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Epitopes for human CD4+ cells on diphtheria toxin: structural features of sequence segments forming epitopes recognized by most subjects.

The sequence regions of diphtheria toxin (DTX) recognized by CD4+ T cells of seven healthy humans of different major histocompatibility complex haplotypes were identified. Overlapping synthetic peptides, screening the DTX sequence, were used to test in proliferation assays unselected blood CD4+ cells, or DTX-specific CD4+ lines propagated by stimulation with DTX of blood mononuclear cells. Blood CD4+ cells and DTX-specific CD4+ lines gave consistent results. Although each subject had an individual pattern of peptide recognition, six peptide sequences (residues 271-290, 321-340, 331-350, 351-370, 411-430 and 431-450) were recognized by all subjects. In the native DTX molecule, these sequence regions are flanked by sequence loops exposed on the DTX surface. They overlap uncharged segments of the DTX sequence. These structural properties may be general requirements for immunodominance in CD4+ cell sensitization in humans.

Adult↗

Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron.

The J4/5 loop of the group I intron in the mouse-derived fungal pathogen Pneumocystis carinii is the docking site for the first step of the RNA-catalyzed self-splicing reaction and thus is a model of a potential drug target. This purine-rich asymmetric internal loop, 5'GGAAG/3'UAGU, is also thermodynamically more stable than other internal loops with two GU closing pairs and three nucleotides opposite two nucleotides. The results from optical melting, nuclear magnetic resonance spectroscopy, and functional group substitution experiments suggest that the GU closing pairs form and that sheared GA pairs form in the internal loop. The NMR spectra show evidence of conformational dynamics, and several GA pairings are possible. Thus, this dynamic loop presents several possible structures for potential binding of drugs that target group I self-splicing introns. The results also contribute to understanding the structural and dynamic basis for the function and thermodynamic stability of this loop.

Adenine↗

DNase I site mapping and micrococcal nuclease digestion of pachytene chromatin reveal novel structural features.

A comparison of the DNase I digestion products of the 32P-5'-end-labeled pachytene nucleosome core particles (containing histones H2A, TH2A, X2, H2B, TH2B, H3, and H4) and liver nucleosome core particles (containing somatic histones H2A, H2B, H3, and H4) revealed that the cleavage sites that are 30, 40, and 110 nucleotides away from the 5'-end are significantly more accessible in the pachytene core particles than in the liver core particles. These cleavage sites correspond to the region wherein H2B interacts with the nucleosome core DNA. These results, therefore, suggest that the histone-DNA interaction at these sites in the pachytene core particles is weaker, possibly because of the presence of the histone variant TH2B interacting at similar topological positions in the nucleosome core as that of its somatic counterpart H2B. Such a loosened structure may also be maintained even in the native pachytene chromatin since micrococcal nuclease digestion of pachytene nuclei resulted in a higher ratio of subnucleosomes (SN4 + SN7) to mononucleosomes than that observed in liver chromatin.

Animals↗

Solvent-dependent structural features of the membrane active peptide trichotoxin A40 as reflected in its dielectric dispersion.

The dielectric dispersion of trichotoxin A40 in solvents of diverse lipophilicity (i.e. n-octanol, dioxane and mixtures of these) has been measured between 100 kHz and 50 MHz. In pure octanol also the weight average molecular weight and the concentration dependence of the circular dichroism spectrum were determined. An analysis of the data leads to the conclusion that in octanol an appreciable amount of the solute exists as single monomeric particles which are about 30 A long and 12.5 A in diameter. There is a dipole moment parallel to the long axis. In addition the evidence points at the presence of small aggregates (mainly dimers and trimers) formed by some kind of head-to-tail association. Evidently dioxane added to octanol favors a different structure of the trichotoxin monomer. It is apparently involved in another aggregation process resulting in aggregates of large size but comparatively low dipole moments.

Anti-Bacterial Agents↗

An immunophilin that binds M(r) 90,000 heat shock protein: main structural features of a mammalian p59 protein.

