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PubMed1996

Structural features of U6 snRNA and dynamic interactions with other spliceosomal components leading to pre-mRNA splicing.

In the spliceosome, the pre-mRNA, U2 and U6 snRNAs fold into a catalytic structure exhibiting striking similarities with domain V and VI of group II introns. Building of this tripartite structure implies that an evolutionary conserved base pairing between U4 and U6 snRNAs should be disrupted to allow potentially U6 catalytic residue to interact with U2 snRNAs and the pre-mRNA. The steps leading to U4/U6 disruption have been recently discovered and have been shown to involve a modification of the 3' end of U6 snRNA and the hnRNP C protein.

Base Composition↗
PubMed2004

GABA receptor antagonists and insecticides: common structural features of 4-alkyl-1-phenylpyrazoles and 4-alkyl-1-phenyltrioxabicyclooctanes.

Fipronil [5-amino-3-cyano-1-(2,6-dichloro-4-trifluoromethylphenyl)-4-trifluoromethylsulfinylpyrazole] is one of the most important insecticides. Structure-activity studies described here reveal that fipronil retains its very high binding potency at the human beta3 and house fly gamma-aminobutyric acid (GABA) receptors and toxicity to house flies on replacing the pyrazole trifluoromethylsulfinyl moiety with tert-butyl or isopropyl and the phenyl trifluoromethyl substituent with ethynyl, trifluoromethoxy, bromo or chloro. Among the compounds studied, those with other alkyl groups at the 4-position of the pyrazole, as well as phenyl substitution without one or both of the 2,6-dichloro groups, are less effective. 5-Amino-4-tert-butyl-3-cyano-1-(2,6-dichloro-4-ethynylphenyl)pyrazole is highly effective and almost isosteric with 4-tert-butyl-3-cyano-1-(4-ethynylphenyl)-2,6,7-trioxabicyclo[2.2.2]octane (the most potent 4-alkyl-1-phenyltrioxabicyclooctane) as a noncompetitive GABA antagonist and insecticide. These findings are interpreted as three binding subsites in the GABA receptor: a hydrophobic site undergoing steric interaction with the tert-butyl or equivalent group; a hydrogen bonding site to pyrazole N-2; a pi bonding site to the face of the phenyl moiety; with supplemental enhancement by the 3-cyano and 4-ethynyl substituents.

Alkylation↗
PubMed1992

Specificity determinants and structural features in the RNA target of the bacterial antiterminator proteins of the BglG/SacY family.

Induction of the Bacillus subtilis sacB gene and sacPA operon and Escherichia coli bgl operon is mediated by structurally homologous antiterminators encoded by the sacY, sacT, and bglG genes, respectively. When activated, these proteins prevent early transcription termination at terminators located in the leader regions of the three operons. BglG was previously shown to bind in vitro to an imperfectly palindromic 29-nucleotide RNA sequence located upstream of the terminator and partially overlapping with it [Houman, F., Diaz-Torres, M.R. & Wright, A. (1990) Cell 62, 1153-1163]. Similar motifs, here termed ribonucleic antiterminators (RATs), strongly conserved in sequence and in position, are found in the leader of both sacB and sacPA. Mutations were created in sacB RAT and tested in B. subtilis; this showed that sacB RAT is the target for SacY-mediated induction of sacB and that a stem-loop structure in the mRNA is required for regulatory function. Mutations increasing the similarity of the sacB RAT with those of sacPA or bgl rendered sacB inducible by SacT or BglG, respectively; most of these changes did not strongly affect induction by SacY, suggesting that the nucleotides at these variable positions act as negative specificity determinants.

Bacillus subtilis↗
PubMed1975

Some structural features of rabbit muscle aldolase as derived from its limited proteolysis.

