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Recognition Mechanism (recognition + mechanism)
Kinds of Recognition Mechanism Selected AbstractsSeparation of enantiomers with charged chiral selectors in CEELECTROPHORESIS, Issue S1 2009Bezhan Chankvetadze Abstract In this short overview the major developments in separation of enantiomers with charged chiral selectors are summarized in CE. The advantages of charged chiral selectors in comparison with their uncharged analogues are emphasized from the viewpoints of higher flexibility, higher and alternative separation selectivity, as well as alternative chiral recognition mechanism. [source] Functional epitope of common , chain for interleukin-4 bindingFEBS JOURNAL, Issue 5 2002Jin-Li Zhang Interleukin 4 (IL-4) can act on target cells through an IL-4 receptor complex consisting of the IL-4 receptor , chain and the common , chain (,c). An IL-4 epitope for ,c binding has previously been identified. In this study, the ,c residues involved in IL-4 binding were defined by alanine-scanning mutational analysis. The epitope comprises ,c residues I100, L102, and Y103 on loop EF1 together with L208 on loop FG2 as the major binding determinants. These predominantly hydrophobic determinants interact with the hydrophobic IL-4 epitope composed of residues I11, N15, and Y124. Double-mutant cycle analysis revealed co-operative interaction between ,c and IL-4 side chains. Several ,c residues involved in IL-4 binding have been previously shown to be mutated in X-linked severe combined immunodeficiency. The importance of these binding residues for ,c function is discussed. These results provide a basis for elucidating the molecular recognition mechanism in the IL-4 receptor system and a paradigm for other ,c -dependent cytokine receptor systems. [source] The lipopolysaccharide-recognition mechanism in cells expressing TLR4 and CD14 but lacking MD-2FEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 1 2007Takahiro Ohnishi Abstract We analysed the lipopolysaccharide (LPS)-recognition mechanism in cells expressing TLR4 and CD14 but lacking MD-2. When TLR4 and CD14 were transiently expressed in HEK293 cells, cell-surface expression of TLR4 was observed, although the expression level was lower than that in cells coexpressing MD-2. We found that membrane CD14,TLR4 complexes were formed in these cells in response to LPS stimulation even in the absence of MD-2 expression, although NF-,B-dependent reporter activity was not induced. A strong activation of NF-,B was observed when these cells were stimulated with LPS followed by soluble MD-2 in this order, even when excess LPS was removed after formation of the CD14,TLR4 complex by washing cells prior to sMD-2 addition. From these results, we propose an additional LPS-recognition mechanism. In cells expressing TLR4 and CD14 but lacking MD-2, LPS is first transferred to membrane CD14 with the aid of LPS binding protein, which leads to the formation of the TLR4,CD14 complex. Then, the binding of soluble MD-2 to this complex triggers the transmembrane signal transduction. Cells expressing TLR4 and CD14 but lacking MD-2, such as airway epithelial cells, may be activated in response to LPS by this mechanism. [source] Visualization of the interaction between archaeal DNA polymerase and uracil-containing DNA by atomic force microscopyGENES TO CELLS, Issue 1 2006Yasuo Asami Deamination of cytosine to uracil is a hydrolytic reaction that is greatly accelerated at high temperatures. The resulting uracil pairs with adenine during DNA replication, thereby inducing G:C to A:T transitions in the progeny. Interestingly, B-family DNA polymerases from hyperthermophilic Archaea recognize the presence of uracil in DNA and stall DNA synthesis. To better understand the recognition mechanism, the binding modes of DNA polymerase B1 of Sulfolobus solfataricus (Pol B1) to uracil-containing DNA were examined by gel mobility shift assays and atomic force microscopy. Although PolB1 per se specifically binds to uracil-containing single-stranded DNA, the binding efficiency was substantially enhanced by the initiation of DNA synthesis. Analysis by the atomic force microscopy showed a number of double-stranded DNA (dsDNA) in the products of DNA synthesis. The generation of ds DNA was significantly inhibited, however, by the presence of template uracil, and intermediates where monomeric forms of Pol B1 appeared to bind to uracil-containing DNA were observed. These results suggest that Pol B1 more efficiently recognizes uracil in DNA during DNA synthesis rather than during random diffusion in solution, and that single molecules of Pol B1 bind to template uracil and stall DNA