or an aspartate residue without the loss of this function. Mutations in basic residues of helix AH4 demonstrated the importance of the lysine K104 for the activator function of cGvpE. A cGvpE protein containing a his-tag at the C-terminus was still able to activate the expression of c-gvpA in vivo. The cGvpE his-purified from Hf. volcanii formed a dimer in Blue-native polyacrylamide gels that could be resolved into monomers by SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Dimers of cGvpE were already seen using SDS-PAGE, but not with cGvpE mutant proteins containing the alterations L166E or L173E/C180L in the leucine zipper. These results imply that the hydrophobic surface of helix AH6 is indeed required for the establishment of cGvpE dimers.
Amino Acid Sequence↗
[Structural features of the inguinal lymph nodes of normal white rats and white rats subjected to dynamic loading].
In histological preparations of the inguinal lymph nodes of white rats subjected to repeated physical loading percentage correlation of structural component areas in the nodes was estimated. A. A. Glagolev's morphometric grid in S. B. Stefanov's modification was used. Dynamic loading for 5 months was stated to produce a number of changes in the lymph nodes under investigation depending on duration of the experiment and on the level of the animals' adaptation to the loading. Most pronounced changes were noted in the medullar substance, with predominance of follicles having light centers, while its area increased sharply at the expense of diffusively outgrowing lymphoid tissue that did not occur under normal conditions. Certain changes were detected in stroma of the nodes--their capsule became more powerful, while trabecules, on the contrary, occupied less area than in the control. The areas in the node occupied by vessels grew larger. Normally trained rats demonstrated maximal changes in 3 months, and then the structure of the node did not differ from that in the control. In overtrained animals, by the 5th month, many indices differed greatly from those in the control.
Animals↗
Structural features of archaebacterial and eukaryotic proteasomes.
The 26S proteasome is the central protease of the ubiquitin-dependent pathway of protein degradation. The molecule has a molecular mass of approximately 2000 kD and has a highly conserved structure in eukaryotes. The 26S proteasome is formed by a barrel-shaped 20S core complex and two polar 19S complexes. The 20S complex has C2 symmetry and is formed by four seven-membered rings of which the outer rings (alpha-type subunits) are rotated by 25.7 degrees relative to the inner rings while the inner rings (beta-type subunits) are in register. From a comparison of the activity and regulation of the 26S and 20S particles it can be deduced that the 20S particle contains the protease activity while the 19S complex contains isopeptidase, ATPase and protein unfolding activities. In this article we describe the structures of various proteasome complexes as determined by electron microscopy and discuss structural implications of their subunit sequences.
Animals↗
Structural feature of the major but not cytokine-inducing molecular species of lipoteichoic acid.
Previously, lipoteichoic acid (LTA) of Enterococcus hirae was found to exhibit definite cytokine-inducing activity but synthetic specimens which share the fundamental structural principles proposed for LTA had no corresponding activity. We also showed recently that several minor components totally less than 5% of the LTA fraction from E. hirae ATCC 9790 possessed the activity, whereas the major component (over 90%) did not [Suda, Y., Tochio, H., Kawano, K., Takada, H., Yoshida, T., Kotani, S., and Kusumoto, S. (1995) FEMS Immun. Med. Microbiol. 12, 97-112]. In the present study, the structure of the major component of LTA was studied in an attempt to elucidate the reason for the lack of the activity in the synthetic compounds. The major component of the LTA was first digested by hydrofluoric acid hydrolysis to cleave phosphodiester linkages present. The hydrolysis products were separated and characterized by means of NMR and MS. The linkage positions of the original phosphodiesters were determined from the NMR spectra of an alkali-treated product without hydrofluoric acid degradation. The compound was proved to consist of 1,3-linked poly(glycerophosphate) and a lipid anchor, Glc(alpha1-2)Glc(alpha1-3)acyl(2)Gro, the former being linked to the 6-position of the distal glucose of the latter. The 2-position of the glycerol residues in the glycerophosphate part were substituted by oligoglucose esterified partially with alanine. The gross structure elucidated here thus coincides with the previous conclusion described by Fischer [Fischer, W. (1990) in Glycolipids, Phosphoglycolipids and Sulfoglycolipids (Kates, M., ed.) pp. 123 234, Plenum Press, New York]. Thus, the molecular species with this so-called "LTA structure" is not responsible for the cytokine-inducing activity.
