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Ion Binding (ion + binding)
Kinds of Ion Binding Terms modified by Ion Binding Selected AbstractsGas Phase, Solution, and Solid State Alkali Ion Binding by the [NbE8]3- (E: As, Sb) Complexes: Synthesis, Structure, and Spectroscopy.CHEMINFORM, Issue 36 2004Banu Kesanli Abstract For Abstract see ChemInform Abstract in Full Text. [source] Ion-Triggered Multistate Molecular Switching Device Based on Regioselective Coordination-Controlled Ion BindingCHEMISTRY - A EUROPEAN JOURNAL, Issue 23 2005Anne Petitjean Dr. Abstract Molecular devices capable of accessing different controlled conformational states, while optically signaling the occupied state, are attractive tools for nanotechnology since they relate to both areas of molecular mechanical devices and logic gates. We report here a simple molecular system that allows access to four distinct conformational and optical states. It is based on the regioselective complexation of metal ions to a heterocyclic ligand triad, which is dictated by the accessible coordination geometry and electrostatic properties of two distinct binding subunits. Thus, local conformational switching is brought about by tetrahedral coordination (of CuI) or octahedral coordination (of M2+ ions) to bidentate and tridentate binding subunits, respectively. The shape modifications undergone represent an ion-controlled nanomechanical device. They give controlled access to four different states that display different physico-chemical (e.g. optical) properties and provide a basis for logic gate operations. [source] Capillary electrophoretic study of the binding of zinc(II) ion to bacitracin A1 in water-2,2,2-trifluoroethanolELECTROPHORESIS, Issue 10 2003Massimo Castagnola Abstract Binding of Zn2+ to bacitracin A1 was studied by capillary electrophoresis in water/2,2,2-trifluoroethanol (70/30 v/v) at different apparent pH values in order to estimate the association constant of metal, the acidic dissociation constants and the Stokes radii of both free and bounded peptide in apolar environment. The Stokes radii of the free peptide species were compared with those in aqueous solution, as obtained in a recent study performed by our group, indicating that apolar environment stabilizes bacitracin A1 in a conformational structure with the lateral chain of apolar amino acids exposed on the external surface. This conformation of the macrocyclic dodecapeptide is ready to interact with Zn2+ ion, as pointed out by the strong increase of the association constant measured in water/2,2,2-trifluoroethanol with respect to the value obtained in aqueous solution. In addition, whereas Zn2+ ion binding in aqueous solution provides a sensible reduction of peptide Stokes radius, no sensible variations following to ion binding were observed in hydro-organic solution. The present results suggest that the apolar environment, rather than the metal ion binding, could be responsible for the conformational transition that brings bacitracin A1 towards its biologically active structure.* [source] Characterization of Mycobacterium tuberculosis nicotinamidase/pyrazinamidaseFEBS JOURNAL, Issue 4 2008Hua Zhang The nicotinamidase/pyrazinamidase (PncA) of Mycobacterium tuberculosis is involved in the activation of the important front-line antituberculosis drug pyrazinamide by converting it into the active form, pyrazinoic acid. Mutations in the pncA gene cause pyrazinamide resistance in M. tuberculosis. The properties of M. tuberculosis PncA were characterized in this study. The enzyme was found to be a 20.89 kDa monomeric protein. The optimal pH and temperature of enzymatic activity were pH 7.0 and 40 °C, respectively. Inductively coupled plasma-optical emission spectrometry revealed that the enzyme was an Mn2+/Fe2+ -containing protein with a molar ratio of [Mn2+] to [Fe2+] of 1 : 1; furthermore, the external addition of either type of metal ion had no apparent effect on the wild-type enzymatic activity. The activity of the purified enzyme was determined by HPLC, and it was shown that it possessed similar pyrazinamidase and nicotinamidase activity, by contrast with previous reports. Nine PncA mutants were generated by site-directed mutagenesis. Determination of the enzymatic activity and metal ion content suggested that Asp8, Lys96 and Cys138 were key residues for catalysis, and Asp49, His51, His57 and His71 were essential for metal ion binding. Our data show that M. tuberculosis PncA may bind metal ions in a manner different from that observed in the case of Pyrococcus horikoshii PncA. [source] Transcriptional profiling of Francisella tularensis infected peripheral blood mononuclear cells: a predictive tool for tularemiaFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 1 2008Chrysanthi Paranavitana Abstract In this study, we analyzed temporal gene expression patterns in human peripheral blood mononuclear cells (PBMCs) infected with the Francisella tularensis live vaccine strain from 1 to 24 h utilizing a whole human Affymetrix® gene chip. We found that a considerable number of induced genes had similar expression patterns and functions as reported previously for gene expression profiling in patients with ulceroglandular tularemia. Among the six uniquely regulated genes reported for tularemia patients as being part of the alarm signal gene cluster, five, namely caspase 1, PSME2, TAP-1, GBP1, and GCH1, were induced in vitro. We also detected four out of the seven potential biomarkers reported in tularemia patients, namely TNFAIP6 at 4 h and STAT1, TNFSF10, and SECTM1 at 16 and 24 h. These observations underscore the value of using microarray expression profiling as an in vitro tool to identify potential biomarkers for human infection and disease. Our results indicate the potential involvement of several host pathways/processes in Francisella infection, notably those involved in calcium, zinc ion binding, PPAR signaling, and lipid metabolism, which further refines the current knowledge of F. tularensis infection and its effects on the human host. Ultimately, this study provides support for utilizing in vitro microarray gene expression profiling in human PBMCs to identify biomarkers of infection and predict in vivo immune responses to infectious agents. [source] The Interaction of Bromide Ions with Graphitic Materials,ADVANCED MATERIALS, Issue 1 2009Apurva Mehta The detailed interactions between hydrated bromine ions and a number of graphene-like surfaces are elucidated for the first time. A common edge site that exhibits preferential binding of bromide is observed for all materials. The local structure around the hydrated bromide in this interaction region is that of the ion binding to a zigzag, convex site on the graphene sheet edge, consistent with predictions of a recent theoretical model. [source] The C-terminal C1 cassette of the N -methyl- d -aspartate receptor 1 subunit contains a bi-partite nuclear localization sequenceJOURNAL OF NEUROCHEMISTRY, Issue 6 2002K. D. Holmes Abstract The N -methyl- d -aspartate receptor (NMDAR) is a multimeric transmembrane protein composed of at least two subunits. One subunit, NR1, is derived from a single gene and can be subdivided into three regions: the N-terminal extracellular domain, the transmembrane regions, and the C-terminal intracellular domain. The N-terminal domain is responsible for Mg2+ metal ion binding and channel activity, while the transmembrane domains are important for ion channel formation. The intracellular C-terminal domain is involved in regulating receptor activity and subcellular localization. Our recent experiments indicated that the intracellular C-terminal domain, when expressed independently, localizes almost exclusively in the nucleus. An examination of the amino acid sequence reveals the presence of a putative nuclear localization sequence (NLS) in the C1 cassette of the NR1 intracellular C-terminus. Using an expression vector designed to test whether a putative NLS sequence is a valid, functional NLS, we have demonstrated that a bi-partite NLS does in fact exist within the NR1-1 C-terminus. Computer algorithms identified a putative helix,loop,helix motif that spanned the C0C1 cassettes of the C-terminus. These data suggest that the NR1 subunit may represent another member of a family of transmembrane proteins that undergo intramembrane proteolysis, releasing a cytosolic peptide that is actively translocated to the nucleus leading to alterations in gene regulation. [source] Cerebellar Gene Expression Profiling and eQTL Analysis in Inbred Mouse Strains Selected for Ethanol SensitivityALCOHOLISM, Issue 9 2005Erik J. MacLaren Background: Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice exhibit striking differences in a number of alcohol and drug related behaviors. This study examined the expression levels of more than 39,000 transcripts in these strains in the cerebellum, a major target of ethanol's actions in the CNS, to find differentially expressed (DE) candidate genes for these phenotypes. Methods: Genes that were differentially expressed between the strains were identified using oligonucleotide arrays as well as complimentary DNA arrays. Sequence alignment was used to locate DE genes in the mouse genome assembly. In silico expression QTL (eQTL) mapping was used to identify chromosomal regions likely to control the