In the rabbit, a p59 protein included in the untransformed, non-DNA binding, "8-9S," steroid receptor complexes binds heat shock protein M(r) approximately 90,000 (hsp90). Sequence data [Lebeau, M. C., Massol, N., Herrick, J., Faber, L. E., Renoir, J. M., Radanyi, C. & Baulieu, E. E. (1992) J. Biol. Chem. 267, 4281-4284] and hydrophobic cluster analysis delineate, from the N terminus, two successive domains closely related to the immunosuppressant FK506 binding immunophilin FKBP (FK506 binding protein), consistent with recent purification of the human p56 immunophilin cognate protein by FK506 affinity chromatography [Yem, A. W., Tomasselli, A. G., Heinrikson, R. L., Zurcher-Neely, H., Ruff, V. A., Johnson, R. A. & Deibel, M. R., Jr. (1992) J. Biol. Chem. 267, 2868-2871]. The first FKBP-like domain demonstrates all structural characteristics known to be necessary for immunosuppressant binding and for peptidylprolyl cis-trans isomerase (rotamase) activity. Hence, p59 is a "hsp binding immunophilin" (HBI). It is thus speculated that hsp binding immunophilin may help the assembly/disassembly mechanisms involved in steroid receptor trafficking and activity and participate in the poorly understood hsp90 function. ATP/GTP binding likely occurs within the second FKBP-like domain, near the FK506 binding site on the FKBP template. A third domain detected by the hydrophobic cluster analysis method is distantly structurally related to the two first FKBP-like domains and is followed by the C-terminal part of the protein, which contains a calmodulin binding consensus sequence. Hsp binding immunophilin may be involved in a number of immunological, endocrinological, and chaperone-mediated pathways.

Amino Acid Sequence↗

New structural features of the polysaccharide from gum ghatti (Anogeissus latifola).

Methylation and 13C NMR analyses were carried out on the high-arabinose, acidic heteropolysaccharide of gum ghatti and the products obtained on three successive, controlled Smith degradations. The side chains contained mainly 2-O- and 3-O-substituted Araf units. Of these the second degradation eliminated remaining alpha-Araf units, and their beta anomers became evident. The proportion of Galp units gradually increased in the form of nonreducing end- and Galp units, although 3,6-di-O- and 3,4,6-tri-O-substituted Galp units diminished. After three degradations groups with consecutive 3-O-substituted beta-Galp units were formed. The proportion of periodate-resistant 3-O- and 2,3-di-O-substituted Manp units was maintained. As a guide to side-chain structures in the polysaccharide, seven of the 10 free reducing oligosaccharide fractions (PC) present in the gum were isolated and examined (NMR, ESIMS, and sometimes methylation analysis). Characterized are alpha-Araf-(1 --> 2)-Ara and three Ara-containing oligosaccharide fractions containing 2-O- and 3-O-substituted units. These gave respectively, ESIMS molecular ions arising from Ara(2), beta-Araf oligosaccharides with four units, beta-Araf oligosaccharides with seven units, and Hex(2)-Ara(4). Alpha-Rhap-(1 --> 4)-GlcA, alpha-Rhap-(1 --> 4)-beta-GlcpA-(1 --> 6)-Gal, and alpha-Rhap-(1 --> 4)-beta-GlcpA-(1 --> 6)-beta-Galp-(1 --> 6)-Gal represented other side chains.

Arabinose↗

Structural features and light-dependent changes in the cytoplasmic interhelical E-F loop region of rhodopsin: a site-directed spin-labeling study.

Thirty consecutive single cysteine substitution mutants in the amino acids Q225-I256 of bovine rhodopsin have been prepared and modified with a sulfhydryl specific nitroxide reagent. This sequence includes the E-F interhelical loop, a transducin interaction site. The accessibilities of the attached nitroxides to collisions with hydrophilic and hydrophobic paramagnetic probes in solution were determined, and the electron paramagnetic resonance spectra analyzed in terms of side chain mobility, both in the dark and after photoactivation. Accessibility cata shows that the rhodopsin polypeptide chain crosses an aqueous/ hydrophobic boundary in the range V227-K231 and again in the range V250-V254. In the hydrophobic segments, both the accessibility and mobility data are consistent with helical structures. In the regions of the sequence located within the aqueous phase, periodic variation in both accessibility and mobility of the spin-labeled side chains indicates that the E-F interhelical loop is largely alpha-helical, being formed by regular extensions of the E and F helices by about 1.5 and 3 turns, respectively. Judging from nitroxide mobilities, the putative extension of helix E in the aqueous phase is more dynamic than that of helix F. Changes in the electron paramagnetic resonance characteristics of the spin-labeled rhodopsin upon photoactivation indicate that chromophore isomerization results in patterns of structural changes that can be interpreted in terms of movements of helices that extend into the aqueous loop regions.