Alkaline Phosphatase↗
Incorporation of the major outer membrane protein of Neisseria gonorrhoeae in saponin-lipid complexes (iscoms): chemical analysis, some structural features, and comparison of their immunogenicity with three other antigen delivery systems.
We incorporated the major outer membrane protein (PI) of Neisseria gonorrhoeae into immunostimulating complexes (iscoms) and examined some analytical, physicochemical, and immunological properties of these structures. The immunogenicity was compared with that of three other PI-containing structures, i.e., liposomes, outer membrane complexes produced by the bacterium, and protein-detergent-adjuvant complexes. AIPO4 and dioctadecyldimethylammonium bromide were used as adjuvants. Our results show that iscoms are much more immunogenic than liposomes and protein-detergent complexes but are also much more toxic. The localization of PI in iscoms was investigated. Therefore, the chymotrypsin susceptibility of PI in iscoms was tested, and the incorporation of fragments of PI was determined. Amphiphilic fragments of PI were incorporated in iscoms, but hydrophilic and hydrophobic fragments were not. Chymotrypsin degradation of PI in iscoms indicated that the protein is exposed to the environment in a similar manner as PI in outer membrane complexes, i.e., with both termini anchored in the iscom.
Adjuvants, Immunologic↗
Structural features of angiotensin-I converting enzyme catalytic sites: conformational studies in solution, homology models and comparison with other zinc metallopeptidases.
Angiotensin-I Converting Enzyme (ACE) is a Zinc Metallopeptidase of which the three-dimensional structure was unknown until recently, when the X-ray structure of testis isoform (C-terminal domain of somatic) was determined. ACE plays an important role in the regulation of blood pressure due to its action in the frame of the Renin-Angiotensin System. Efforts for the specific inhibition of the catalytic function of this enzyme have been made on the basis of the X-ray structures of other enzymes with analogous efficacy in the hydrolytic cleavage of peptide substrate terminal fragments. Angiotensin-I Converting Enzyme bears the sequence and topology characteristics of the well-known gluzincins, a sub-family of zincins metallopeptidases and these similarities are exploited in order to reveal common structural elements among these enzymes. 3D homology models are also built using the X-ray structure of Thermolysin as template and peptide models that represent the amino acid sequence of the ACE's two catalytic, zinc-containing sites are designed and synthesized. Conformational analysis of the zinc-free and zinc-bound peptides through high resolution 1H NMR Spectroscopy provides new insights into the solution structure of ACE catalytic centers. Structural properties of these peptides could provide valuable information towards the design and preparation of new potent ACE inhibitors.
Amino Acid Motifs↗
Chemical composition and structural features of the macromolecular components of plantation Acacia mangium wood.
The wood of Acacia mangium, a prominent fast-growing plantation species used in the pulp-and-paper industry and, so far, poorly investigated for its chemical structure, was submitted to a detailed characterization of its main macromolecular components. Lignin (28% wood weight) isolated by mild acidolysis and characterized by permanganate oxidation, 1H and 13C NMR, and GPC, showed a very low content of syringylpropane-derived units (S:G:H of 48:49:3), a high degree of condensation, a low content of beta-O-4 ( approximately 0.40-0.43 per C6) structures, and a Mw of 2230. Glucuronoxylan (14% wood weight) isolated by alkaline (KOH) or by dimethyl sulfoxide extraction was characterized by methylation analysis, 1H NMR, and GPC. About 10% of the xylopyranose (Xylp) units constituting the linear backbone were substituted at O-2 with 4-O-methylglucuronic acid residues. Almost half of the Xylp units (45%) were O-2 (18%), O-3 (24%) or O-2,3 (3%) acetylated. X-ray diffraction analysis of cellulose (46% wood weight), isolated according to the Kürschner-Hoffer method, showed a degree of crystallinity of 67.6%.
Acacia↗
Active site structural features for chemically modified forms of rhodanese.
In the course of the reaction catalyzed by rhodanese, the enzyme cycles between two catalytic intermediates, the sulfur-free and the sulfur-substituted (persulfide-containing) forms. The crystal structure of sulfur-free rhodanese, which was prepared in solution and then crystallized, is highly similar to that of sulfur-substituted enzyme. The inactivation of sulfur-free rhodanese with a small molar excess of hydrogen peroxide relies essentially on a modification limited to the active site, consisting of the oxidation of the essential sulfhydryl to sulfenyl group (-S-OH). Upon reaction of the sulfur-free enzyme with monoiodoacetate in the crystal, the Cys-247 side chain with the bound carboxymethyl group is forced into a conformation that allows favorable interactions of the carboxylate with the four peptide NH groups that participate in hydrogen bonding interactions with the transferable sulfur atom of the persulfide group in the sulfur-substituted rhodanese. It is concluded that active site-specific chemical modifications of sulfur-free rhodanese do not lead to significant changes of the protein structure, consistent with a high degree of similarity of the structures of the sulfur-free and sulfur-substituted forms of the enzyme both in solution and in the crystal.