synthesis. [source] Molecular Recognition of a Peptide by the Nickel(II) Complex of 1,4,7,10-Tetraazacyclododecane-2,9-dioneHELVETICA CHIMICA ACTA, Issue 3 2003Jian Gao The nickel(II) complex of the macrocycle 1,4,7,10-tetraazacyclododecane-2,9-dione (dota) was found to be efficient in the recognition of the dipeptide, glycyl-glycine (Gly-Gly) in aqueous solution. This (dota)NiII complex serves as a targeting molecule to form a stable ternary complex with the dipeptide at pH,8.3 in aqueous solution. The recognition constant (log K=19.20) and the recognition mechanism were investigated based on the potentiometric method. The single-crystal of a six-coordinated (dota)2NiII complex is also reported. [source] New mathematic model for predicting chiral separation using molecular docking: Mechanism of chiral recognition of triadimenol analoguesJOURNAL OF SEPARATION SCIENCE, JSS, Issue 14 2009Guoqing Zhang Abstract The purpose of this paper was to study the enantioseparation mechanism of triadimenol compounds by carboxymethylated (CM)-,-CD mediated CE. All the enantiomers were separated under the same experimental conditions to study the chiral recognition mechanism using a 30 mM sodium dihydrogen phosphate buffer at pH 2.2 adjusted by phosphoric acid. The inclusion courses between CM-,-CD and enantiomers were investigated by the means of molecular docking technique. It was found that there were at least three points (one hydrophobic bond and two hydrogen bonds) involved in the interaction of each enantiomer with the chiral selectors. A new mathematic model has been built up based on the results of molecular mechanics calculations, which could analyze the relationship between the resolution of enantioseparation and the interaction energy in the docking area. Comparing the results of the separation by CE, the established mathematic model demonstrated good capability to predict chiral separation of triadimenol enantiomers using CM-,-CD mediated CE. [source] Thermodynamic origin of the chiral recognition of tryptophan on teicoplanin and teicoplanin aglycone stationary phasesJOURNAL OF SEPARATION SCIENCE, JSS, Issue 5 2005Mohamed Haroun Abstract The D-, L-tryptophan binding and the chiral recognition properties of the teicoplanin and teicoplanin aglycone (TAG) chiral stationary phase (CSPs) were compared at various column temperatures. The solute adsorption isotherms (bi-Langmuir model) were determined for both the two CSPs using the perturbation method. It was demonstrated that the sugar units were involved in the reduction of the apparent enantioselectivity through two phenomena: (i) the inhibition of some enantioselective contacts with low-affinity binding regions of the aglycone and (ii) a decrease in the stereoselective properties of the aglycone high-affinity binding pocket. The phenomenon (ii) was governed by both a decrease in the ratio of the enantiomer adsorption constant and a strong reduction of the site accessibility for D- and L-tryptophan. In addition, a temperature effect study was performed to investigate the chiral recognition mechanism at the aglycone high-affinity pocket. An enthalpy-entropy compensation analysis derived from the Grunwald model as well as the comparison with the literature data demonstrated that the enantioselective binding mode was dependent on an interface dehydration process. The change in the enantioselective process observed between the TAG and teicoplanin CSP was characterized by a difference of ca. 2,3 ordered water molecules released from the species interface. [source] Cysteine-independent polymerization of metallothioneins in solutions and in crystalsPROTEIN SCIENCE, Issue 12 2000Tingjun Hou Abstract Polymerization of metallothioneins is one of the usually encountered puzzles during the research process of metallothioneins' structure and function. Our work focuses on the cysteine independently occurred polymerization from metallothioneins monomers in different milieus, while it leaves out the aggregation caused by the oxidation of cysteine, because the latter circumstance is the result of purification lapsus. After the purification of metallothioneins monomers, a dynamic light-scattering technique is used to detect the polymerized states of rabbit liver metallothionein I and II in different buffers, which is the first systematical detection of polymerized states of metallothioneins in solutions. The effects of different compositions of each buffer are discussed in details. Steric complementarity, hydrophobic, and electrostatic interaction characteristics are studied, following the modeling of monomers and relevant polymers of rat metallothionein II, rabbit liver metallothionein