The peptides released during the limited tryptic proteolysis of rabbit muscle aldolase (Biszku et al., 1973) were located in the primary structure. The pattern of peptide liberation, peptide bond splitting and activity decrease in compatible with two structural models for the truncated tetrameric product, named aldolase-T. According to the more probable model aldolase-T has the structure A+A+B++B++. Subunits B++ are deprived of the segments comprising residues 1-27, 42-71 and 306-364 of the intact enzyme and are inactive. The fragment comprising residues 28-41 is non-covalently attached to these subunits. Subunits A+ are depleted only of peptides 1-27 and 324-332 and retain 70% activity. In these subunits the fragment comprising residue 333-364 remains non-covalently bound. The molecular weights of the truncated subunits, determined with polyacrylamide-gel electrophoresis in the presence of sodium dodecylsulfate support the above conclusions. Aldolase-T can be reversibly denatured at pH 2 or in 4 M urea. The recovery of enzymatic activity after decreasing urea or acid concentration indicates the non-covalent rebinding of fragment 333-364. This fragment is named the "T-peptide" of trypsin-treated aldolase. It is suggested that segments 1-27 and 324-364 are not necessary for the renaturation process. Since aldolase-T is a tetramer it seems that large parts of the N- and C-terminal regions of the enzyme are not involved in the intersubunit interactions. The C-terminal region of aldolase, starting around residue 324, appears to be necessary to the structure of the active site. In contrast to this, the N-terminal region up to residue 27 and probably to residue 60, is not part of the active center.

Amino Acid Sequence↗
PubMed1995

Structural features mediating fibrin selectivity of vampire bat plasminogen activators.

The distinguishing characteristic of vampire bat (Desmodus rotundus) salivary plasminogen activators (DSPAs) is their strict requirement for fibrin as a cofactor. DSPAs consist of structural modules known from urokinase (u-PA) and tissue-type plasminogen activator (t-PA) such as finger (F), epidermal growth factor (E), kringle (K), and protease (P), combining to four genetically and biochemically distinct isoenzymes, exhibiting the formulas FEKP (DSPA alpha 1 and alpha 2) and EKP and KP (DSPA beta and DSPA gamma). Only DSPA alpha 1 and alpha 2 bind to fibrin. All DSPAs are single-chain molecules, displaying substantial amidolytic activity. In a plasminogen activation assay, all four DSPAs are almost inactive in the absence of fibrin but strongly stimulated by fibrin addition. The catalytic efficiency (kcat/Km) of DSPA alpha 1 increases 10(5)-fold, whereas the corresponding value of t-PA is only 550. The ratio of the bimolecular rate constants of plasminogen activation in the presence of fibrin versus fibrinogen (fibrin selectivity) of DSPA alpha 1, alpha 2, beta, gamma, and t-PA was found to be 13,000, 6500, 250, 90, and 72, respectively. Whereas all DSPAs are therefore more fibrin dependent and fibrin selective than t-PA, the extent depends on the respective presence of the various domains. The introduction of a plasmin-sensitive cleavage site in a position akin to the one in t-PA partially obliterates fibrin cofactor requirement. Fibrin dependence and fibrin selectivity of DSPAs are accordingly mediated by fibrin binding, which involves the F domain, as yet undefined determinants within the K and P domains, and by the absence of a plasmin-sensitive activation site. These findings transcend the current understanding of fibrin-mediated stimulation of plasminogen activation: in addition to fibrin binding, specific protein-protein interactions come into play, which stabilize the enzyme in its active conformation.

Aminocaproic Acid↗
PubMed2004

Characterization of novel structural features in the lipopolysaccharide of nondisease associated nontypeable Haemophilus influenzae.