Animals↗
Unique structural features of a novel class of small heat shock proteins.
Small heat shock proteins (smHSPs) and alpha-crystallins constitute a family of related molecular chaperones that exhibit striking variability in size, ranging from 16 to 43 kDa. Structural studies on these proteins have been hampered by their tendency to form large, often dynamic and heterogeneous oligomeric complexes. Here we describe the structure and expression of HSP12.6, a member of a novel class of smHSPs from the nematode Caenorhabditis elegans. Like other members of its class, HSP12.6 possesses a conserved alpha-crystallin domain but has the shortest N- and C-terminal regions of any known smHSP. Expression of HSP12.6 is limited to the first larval stage of C. elegans and is not significantly up-regulated by a wide range of stressors. Unlike other smHSPs, HSP12.6 does not form large oligomeric complexes in vivo. HSP12.6 was produced in Escherichia coli as a soluble protein and purified. Cross-linking and sedimentation velocity analyses indicate that the recombinant HSP12.6 is monomeric, making it an ideal candidate for structure determination. Interestingly, HSP12.6 does not function as a molecular chaperone in vitro, since it is unable to prevent the thermally induced aggregation of a test substrate. The structural and functional implications of these findings are discussed.
Amino Acid Sequence↗
Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops.
The most frequently occurring RNA hairpins in 16S and 23S ribosomal RNA contain a tetranucleotide loop that has a GNRA consensus sequence. The solution structures of the GCAA and GAAA hairpins have been determined by nuclear magnetic resonance spectroscopy. Both loops contain an unusual G-A base pair between the first and last residue in the loop, a hydrogen bond between a G base and a phosphate, extensive base stacking, and a hydrogen bond between a sugar 2'-end OH and a base. These interactions explain the high stability of these hairpins and the sequence requirements for the variant and invariant nucleotides in the GNRA tetranucleotide loop family.
Base Sequence↗
Structural features of the extracellular portion of membrane-anchoring peptides on membrane-bound immunoglobulins.
Membrane-bound immunoglobulins, mIgs, are displayed as transmembrane proteins on the surface of B cells, where they serve as antigen receptors. The mIgs are anchored to the membrane through a carboxy-terminal extension of the immunoglobulin heavy chain. Three distinct structural regions of these membrane-anchor peptides, of mouse and human mIgs, have been delineated: (1) a central conserved stretch of 25 hydrophobic, unchanged amino acid residues, which spans the membrane lipid bilayer; (2) a C-terminal hydrophilic region of 3-28 amino acids, which is intracytoplasmic; and (3) an N-terminal extracellular hydrophilic region of 13-67 amino acids, which is isotype-specific. Here we report predicted secondary and tertiary structures of the third structural region of the membrane anchoring peptide along with corroborating experimental evidence. The predictions of secondary and tertiary structure indicate that most of these regions can assume an chi-helical conformation. Circular dichroism spectroscopy of corresponding synthetic peptide confirms this essential feature. The choice of solvent and pH have dramatic effects on peptide helicity; solvent conditions consistent with a membrane-proximal environment promote helicity. Additional studies suggest that the two adjacent extracellular peptides may be stabilized through coiled-coil interactions similar to those described for some other transmembrane proteins.
Amino Acid Sequence↗
The hemidesmosome: new fine structural features revealed by freeze-fracture techniques.
Hemidesmosomes along the dermal-epidermal junction of larval and post-metamorphic newt skin have been examined in freeze-fracture replica images correlated with electron micrographs of sectioned material. Larval hemidesmosomal sites are characterized by large (200-300 A) intramembranous granules arranged into clusters, each of which is aligned with a cytoplasmic hemidesmosomal plaque. In unfixed epidermis the granules remain attached to the A-face, while after glutaraldehyde fixation they are found on both A- and B-faces. Following metamorphosis the clusters are less distinct and localized. Replicas of unfixed B-faces and nearby cytoplasm display elongate, filamentous profiles which traverse the cytoplasmic leaflet and extend onto the B-face. The possibility that these components constitute a filamentous network serving to link tonofilaments, hemidesmosomal plaque, and basal plasmalemma is considered in view of the evidence to date. Hemidesmosomal fine structure as revealed by these studies is compared to features of desmosomes as detailed in the following report.