Amino Acid Sequence↗

Structural features underlying the unusual mode of calmodulin phosphorylation by protein kinase CK2: A study with synthetic calmodulin fragments.

To shed light on the paradoxical behaviour of calmodulin, whose phosphorylation is inhibited by the regulatory beta-subunit of protein kinase CK2, a series of peptides encompassing the phosphoacceptor sites of calmodulin have been synthesized and assayed as substrates of CK2 alpha-subunit either alone or combined with the beta-subunit. The shortest peptide whose phosphorylation is reduced instead of being enhanced by the beta-subunit encompasses the sequence 68-106, including the central helix and the Ca2+-binding loop-III. In contrast, the phosphorylation of a peptide encompassing loop II and the central helix (54-92) is stimulated, like that of several shorter peptides, by the beta-subunit. Our data localize to the C-terminal domain of calmodulin the structural elements that are responsible for inverted susceptibility to beta-subunit regulation.

Amino Acid Sequence↗

Cysteine scanning mutagenesis at 40 of 76 positions in villin headpiece maps the F-actin binding site and structural features of the domain.

Villin headpiece, the 76 amino acid, C-terminal domain of villin, is one of the two F-actin binding sites in villin necessary for F-actin bundling activity. Expression and study of recombinant headpiece revealed the domain to be remarkably thermostable (Tm = 74 degrees C) for a non-disulfide-bonded domain. Forty independent point mutations to cysteine of headpiece have been purified and tested for their actin binding activity, cysteine reactivity, and thermal stability. These assays identify two segments of headpiece, near amino acids 38 and 70 of headpiece, in which mutations to cysteine significantly disrupt cosedimentation of headpiece with F-actin. Assay of the thermal stability of these mutants and assay of the reactivity of the introduced cysteine show that these amino acids are mutations at the protein surface that do not perturb the overall structure of the domain. The actin binding mutants are replacements to cysteine of Lys38, Glu39, Lys65, Lys70, Lys71, Leu75, and Phe76 of headpiece. We propose that these discontinuous segments of charged amino acids define the F-actin binding contacts of the headpiece domain. The assay of mutants for effects on the thermal stability of helical structure as well as the assay of reactivity of the introduced sulfhydryl group identify candidate positions that are involved in the stabilizing core and internal structure of the domain. The cysteine scanning mutagenesis also identifies an amino-terminal subdomain (Val1-Leu35) and a predominantly helical carboxy-terminal subdomain (Pro36-Phe76).

Actins↗

Effect of alanine ester substitution and other structural features of lipoteichoic acids on their inhibitory activity against autolysins of Staphylococcus aureus.

Native substitution with the D-alanine ester of lipoteichoic acids (LTAs) affects their immunological properties, the capacity to bind divalent cations, and LTA carrier activity. In this study we tested the influence of the D-alanine ester on anti-autolytic activity, using extracellular autolysin from Staphylococcus aureus and nine LTAs with alanine/phosphorus molar ratios of between 0.23 and 0.71. The inhibitory activity, highest with alanine-free LTA, exponentially decreased with increasing alanine content, approaching zero at substitutions of greater than 0.6. Correspondingly, dipolar ionic phospholipids were not inhibitory, in contrast to negatively charged ones. Glycosylation of LTA up to an extent of 0.5 did not depress inhibitory activity, and even at a degree of 0.8 the effect was comparatively small. On comparison of LTAs from various sources, differences in lipid structures and chain lengths were without effect. The inhibitory activity drastically decreased when the glycolipid carried a single glycerophosphate residue or the hydrophilic chain had the unusual structure [6 leads to Gal(alpha 1--6)Gal(alpha 1--3)Gro-(2 comes from 1 alpha Gal)-P]n, in which digalactosyl moieties connect the alpha-galactosylated glycerophosphate units. Principally, the same results were obtained with the more complex system of autolysis of S. aureus cells. We hypothesize that the anti-autolytic activity of LTA resides in a sequence of glycerophosphate units and that the negative charges of appropriately spaced phosphodiester groups play a crucial role. The alanine ester effect is discussed with respect to the putative in vivo regulation of autolysins by LTA.