Nontypeable Haemophilus influenzae (NTHi) is a common commensal of the human upper respiratory tract and is associated with otitis media in children. The structures of the oligosaccharide portions of NTHi lipopolysaccharide (LPS) from several otitis media isolates are now well characterized but it is not known whether there are structural differences in LPS from colonizing, nondisease associated strains. Structural analysis of LPS from nondisease associated NTHi strains 11 and 16 has been achieved by the application of high-field NMR techniques, ESI-MS, ESI-MSn, capillary electrophoresis coupled to ESI-MS, composition and linkage analyses on O-deacylated LPS and core oligosaccharide material. This is the first study to report structural details on LPS from strains taken from the nasopharynx from healthy individuals. Both strains express identical structures and contain the common element of H. influenzae LPS, L-alpha-D-Hepp-(1-->2)-[PEtn-->6]-L-alpha-D-Hepp-(1-->3)-[beta-D-Glcp-(1-->4)]-L-alpha-D-Hepp-(1-->5)-[PPEtn-->4]-alpha-Kdop-(2-->6)-lipid A, in which each heptose is elongated by a single hexose residue with no further oligosaccharide extensions. In the major Hex3 glycoform, the terminal Hepp residue (HepIII) is substituted at the O-2 position by a beta-D-Galp residue and the central Hepp residue (HepII) is substituted at O-3 by a alpha-D-Glcp residue. Notably, the strains express two phosphocholine (PCho) substituents, one at the O-6 position of alpha-D-Glcp and the other at the O-6 position of beta-D-Galp. Major acetylation sites were identified at O-4 of Gal and O-3 of HepIII. Additionally, both strains express glycine, and strain 11 also expresses detectable amounts of N-acetylneuraminic acid.

Carbohydrate Conformation↗
PubMed2000

Potential drugs and nondrugs: prediction and identification of important structural features

Using decision trees, a model to discriminate between potential drugs and nondrugs has been developed. Compounds from the Available Chemical Directory and the World Drug Index databases were used as training set; the molecular structures were represented using extended atom types. The error rate on an independent validation data set is 17.4%. The number of false negatives can be reduced by penalizing the misclassification of drugs so that 92 out of 100 potential drugs are correctly recognized. At the same time, 34 out of 100 nondrugs are classified as potential drugs. The predictions of the model can be used to guide the purchase or selection of compounds for biological screening or the design of combinatorial libraries. The visualization of the generated models in the form of colored trees allowed us to identify a few, surprisingly simple features that explain the most significant differences between drugs and nondrugs in the training set: Just by testing the presence of hydroxyl, tertiary or secondary amino, carboxyl, phenol, or enol groups, already three quarters of all drugs could be correctly recognized. The nondrugs, on the other hand, are characterized by their aromatic nature with a low content of functional groups besides halogens. The general applicability of the model is shown by the predictions made for several Organon databases.

Journal Article↗
PubMed1998

Similarity of structural features and evolution of satellite DNAs from palorus subdepressus (Coleoptera) and related species

A novel highly abundant satellite DNA comprising 20% of the genome has been characterized in Palorus subdepressus (Insecta, Coleoptera). The 72-bp-long monomer sequence is composed of two copies of T2A5T octanucleotide alternating with 22-nucleotide-long elements of an inverted repeat. Phylogenetic analysis revealed clustering of monomer sequence variants into two clades. Two types of variants are prevalently organized in an alternating pattern, thus showing a tendency to generate a new complex repeating unit 144 bp in length. Fluorescent in situ hybridization revealed even distribution of the satellite in the region of pericentric heterochromatin of all 20 chromosomes. P. subdepressus satellite sequence is clearly species specific, lacking similarity even with the satellite from congeneric species P. ratzeburgii. However, on the basis of similarity in predicted tertiary structure induced by intrinsic DNA curvature and in repeat length, P. subdepressus satellite can be classified into the same group with satellites from related tenebrionid species P. ratzeburgii, Tenebrio molitor, and T. obscurus. It can be reasonably inferred that repetitive sequences of different origin evolve under constraints to adopt and conserve particular features. Obtained results suggest that the higher-order structure and repeat length, but not the nucleotide sequence itself, are maintained through evolution of these species.

Journal Article↗
PubMed1987

Structural features of the terminal loop region of frog retinal rod outer segment disk membranes: I. Organization of lipid components.

We have applied thin sectioning and freeze-fracture techniques to investigate the terminal loop structure of photoreceptive disks in frog retinal rod outer segments. Our studies of this region demonstrate a highly curved terminal loop bilayer that is continuous with both lamellar bilayers of the disk, and equivalent to them in dimensions and staining properties. Rhodopsin, however, appears to be excluded from this region of high curvature.

Animals↗
PubMed1997

Structural features of aminoquinolines necessary for antagonist activity against botulinum neurotoxin.