Animals↗
Structural features and antigenic properties of carbohydrate-containing components of Trypanosoma conorhini.
Aqueous and phenolic extracts of Trypanosoma conorhini were fractionated and high molecular weight, carbohydrate-rich fractions obtained. Their antigenic characteristics, reactivity with lectins and partial chemical structure were determined. The major component, the phenolic extract, was electrophoretically diffuse and consisted of 15% protein, 5% phosphorus, hexosamine, and 67% neutral carbohydrate, which contained mannose, galactose, and xylose in a molar ratio of 1.0:1.8:1.8. Chemical analyses and lectin agglutination experiments showed nonreducing end-groups of beta-D-galactopyranose, beta-xylopyranose, and alpha-D-mannopyranose. Phosphate esters occurred, apparently, at O-6 of hexopyranosyl units. Hexosamine was present as nonacetylated units of 2-amino-2-deoxy-alpha-D-glucopyranosyl units that were extremely resistant to acid hydrolysis. On double immunodiffusion tests, the major component gave a precipitation line with rabbit serum against whole cells of Trypanosoma cruzi, suggesting the presence of common antigenic determinant(s) on the cell surface of each trypanosomatid.
Agglutination Tests↗
Intensely luminescent gold(I)-silver(I) cluster complexes with tunable structural features.
A new series of isostructural, brilliantly luminescent gold-silver complexes having the formula [Au3(mu3-E)Ag(PPh2py)3](BF4)2 where E = O, S, Se and Ph2Ppy = 2-diphenylphosphinopyridine has been synthesized and characterized. The structural core of these complexes is a Au3Ag metallophilically linked tetrahedron with a group-16 atom functioning as a mu3-ligand capping the three gold atoms. In the solid state, pairs of clusters are joined by two unsupported aurophilic interactions. The emission energy changes strikingly in going from O (blue) to S (yellow) and Se (orange). The luminescence from the E = O system is the first to be reported for a gold(I) oxo system. Additionally, the luminescent 4-methylpyridyl analogue with E = S has been prepared and structurally characterized. For E = S, Se, the change in emission energy with mu3-bridging atom provides a sound basis for an LMMCT assignment of the excited state while lifetime measurements support its spin-forbidden nature. Frozen glass measurements indicate the presence of a higher-energy emitting state for these systems, and for the E = O system, either LMMCT or metal-centered cluster-based emission can be proposed.
Journal Article↗
Structural features and hydration of d(C-G-C-G-A-A-T-T-A-G-C-G); a double helix containing two G.A mispairs.
Single crystal X-ray diffraction techniques have been used to characterise the molecular structure of the title compound to 2.5A resolution. The structure consists of ten standard Watson-Crick base pairs and two G.A mismatched base pairs. The purine-purine mismatches have guanine in the usual anti orientation with respect to the sugar and adenine in syn orientation. There are two hydrogen bonds formed between the mismatch bases, N-1 and O-6 of guanine with N-7 and N-6 of adenine respectively. The bulky purine-purine mismatches are accommodated with minor perturbation of the sugar-phosphate backbone. There is a slight improvement in base pair overlap at the mismatch sites. Details of the backbone conformation, base stacking interactions and hydration are presented and compared with those of the parent compound d(C-G-C-G-A-A-T-T-C-G-C-G).
Base Composition↗
Structural features of allergenic molecules.
In this paper the relation between protein allergenicity (the capacity to induce IgE antibody production or the capacity to activate mast cells sensitized with IgE antibodies induced by a cross-reactive allergen) and protein structure is discussed. While cross-reactivity is to a large degree predictable from primary sequence comparisons, the IgE-inducing capacity is mostly determined by factors other than the primary sequence. Two routes to IgE are discussed: (1) the atopic route (used by allergens from pollen and mites) in which a direct switch from mu to epsilon is common and (2) the 'modified Th2' route (used by allergens from pets) in which the class switch to IgE is often preceded by a switch to IgG4. According to this working hypothesis, the choice between these two routes is determined at the level of the germinal center activity.
Allergens↗