Alanine↗

Tachykinins with unusual structural features from a urodele, the amphiuma, an elasmobranch, the hammerhead shark, and an agnathan, the river lamprey.

Tachykinins were purified from extracts of gastrointestinal tissues of the urodele, Amphiuma tridactylum (three-toed amphiuma), and the elasmobranch Sphyrna lewini (hammerhead shark), and from the brain of the agnathan Lampetra fluviatilis (river lamprey). The amphiuma substance P (SP) (DNPSVGQFYGLM-NH2) contains 12 amino residues compared with 11 for mammalian SP and lacks the Arg/Lys-Pro-Xaa-Pro motif that is characteristic of NK1 receptor-selective agonists. Lampetra SP (RKPHPKEFVGLM-NH2) is identical to SP from the sea lamprey and the shark SP-related peptide (AKFDKFYGLM-NH2) is identical to dogfish scyliorhinin I. Amphiuma neurokinin A (NKA) (HKDAFIGLM-NH2) and lamprey NKA (HFDEFVGLM-NH2) contain 9 amino acid residues compared with 10 for mammalian NKA. The shark NKA-related peptide (ASGPTQAGIV10GRKRQKGEMF20VGLM-NH2) shows limited structural similarity to mammalian neuropeptide gamma and the teleost tachykinin, carassin but contains 24 rather than 21 amino acid residues. The data show that the primary structures of the tachykinins have been very poorly conserved during vertebrate evolution and that pressure has acted only to maintain the functionally important sequence -Phe-Xaa-Gly Leu-Met-NH2 at the COOH-termini of the peptides.

Amino Acid Sequence↗

Atypical adenomatous hyperplasia of lung: its incidence and analysis of clinical, glycohistochemical and structural features including newly defined growth regulators and vascularization.

BACKGROUND: Adenomatous hyperplasia of the peripheral lung has been suggested to be a preneoplastic lesion leading to peripherally localized lung carcinomas. The paucity of data about cellular and vascular characteristics of this lesion in comparison to normal lung prompted this investigation. MATERIAL AND METHODS: We describe results of two investigations comprising 75 cases and 70 cases, respectively, with atypical adenomatous hyperplasia (AAH) of the lung, respectively: (a) a prospective study part with thorough analysis of surgical lung specimens (lobes and lungs) for light microscopical detection of the lesion; and (b) a retrospective study part with immuno- and lectin histochemical analysis of AAH and non-neoplastic lung parenchyma monitoring expression of growth-related markers and changes in vascularization patterns. Sections of the individual cases were examined by an image-analyzing system including automated measurement of staining intensities and structure analysis. RESULTS: The prospective study part revealed an incidence of AAH in 2/31 cases with squamous cell carcinoma and in 5/32 cases with adenocarcinomas. No relation to pT- or pN stages was detectable, high grade AAHs were seen to be close to the tumor lesions (<2 cm distance) and those with low grade at greater distances. Statistically significantly increased levels of expression of anti-apoptotic bcl-2, macrophage migration inhibitory factor (MIF) capable to suppress p53 activities, heparin-binding lectin, interleukin-2, galectin-1 and of binding sites for the endogenous lectins galectins-1, -3 and -7 were determined. In addition, alveolar-lining cells, which express these markers, formed spatial clusters, which harbor different levels of structural entropy. AAH displayed an increased level of vascularization characterized by regular size and increased number of newly formed vessels. INTERPRETATION: The prospective and retrospective study parts point to a close association of AAH with peripherally localized adenocarcinoma of the lung. AAH is characterized by pronounced alteration of expression of several growth-related markers and probably non-reversible changes in vascularization.

Adenocarcinoma↗

Analysis of sequence and structural features that identify the B/C motif of U3 small nucleolar RNA as the recognition site for the Snu13p-Rrp9p protein pair.

