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Common Motif (common + motif)
Selected AbstractsSelf-Assembled Robust Dipeptide Nanotubes and Fabrication of Dipeptide-Capped Gold Nanoparticles on the Surface of these Nanotubes,ADVANCED FUNCTIONAL MATERIALS, Issue 12 2009Samit Guha Abstract Three water-soluble dipeptides containing N-terminally located , -alanine residue and C-terminally located , -amino acid residues (, -Ala- L -Xaa, Xaa,=,Val/Ile/Phe) form robust crystalline nanotubes. These dipeptide nanotubes contain a common motif, a hybrid of ,,, -amino acids, which are stable against heat up to 80,°C, a wide range of pH (2,10), and proteolytic degradation. These robust crystalline dipeptide nanotubes are used as a template for fabricating dipeptide-capped gold nanoparticles on their outer surfaces. This is an easy way to develop nanotube/nanoparticle hybrid materials under mild conditions. [source] The active site of hydroxynitrile lyase from Prunus amygdalus: Modeling studies provide new insights into the mechanism of cyanogenesisPROTEIN SCIENCE, Issue 2 2002Ingrid Dreveny Abstract The FAD-dependent hydroxynitrile lyase from almond (Prunus amygdalus, PaHNL) catalyzes the cleavage of R -mandelonitrile into benzaldehyde and hydrocyanic acid. Catalysis of the reverse reaction,the enantiospecific formation of ,-hydroxynitriles,is now widely utilized in organic syntheses as one of the few industrially relevant examples of enzyme-mediated C,C bond formation. Starting from the recently determined X-ray crystal structure, systematic docking calculations with the natural substrate were used to locate the active site of the enzyme and to identify amino acid residues involved in substrate binding and catalysis. Analysis of the modeled substrate complexes supports an enzymatic mechanism that includes the flavin cofactor as a mere "spectator" of the reaction and relies on general acid/base catalysis by the conserved His-497. Stabilization of the negative charge of the cyanide ion is accomplished by a pronounced positive electrostatic potential at the binding site. PaHNL activity requires the FAD cofactor to be bound in its oxidized form, and calculations of the pKa of enzyme-bound HCN showed that the observed inactivation upon cofactor reduction is largely caused by the reversal of the electrostatic potential within the active site. The suggested mechanism closely resembles the one proposed for the FAD-independent, and structurally unrelated HNL from Hevea brasiliensis. Although the actual amino acid residues involved in the catalytic cycle are completely different in the two enzymes, a common motif for the mechanism of cyanogenesis (general acid/base catalysis plus electrostatic stabilization of the cyanide ion) becomes evident. [source] ,-Catenin dysregulation in cancer: interactions with E-cadherin and beyond,THE JOURNAL OF PATHOLOGY, Issue 2 2010Qun Lu Abstract Stable E-cadherin-based adherens junctions are pivotal in maintaining epithelial tissue integrity and are the major barrier for epithelial cancer metastasis. Proteins of the p120ctn subfamily have emerged recently as critical players for supporting this stability. The identification of the unique juxtamembrane domain (JMD) in E-cadherin that binds directly to ,-catenin/NPRAP/neurojungin (CTNND2) and p120ctn (CTNND1) provides a common motif for their interactions. Recently, crystallographic resolution of the JMD of p120ctn further highlighted possibilities of intervening between interactions of p120ctn subfamily proteins and E-cadherin for designing anti-cancer therapeutics. For most epithelial cancers, studies have demonstrated a reduction of p120ctn expression or alteration of its subcellular distribution. On the other hand, ,-catenin, a primarily neural-enriched protein in the brain of healthy individuals, is up-regulated in all cancer types that have been studied to date. Two research articles in the September 2010 issue of The Journal of Pathology increase our understanding of the involvement of these proteins in lung cancer. One reports the identification of rare p120ctn (CTNND1) gene amplification in lung cancer. One mechanism by which ,-catenin and p120ctn may play a role in carcinogenesis is their competitive binding to E-cadherin through the JMD. The other presents the first vigorous characterization of ,-catenin overexpression in lung cancer. Unexpectedly, the authors observed that ,-catenin promotes malignant phenotypes of non-small cell lung cancer by non-competitive binding to E-cadherin with p120ctn in the cytoplasm. Looking towards the future, the understanding of ,-catenin and p120ctn with and beyond their localization at the cell,cell junction should provide further insight into their roles in cancer pathogenesis. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Invited Commentary for Castillo et al. Gene amplification of the transcription factor DP1 and CTNND1 in human lung cancer, Journal of Pathology, 2010; 222: 89,98. And for Zhang et al. ,-Catenin promotes malignant phenotype of non-small cell lung cancer by non-competative binding to E-cadherin with p120ctn in cytoplasm. Journal of Pathology, 2010; 222: 76,88. [source] DOMINO1, a member of a small plant-specific gene family, encodes a protein essential for nuclear and nucleolar functionsTHE PLANT JOURNAL, Issue 6 2004Sylvie Lahmy Summary Arabidopsis embryos carrying the domino1 mutation grow slowly in comparison with wild type embryos and as a consequence reach only the globular stage at desiccation. The primary defect of the mutation at the cellular level is the large size of the nucleolus that can be observed soon after fertilization in the nuclei of both the embryo and the endosperm. The ultrastructure of mutant nucleoli is drastically different from wild type and points to a fault in ribosome biogenesis. DOMINO1 encodes a protein, which belongs to a plant-specific gene family sharing a common motif of unknown function, present in the tomato DEFECTIVE CHLOROPLASTS AND LEAVES (LeDCL) protein. Using a GFP protein fusion, we show that DOMINO1 is targeted to the nucleus. We propose that inactivation of DOMINO1 has a negative effect on ribosome biogenesis and on the rate of cell division. [source] Experimental and theoretical charge-density study of a tetranuclear cobalt carbonyl complexACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2009Jacob Overgaard Details of the complex bonding environment present in the molecular centre of an alkyne-bridged dicobalt complex have been examined using a combination of experimental and theoretical charge-density modelling for two compounds which share a central Co2C2 tetrahedral moiety as their common motif. Topological analysis of the experimental electron density illustrates the problem of separating the Co,C bond-critical points (b.c.p.s) from the intervening ring-critical point (r.c.p.), due largely to the flat nature of the electron density in the CoC2 triangles. Such a separation of critical points is immediately obtained from a topological analysis of the theoretical electron density as well as from the multipole-projected theoretical density; however, the addition of random noise to the theoretical structure factors prior to multipole modelling leads to a failure in consistently distinguishing two b.c.p.s and one r.c.p. in such close proximity within the particular environment of this Co2C2 centre. [source] Crystal packing in vicinal diols CnHm(OH)2ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2002Carolyn Pratt Brock The O,H,O bonds in vic -diols CnHm(OH)2 have been studied using data retrieved from the Cambridge Structural Database. About half of these diols form complete, or almost complete, sets of intermolecular O,H,O bonds (i.e. two satisfied donors per molecule). For this half of the structures the frequencies of high-symmetry space groups and of structures with Z,,>,1 (more than one molecule in the asymmetric unit) are substantially elevated. The most common motif among fully bonded structures is an dimer, which can be linked in a variety of ways to form one-, two- or even three-dimensional patterns. Most of the other half of the vic -diols form simple O,H,O chains in which each OH group participates in only one intermolecular hydrogen bond. The space-group frequencies for this second group of structures are unexceptional. The most important factor determining the extent of O,H,O bond formation is the degree of substitution of the vic -diol. The spatial segregation of OH groups that is necessary for the formation of O,H,O bonds is found to make the dense filling of space more