I and II. These theoretical calculations are the first complete computer simulations on different factors affecting metallothioneins' polymerization. A molecular recognition mechanism of metallothioneins' polymerization in solutions is proposed on the bases of experimental results and theoretical calculations. Preliminary X-ray studies of two crystal forms of rabbit liver metallothionein II are compared with the crystal structure of rat metallothionein II, and the polymerized states in crystal packing are discussed with the knowledge of polymerization of metallothioneins in solutions. The hypothesis, which is consistent with theoretical calculations and experimental results, is expected to construct a connection between the biochemical characteristics and physiological functions of metallothioneins, and this research may give some enlightenment to the topics of protein polymerizations. [source] Nucleotide,amino acid interactions in the l -His,IMP·MeOH·H2O complexACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2010Katarzyna, lepokura In the crystal structure of the methanol-solvated monohydrated complex of l -histidine (His) with inosine 5,-monophosphate (IMP), namely l -histidinium inosine-5,-phosphate methanol solvate monohydrate, C6H10N3O2+·C10H12N4O8P,·CH3OH·H2O, most of the interactions between IMP anions (anti/C3,- endo/gauche,gauche conformers) are realized between the riboses and hypoxanthine bases in a trans sugar-edge/sugar-edge geometry, and between the phosphate groups. The base Watson,Crick edge is involved in additional methanol-mediated IMP...MeOH...IMP contacts. Specific and nonspecific nucleotide,amino acid (IMP...His) interactions engage the Hoogsteen edges of the base and phosphate group, respectively. Additional stabilization of His...IMP contacts is provided by ,,, stacking between the imidazolium ring of His and the hypoxanthine base of IMP. The results may indicate the possible recognition mechanism between His and IMP. [source] Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodonsACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2007Yoshiteru Sato In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing. It is believed that AspRS instead produces Asp-tRNAAsn in addition to Asp-tRNAAsp. In order to reveal the recognition mechanism for the two anticodons, GUC for aspartate and GUU for asparagine, the crystal structure of St -AspRS (nondiscriminating type) has been determined at 2.3,Å resolution as the first example of the nondiscriminating type of AspRS from crenarchaea. A structural comparison with structures of discriminating AspRSs indicates that the structures are similar to each other overall and that the catalytic domain is highly conserved as expected. In the N-terminal domain, however, the binding site for the third anticodon nucleotide is modified to accept two pyrimidine bases, C and U, but not purine bases. The C base can bind to form a hydrogen bond to the surrounding main-chain amide group in the discriminating AspRS, while in the nondiscriminating AspRS the corresponding amino-acid residue is replaced by proline, which has no amide H atom for hydrogen-bond formation, thus allowing the U base to be accommodated in this site. In addition, the residues that cover the base plane are missing in the nondiscriminating AspRS. These amino-acid changes make it possible for both C and U to be accepted by the nondiscriminating AspRS. It is speculated that this type of nondiscriminating AspRS has been introduced into Thermus thermophilus through horizontal gene transfer. [source] Importance of hydrogen-bonding sites in the chiral recognition mechanism between racemic D3 terbium(III) complexes and amino acidsCHIRALITY, Issue 5 2009Ahmed Moussa Abstract The perturbation of the racemic equilibrium of luminescent D3 terbium(III) complexes with chelidamic acid (CDA), a hydroxylated derivative of 2,6-pyridine-dicarboxylic acid (DPA), by added chiral biomolecules such as L -amino acids has been studied using circularly polarized luminescence and 13C NMR spectroscopy. It is shown in this work that the chiral-induced equilibrium shift of [Tb(CDA)3]6, by L -amino acids (i.e. L -proline or L -arginine) was largely influenced by the hydrogen-bonding networks formed between the ligand interface of racemic [Tb(CDA)3]6, and these added chiral agents. The capping of potential hydrogen-bonding sites by acetylation in L -proline led to a ,100-fold drop in the induced optical activity of the [Tb(CDA)3]6,:N -acetyl- L -proline system. This result suggested that the hydrogen-bonding networks serve as the basis for further noncovalent discriminatory interactions between racemic [Tb(CDA)3]6, and added