The eukaryal Snu13p/15.5K protein binds K-turn motifs in U4 snRNA and snoRNAs. Two Snu13p/15.5K molecules bind the nucleolar U3 snoRNA required for the early steps of preribosomal processing. Binding of one molecule on the C'/D motif allows association of proteins Nop1p, Nop56p, and Nop58p, whereas binding of the second molecule on the B/C motif allows Rrp9p recruitment. To understand how the Snu13p-Rrp9p pair recognizes the B/C motif, we first improved the identification of RNA determinants required for Snu13p binding by experiments using the systematic evolution of ligands by exponential enrichment. This demonstrated the importance of a U.U pair stacked on the sheared pairs and revealed a direct link between Snu13p affinity and the stability of helices I and II. Sequence and structure requirements for efficient association of Rrp9p on the B/C motif were studied in yeast cells by expression of variant U3 snoRNAs and immunoselection assays. A G-C pair in stem II, a G residue at position 1 in the bulge, and a short stem I were found to be required. The data identify the in vivo function of most of the conserved residues of the U3 snoRNA B/C motif. They bring important information to understand how different K-turn motifs can recruit different sets of proteins after Snu13p association.

Base Pairing↗

Structural features of ribonucleotide reductase.

Herpes simplex virus type 1 (HSV-1) encodes a ribonucleotide reductase which comprises two polypeptides with sizes of 136,000 (RR1) and 38,000 mol. wt. (RR2). We have determined the entire DNA sequence specifying HSV-1 RR1 and have identified two adjacent open reading frames in varicella-zoster virus (VZV) which have homology to HSV RR1 and RR2; the predicted sizes for the VZV RR1 and RR2 polypeptides are 87,000 and 35,000 mol. wt. respectively. Amino acid comparisons with RR1 and RR2 polypeptides from other organisms indicate that HSV-1 RR1 contains a unique N-terminal domain which is absent from other RR1 polypeptides apart from HSV-2 RR1. These N-terminal amino acid sequences are poorly conserved between HSV-1 and HSV-2 in contrast to the remainder of the protein which shows greater than 90% homology. Polypeptide structural predictions suggest that the HSV-1 N-terminal domain may be separated into two regions, namely, a beta-sheet structure followed by a nonstructured area. Across the remainder of RR1 and RR2, comparisons also reveal blocks of amino acids conserved between the different ribonucleotide reductases, and these may be important for enzyme activity. From predictions on the structure of these conserved blocks, we have proposed that the location of a substrate binding site within RR1 is centered on three conserved glycine residues in a region which is predicted to adopt a beta-sheet/turn/alpha-helical structure; this approximates to the structure for ADP nucleotide binding folds. Finally, we propose that the promoters for the HSV and Epstein-Barr virus (EBV) RR2 transcripts have evolved by separate evolutionary routes.

Amino Acid Sequence↗

Some structural features of an insoluble alpha-D-glucan from a mutant strain of Leuconostoc mesenteroides NRRL B-1355.

Leuconostoc mesenteroides strain NRRL B-1355 produces two soluble extracellular alpha-D-glucans from sucrose: alternan and dextran. An unusual mutant strain derived from NRRL B-1355 has recently been isolated which produces practically no soluble polysaccharide, but significant amounts of an insoluble D-glucan. Methylation analysis shows it contains linear (1-->3) and (1-->6) linkages as well as (1-->2) and (1-->3) branch linkages. The insoluble glucan was partially digestible by endodextranase, giving rise to a series of oligosaccharides, a high-molecular weight soluble fraction and an insoluble residue. Treatment of the soluble dextranase-limit fraction with an alpha(1-->2) debranching enzyme led to further dextranase susceptibility. Methylation, FTIR and NMR analyses of the dextranase-treated fractions indicate a non-uniform structure with domains bearing similarities to L. mesenteroides strain NRRL B-1299 dextran and to insoluble streptococcal D-glucans.

Carbohydrates↗

Structural features involved in the mitogenic activity of Bordetella pertussis lipopolysaccharides for spleen cells of C3H/HeJ mice.