transcription level of DE genes, and the EASE program identified overrepresented functional themes. The genomic region immediately upstream of the cyclase associated protein homolog 1 (Cap1) gene was directly sequenced from PCR products. Results: Nearly 300 genes were identified as differentially expressed between the cerebella of ILS and ISS. These genes and their corresponding eQTLs map to genomic regions linked to several phenotypes that differ between the ILS and ISS strains, including ethanol preference and cocaine-induced locomotor activation on Chromosomes 4 and 7 respectively. Eight genes were cross-platform validated, four of which are more highly expressed in ILS cerebellum. Three SNPs, one of which disrupts a predicted Sp1 binding site, were found in the upstream region of Cap1, a strong candidate for influencing ethanol phenotypes. Conclusions: Many of these DE genes are candidates to influence ethanol and drug regulated phenotypes because they either map to ethanol related QTLs in the genome or are linked to them through eQTL mapping. Genes involved in calcium ion binding and transcriptional regulation are overrepresented and therefore these gene classes may influence ethanol behaviors in mice and humans. [source] Cofactor effects on the protein folding reaction: Acceleration of ,-lactalbumin refolding by metal ionsPROTEIN SCIENCE, Issue 4 2006Natalia A. Bushmarina Abstract About 30% of proteins require cofactors for their proper folding. The effects of cofactors on the folding reaction have been investigated with ,-lactalbumin as a model protein and metal ions as cofactors. Metal ions accelerate the refolding of ,-lactalbumin by lessening the energy barrier between the molten globule state and the transition state, mainly by decreasing the difference of entropy between the two states. These effects are linked to metal ion binding to the protein in the native state. Hence, relationships between the metal affinities for the intermediate states and those for the native state are observed. Some residual specificity for the calcium ion is still observed in the molten globule state, this specificity getting closer in the transition state to that of the native state. The comparison between kinetic and steady-state data in association with the , value method indicates the binding of the metal ions on the unfolded state of ,-lactalbumin. Altogether, these results provide insight into cofactor effects on protein folding. They also suggest new possibilities to investigate the presence of residual native structures in the unfolded state of protein and the effects of such structures on the protein folding reaction and on protein stability. [source] Copper binding to octarepeat peptides of the prion protein monitored by mass spectrometryPROTEIN SCIENCE, Issue 2 2000Randy M. Whittal Abstract Electrospray ionization mass spectrometry (ESI-MS) was used to measure the binding of Cu2+ ions to synthetic peptides corresponding to sections of the sequence of the mature prion protein (PrP). ESI-MS demonstrates that Cu2+ is unique among divalent metal ions in binding to PrP and defines the location of the major Cu2+ binding site as the octarepeat region in the N-terminal domain, containing multiple copies of the repeat ProHisGlyGlyGlyTrpGlyGln. The stoichiometries of the complexes measured directly by ESI-MS are pH dependent: a peptide containing four octarepeats chelates two Cu2+ ions at pH 6 but four at pH 7.4. At the higher pH, the binding of multiple Cu2+ ions occurs with a high degree of cooperativity for peptides C-terminally extended to incorporate a fifth histidine. Dissociation constants for each Cu2+ ion binding to the octarepeat peptides, reported here for the first time, are mostly in the low micromolar range; for the addition of the third and fourth Cu2+ ions to the extended peptides at pH 7.4, KD's are <100 nm. n-terminal acetylation of the peptides caused some reduction in the stoichiometry of binding at both ph's. cu2+ also binds to a peptide corresponding to the extreme N-terminus of PrP that precedes the octarepeats, arguing that this region of the sequence may also make a contribution to the Cu2+ complexation. Although the structure of the four-octarepeat peptide is not affected by pH changes in the absence of Cu2+, as judged by circular dichroism, Cu2+ binding induces a modest change at pH 6 and a major structural perturbation at pH 7.4. It is possible that PrP functions as a Cu2+ transporter by binding Cu2+ ions from the extracellular medium under physiologic conditions and then releasing some or all of this metal upon exposure to acidic pH in endosomes or secondary lysosomes. [source] Electrochemical