Certain aminoquinoline antimalarial compounds, such as chloroquine, antagonize the paralytic actions of botulinum neurotoxins (BoNT). These studies have been extended to determine the critical structural groups necessary for synthetic aminoquinolines to have antagonist activity against BoNT. Isolated mouse hemidiaphragms were maintained at 36 degrees C and indirectly stimulated; the resulting isometric twitch tensions were recorded as a measure of synaptic function. The muscles were exposed to the test compounds before being treated with a challenge concentration of BoNT (typically 0.2 nM of serotype A). The time to onset of 50% muscle paralysis due to BoNT was used to assess quantitatively the efficacy of the test compounds, which were then ranked on the basis of the concentrations necessary to delay paralysis by a specified time increment. Of the compounds tested, those having a 7-chloro-4-aminoquinoline configuration, similar to chloroquine (or the structurally similar 6-chloro-9-amino acridine group in quinacrine), were most effective. Truncation of the alkyl-amino-alkyl group from chloroquine and conversion of the 4-amino nitrogen to a primary amine did not significantly alter its effectiveness as a BoNT antagonist. However, the 6-chloro- or 8-chloro- isomers of chloroquine were essentially ineffective. These results suggest that aminoquinolines antagonize the paralytic actions of BoNT through interaction with a selective, stereospecific site that is not well correlated with antimalarial activity.

Aminoquinolines↗
PubMed2005

Crystal structure of phosphorylcholine esterase domain of the virulence factor choline-binding protein e from streptococcus pneumoniae: new structural features among the metallo-beta-lactamase superfamily.

Streptococcus pneumoniae is the worldwide leading cause of deaths from invasive infections such as pneumoniae, sepsis, and meningitidis in children and the elderly. Nasopharyngeal colonization, which plays a key role in the development of pneumococcal disease, is highly dependent on a family of surface-exposed proteins, the choline-binding proteins (CBPs). Here we report the crystal structure of phosphorylcholine esterase (Pce), the catalytic domain of choline-binding protein E (CBPE), which has been shown to be crucial for host/pathogen interaction processes. The unexpected features of the Pce active site reveal that this enzyme is unique among the large family of hydrolases harboring the metallo-beta-lactamase fold. The orientation and calcium stabilization features of an elongated loop, which lies on top of the active site, suggest that the cleft may be rearranged. Furthermore, the structure of Pce complexed with phosphorylcholine, together with the characterization of the enzymatic role played by two iron ions located in the active site allow us to propose a reaction mechanism reminiscent of that of purple acid phosphatase. This mechanism is supported by site-directed mutagenesis experiments. Finally, the interactions of the choline binding domain and the Pce region of CBPE with chains of teichoic acids have been modeled. The ensemble of our biochemical and structural results provide an initial understanding of the function of CBPE.

Amino Acid Sequence↗
PubMed1999

Structural features of the gamma subunit of the Escherichia coli F(1) ATPase revealed by a 4.4-A resolution map obtained by x-ray crystallography.

The F(1) part of the F(1)F(O) ATP synthase from Escherichia coli has been crystallized and its structure determined to 4.4-A resolution by using molecular replacement based on the structure of the beef-heart mitochondrial enzyme. The bacterial F(1) consists of five subunits with stoichiometry alpha(3), beta(3), gamma, delta, and epsilon. delta was removed before crystallization. In agreement with the structure of the beef-heart mitochondrial enzyme, although not that from rat liver, the present study suggests that the alpha and beta subunits are arranged in a hexagonal barrel but depart from exact 3-fold symmetry. In the structures of both beef heart and rat-liver mitochondrial F(1), less than half of the structure of the gamma subunit was seen because of presumed disorder in the crystals. The present electron-density map includes a number of rod-shaped features which appear to correspond to additional alpha-helical regions within the gamma subunit. These suggest that the gamma subunit traverses the full length of the stalk that links the F(1) and F(O) parts and makes significant contacts with the c subunit ring of F(O).

Amino Acid Sequence↗
PubMed1986

Structural features of absorptive cell and microvillus membrane preparations from rat small intestine.