difficult because the intermolecular spacings that are appropriate for the O,H,O bonds may be inappropriate for the rest of the molecule. [source] An Unexpected Michael,Aldol,Smiles Rearrangement Sequence for the Synthesis of Versatile Optically Active Bicyclic Structures by Using Asymmetric OrganocatalysisCHEMISTRY - A EUROPEAN JOURNAL, Issue 14 2010Nicole Holub Dr. Abstract A facile and simple organocatalytic procedure to generate optically active 6-alkyl- and 6-aryl-substituted bicyclo[2.2.2]oct-5-en-2-ones is presented. The reaction is catalysed by a 9-amino-9-deoxyepiquinine trifluoroacetic acid salt, which activates ,,,-unsaturated cyclic ketones for the 1,4-addition of ,-keto benzothiazoyl sulfones in a stereoselective fashion. Subsequent intramolecular aldol reaction and Smiles rearrangement gives rise to important optically active bicycles, which are a common motif in natural products, ligands in asymmetric catalysis and substrates for Cope rearrangements, photochemical reactions, radical cyclisations and metathesis. Different bicyclic structures were obtained by utilisation of various cyclic enones or by performing ring-expanding reactions. Furthermore, two possible mechanistic pathways are outlined and discussed. [source] Hydrogen-Bond Networks in Water Clusters (H2O)20: An Exhaustive Quantum-Chemical AnalysisCHEMPHYSCHEM, Issue 2 2010Andrei M. Tokmachev Dr. Abstract Water aggregates allow for numerous configurations due to different distributions of hydrogen bonds. The total number of possible hydrogen-bond networks is very large even for medium-sized systems. We demonstrate that targeted ultra-fast methods of quantum chemistry make an exhaustive analysis of all configurations possible. The cage of (H2O)20 in the form of the pentagonal dodecahedron is a common motif in water structures. We calculated the spatial and electronic structure of all hydrogen-bond configurations for three systems: idealized cage (H2O)20 and defect cages with one or two hydrogen bonds broken. More than 3 million configurations studied provide unique data on the structure and properties of water clusters. We performed a thorough analysis of the results with the emphasis on the cooperativity in water systems and the structure-property relations. [source] Substrate interactions of the electroneutral Na+ -coupled inorganic phosphate cotransporter (NaPi-IIc)THE JOURNAL OF PHYSIOLOGY, Issue 17 2009Chiara Ghezzi The SLC34 solute carrier family comprises the electrogenic NaPi-IIa/b and the electroneutral NaPi-IIc, which display Na+ : Pi cotransport stoichiometries of 3 : 1 and 2 : 1, respectively. We previously proposed that NaPi-IIc lacks one of the three Na+ interaction sites hypothesised for the electrogenic isoforms, but, unlike NaPi-IIa/b, its substrate binding order is undetermined. By expressing NaPi-IIc in Xenopus oocytes, isotope influx and efflux assays gave results consistent with Na+ being the first and last substrate to bind. To further investigate substrate interactions, we applied a fluorometry-based technique that uses site-specific labelling with a fluorophore to characterize substrate-induced conformational changes. A novel Cys was introduced in the third extracellular loop of NaPi-IIc that could be labelled with a reporter fluorophore (MTS-TAMRA). Although labelling resulted in suppression of cotransport as previously reported for the electrogenic isoforms, changes in fluorescence were induced by changes in extracellular Na+ concentration in the absence of Pi and by changes in extracellular Pi concentration in presence of Na+. These data, combined with 32P uptake data, also support a binding scheme in which Na+ is the first substrate to interact. Moreover, the apparent Pi affinity from fluorometry agreed with that from 32P uptake, confirming the applicability of the fluorometric technique for kinetic studies of electroneutral carriers. Analysis of the fluorescence data showed that like the electrogenic NaPi-IIb, 2 Na+ ions interact cooperatively with NaPi-IIc before Pi binding, which implies that only one of these is translocated. This result provides compelling evidence that SLC34 proteins share common motifs for substrate interaction and that cotransport and substrate binding stoichiometries are not necessarily equivalent. [source] | |||||||||||||