functions of metallosupramolecular nanomaterialsTHE CHEMICAL RECORD, Issue 4 2007Masayoshi Higuchi Abstract Self-assembly of metal ions and organic ligands results in the formation of extended or discrete metallosupramolecular structures. In case of neutral ditopic ligands such as bisterpyridines, extended metallosupramolecular coordination polyelectrolytes (MEPEs) are formed. Metal ion-induced self-assembly of 1,4-bis(2,2,:6,,2,-terpyridin-4,-yl)benzene with Fe(II) or Co(II) results in MEPEs with interesting electrochemical properties. These MEPEs reversibly change their color when oxidized or reduced. The heterometallic MEPE consisting of Fe(II) and Co(II) combines the properties of the individual MEPEs and therefore shows their different states: red-purple, blue, and transparent. On the other hand, complexation of cyclic phenylazomethines with metal ions results in discrete metallosupramolecular structures. We find that metal ion assembly to the organic module occurs in a stepwise fashion because of a difference in the basicity of the imine conformers, and the metal ion assembly can be controlled electrochemically. This example illustrates how metal ion binding can be controlled by the conformation of the receptor, an important step toward assembling organic ligands and metal ions in predictable ways. © 2007 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 7: 203,209; 2007: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20118 [source] Asymmetries in the nucleosome core particle at 2.5,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2000Joel M. Harp The 2.5,Å X-ray crystal structure of the nucleosome core particle presented here provides significant additions to the understanding of the nucleosome, the fundamental unit of chromatin structure. Extensions are made to the structure of the N-terminal histone tails and details are provided on hydration and ion binding. The structure is composed of twofold symmetric molecules, native chicken histone octamer cores and the DNA palindrome, which were expected to form a perfectly twofold symmetric nucleosome core particle. In fact, the result is asymmetric owing to the binding of the DNA to the protein surface and to the packing of the particles in the crystal lattice. An analysis is made of the asymmetries by comparisons both within the nucleosome core particle and to the structure of the histone octamer core of the nucleosome. [source] Metal Binding Properties of Fluorescent Analogues of Trichogin GA,IV: A Conformational Study by Time-Resolved Spectroscopy and Molecular Mechanics InvestigationsCHEMBIOCHEM, Issue 1 2009Mariano Venanzi Prof. Abstract The metal ion binding properties of two fluorescent analogues of trichogin GA,IV, which is a natural undecapeptide showing significant antimicrobial activity, were studied by circular dichroism, time-resolved optical spectroscopy, and molecular mechanics calculations. Binding of CaII and GdIII to the peptides investigated was shown to promote a structural transition from highly helical conformations to folded structures characterized by formation of a loop that embedded the metal ion. Time-resolved spectroscopy revealed that peptide dynamics is also remarkably affected by ion binding: peptide-backbone motions slowed down to the microsecond time scale. Finally, molecular mechanics calculations emphasized the role of the central Gly5-Gly6 motif, which allowed for the twisting of the peptide segment that gave rise to the formation of the binding cavity. [source] Ion and pH Sensing with Colloidal Nanoparticles: Influence of Surface Charge on Sensing and Colloidal PropertiesCHEMPHYSCHEM, Issue 3 2010Feng Zhang Dr. Abstract Ion sensors based on colloidal nanoparticles (NPs), either as actively ion-sensing NPs or as nanoscale carrier systems for organic ion-sensing fluorescent chelators typically require a charged surface in order to be colloidally stable. We demonstrate that this surface charge significantly impacts the ion binding and affects the read-out. Sensor read-out should be thus not determined by the bulk ion concentration, but by the local ion concentration in the nano-environment of the NP surface. We present a conclusive model corroborated by experimental data that reproduces the strong distance-dependence of the effect. The experimental data are based on the capability of tuning the distance of a pH-sensitive fluorophore to the surface of NPs in the nanometer (nm) range. This in turn allows for modification of the effective acid dissociation constant value (its logarithmic form, pKa) of analyte-sensitive fluorophores by tuning their distance to the underlying colloidal NPs. [source] | ||||||||||||||||