Spleen cells from the C3H/HeJ mouse strain cannot be stimulated by many smooth-type lipopolysaccharides (LPSs), and by the main biologically-active region (lipid A) of these molecules. The genetic origin of this defect (expression of the mutant allele Lpsd at the chromosome 4 locus) was established over 20 years ago, but its biochemical nature has remained undefined. Several investigators have noted, however, that some particular LPSs can bypass this defect, and stimulate the proliferation of C3H/HeJ B lymphocytes. In this study we compare the mitogenic activities of the LPSs isolated from a wild strain (1414) and from a mutant 'rough' strain (A100) of Bordetella pertussis. Both LPS-1414 and LPS-A100 were mitogenic for C3H/HeJ spleen cells, but their lipid A fragments were not. This indicates that a carbohydrate structure proximal to lipid A is involved in the mitogenic activity. However, the isolated polysaccharides were not mitogenic. Four sugars are common to both LPS-1414 and LPS-A100: an heptose, and three sugars bearing free amino groups. After removal of these four sugars from the LPSs by nitrous acid treatment, the recovered lipooligosaccharides were not mitogenic in Lpsd spleen cells. The results suggest that substructures present in lipid A and in this group of four sugars are both required for induction of a mitogenic effect in Lpsd splenocytes, whereas lipid A alone can stimulate Lpsn spleen cells.

Animals↗

New structural features of unsupported chains of metal ions in luminescent [(NH3)4Pt][Au(CN)2]2 x 1.5(H2O) and related salts.

Luminescent [(NH(3))(4)Pt][Au(CN)(2)](2).1.5(H(2)O), which forms from aqueous solutions of [(NH(3))(4)Pt]Cl(2) and K[Au(CN)(2)], crystallizes with extended chains of the two ions with multiple close Pt...Au (3.2804(4) and 3.2794(4) A) and Au...Au (3.2902(5), 3.3312(5), and 3.1902(4) A) contacts. Nonluminescent [(NH(3))(4)Pt][Ag(CN)(2)](2).1.4(H(2)O) is isostructural with [(NH(3))(4)Pt][Au(CN)(2)](2).1.5(H(2)O). Treatment of [(NH(3))(6)Ni]Cl(2) with K[Au(CN)(2)] forms [(NH(3))(2)Ni][Au(CN)(2)](2) in which the [Au(CN)(2)](-) ions function as nitrile ligands toward nickel, which assumes a six-coordinate structure with trans NH(3) ligands. The [Au(CN)(2)](-) ions self-associate into linear columns with close Au...Au contacts of 3.0830(5) A, and pairs of gold ions in these chains make additional but longer (3.4246(5) A) contacts with other gold ions.

Journal Article↗

RNA adducts with chlorophyll and chlorophyllin: stability and structural features.

Porphyrins and their metal derivatives are strong nucleic acids binders. Some of these compounds have been used for radiation sensitization therapy of cancer and are targeted to interact with cellular DNA. Chlorophyll (Chl) binds DNA via guanine N-7 atom (major groove) and the backbone phosphate group (Neault and Tajmir-Riahi. Biophys. J. 76, 2177, 1999), whereas chlorophyllin (Chln) intercalates into A-T and G-C regions (Neault and Tajmir-Riahi. J. Phys. Chem. B. 102, 1610, 1998). This study was designed to examine the interaction of RNA with chlorophyll a and chlorophyllin in aqueous solution at physiological pH with pigment/RNA(phosphate) ratios (r) of 1/80 to 1/2. Fourier transform infrared (FTIR) and UV-visible difference spectroscopic methods were used to characterize the nature of pigment-RNA interaction and to establish correlation between spectral changes and the pigment binding mode, binding constant, RNA secondary structure and structural variations of pigment-RNA complexes in aqueous solution. Spectroscopic results showed that Chl and Chln bind RNA through G-C and A-U bases and the backbone phosphate group with overall binding constants of KChl = 1.95 x 10(5) M(-1) and KChln = 1.61 x 10(5) M(-1). The larger K value obtained for Chl-RNA complexes is attributed to the formation of more stable five or six-coordinate Mg cation in the RNA adducts, while the four-coordination Cu(II) in Chln can be more stable than that of the five or six-coordinated copper ion in the Chln-RNA complexes. Aggregation of pigment-RNA complexes occurs at high metalloporphyrin concentrations. No biopolymer secondary structural changes were observed upon pigment interaction and RNA remains in the A-family structure in these pigment complexes.

Antimutagenic Agents↗