Absorptive cells of the small intestine are highly polarized cells with distinct microvillus membrane (MVM) and basolateral plasma membrane domains. We compared membrane structure in the following preparations of rat small intestine commonly used for in vitro study of MVM function: epithelial sheets, isolated epithelial cells, and four different MVM vesicle preparations, using electron microscopy of thin sections and freeze fracture replicas. We also quantitated mean vesicle diameter of the four MVM preparations by quasielastic light scattering and determined their actin content. Epithelial sheets maintained their plasma membrane polarity as judged by intramembrane particle (IMP) distribution for at least 30 min after isolation. In contrast, the plasma membrane of isolated cells showed redistribution of IMPs, indicating considerable loss of polarity in the few minutes required for cell recovery. The P-face IMPs in MVM prepared by Ca++ precipitation were randomly distributed but became aggregated after exposure to potassium thiocyanate, which removed approximately 50% of core actin. The P-face IMPs in Mg++ precipitated MVM were aggregated whether or not core actin was depleted with potassium thiocyanate. The shape and size of MVM vesicles differed considerably with different preparative techniques. The extremely rapid loss of plasma membrane polarity of isolated intestinal epithelial cells and the striking structural heterogeneity of MVM vesicles prepared by commonly used techniques should be considered in the interpretation of functional studies with these preparations.

Animals↗
PubMed2000

Structural features of normal and mutant human lysosomal glycoside hydrolases deduced from bioinformatics analysis.

Lysosomal storage diseases are due to inherited deficiencies in various enzymes involved in basic metabolic processes. As with other genetic diseases, accurate structure data for these enzymatic proteins should help in better understanding the molecular effects of mutations identified in patients with the corresponding lysosomal diseases; however, no such three-dimensional (3D) structure data are available for many lysosomal enzymes. Thus, we herein intend to illustrate for an audience of molecular geneticists how structure information can nonetheless be obtained via a bioinformatics approach in the case of five human lysosomal glycoside hydrolases. Indeed, using the two-dimensional hydrophobic cluster analysis method to decipher the sequence information available in data banks for the large group of glycoside hydrolases (clan GH-A) to which these human lysosomal enzymes belong, we could deduce structure predictions for their catalytic domains and propose explanations for the molecular effects of mutations described in patients. In addition, in the case of human beta-glucuronidase for which experimental 3D data have been reported, we also show here that bioinformatics methods relying on the available 3D structure information can be used to obtain further insights into the effects of various mutations described in patients with Sly disease. In a broader perspective, our work stresses that, in the context of a rapid increase in protein sequence information through genome sequencing, bioinformatics approaches might be highly useful for generating structure-function predictions based on sequence-structure interrelationships.

Crystallography, X-Ray↗
PubMed1977

Leukemic reticuloendotheliosis: "hairy cell leukemia," functional and structural features of the abnormal cell in a patient with profound leukocytosis.

The development of profound leukocytosis in a patient with leukemic reticuloendotheliosis (LRE) enabled us to obtain purified LRE cells for the investigation of their structural and functional characteristics. The LRE cells of our patient bore surface immunoglobulin and had complement receptors but did not bear Fc receptors and did not form rosettes with sheep erythrocytes. By electron microscopy, the cells were observed to contain typical ribosome lamella structures and to phagocytize both 0.81 micron latex particles and complement-coated zymosan particles. They were adherent to both glass and nylon wool fibers. The mitogenic response to erythroagglutinating phytohemagglutinin was normal to magnitude but delayed chronologically. The binding of 125I-labeled plant lectins was used to characterize the surface topography of LRE cells. Results of these studies indicated that the LRE cell surface differed significantly from the surface of normal T and B lymphocytes and chronic lymphatic leukemia cells. The LRE cells were capable of both stimulating and responding in a one-way mixed lymphocyte culture. However, the LRE cells were not active as effector cells of either cell-mediated lympholysis, a T cell function, or antibody-dependent cellular cytotoxicity, a null cell function. In contrast, they were effector cells of lectin-induced cellular cytotoxicity showing that they did possess the capacity to function as cytotoxic effector cells. These data indicated that the LRE cells in our patient had surface and functional characteristics of both lymphocytes and monocytes.

Binding Sites↗