L -amino acids. Chirality, 2009. © 2008 Wiley-Liss, Inc. [source] Chiral recognition mechanisms with macrocyclic glycopeptide selectors,CHIRALITY, Issue 1 2009Alain Berthod Abstract Macrocyclic glycopeptide selectors are naturally occurring antibiotics produced by microorganisms. They were found to be excellent chiral selectors for a wide range of enantiomers, including amino acids. Four selectors are commercialized as chiral stationary phases (CSP) for chromatography. They are ristocetin, teicoplanin, vancomycin, and the teicoplanin aglycone (TAG). The key docking interaction for amino acid recognition was established to be a charge,charge interaction between the anionic carboxylate group of the amino acid and a cationic amine group of the macrocyclic peptidic selector basket. The carbohydrate units are responsible for secondary interactions. However, they hinder somewhat the charge,charge docking interaction. The TAG selector is more effective for amino acid enantioseparations than the other CSPs. The "sugar" units are however useful allowing for chiral recognitions of other analytes, e.g., ,-blockers, not possible with the aglycone. Thermodynamic studies established that normal phase and reversed phase enantioseparations were enthalpy-driven. With polar waterless mobile phases used in the polar ionic mode, some separations were enthalpy-driven and others were entropy-driven. The linear solvation energy method was tentatively used to gain knowledge about the chiral recognition mechanism. It appeared to be a viable approach with neutral molecules but it failed with ionizable solutes. With molecular solutes and the teicoplanin CSP, the study showed a significant role of the surface charge-induced dipole interaction and steric effects. The remarkable complementary enantioselectivity effect observed with the four CSPs is discussed. Chirality, 2009. © 2008 Wiley-Liss, Inc. [source] Comparative HPLC enantioseparation of ferrocenylalcohols on two cellulose-based chiral stationary phasesCHIRALITY, Issue 5 2007Angela Patti Abstract The direct HPLC enantiomeric separation of several ferrocenylalcohols on the commercially available Chiralcel OD and Chiralcel OJ columns has been evaluated in normal-phase mode. Almost all the compounds were resolved on one or both chiral stationary phases (CSPs) with separation factor (,) ranging from 1.06 to 2.88 while the resolution (Rs) varied from 0.63 to 12.70 In the separation of the ,-ferrocenylalcohols 1a,e and the phenyl analogues 2a,e, which were all resolved except 1c, a similar trend in the retention behavior for the two series of alcohols was evidenced and the selectivity was roughly complementary on the two investigated CSP. For three ferrocenylacohols, chosen as model compounds, the influence of the mobile phase composition and temperature on the enantioseparation were investigated and additional information on the chiral recognition mechanism were deduced from the chromatographic behavior of their acetylderivatives. Chirality, 2007. © 2007 Wiley-Liss, Inc. [source] Helical- and ahelical-dependent chiral recognition mechanisms in capillary electrophoresis using amylose as the selectorELECTROPHORESIS, Issue 8 2009Weili Wei Abstract The present study discovered that helical structures of amylose were not always responsible for its chiral recognition abilities in CE. Several enantiomers with different structures were selected as models. Based on ultraviolet,visible spectroscopy and 13C NMR measurements, it was found that helical structures were gradually destroyed by temperature elevation and almost entirely transformed to extended ahelical structures above 60°C. Then, CE and 1H NMR chiral recognitions were investigated at different temperatures; chiral selectivity of the enantiomers varied in two different ways. Summarily, helical structures were necessary only for chiral separations of the enantiomers with small (<0.78,nm) and flexible molecular structures. However, for the gauche enantiomers (>0.78,nm) with high steric hindrances over their chiral centers, ahelical structures alone can realize chiral recognitions. By using iodine as a helix including competitor, it was further proved that helical structures functioned through the inclusive complexations only in the chiral separations of small enantiomers and had no effect for the others. The underlying mechanisms of the functions of helical and ahelical structures in molecular level were discussed as well. [source] Development of molecular immunoassay system for probiotics via toll-like receptors based on food immunologyANIMAL SCIENCE JOURNAL, Issue 1 2008Haruki KITAZAWA ABSTRACT Recent interest has focused on the importance of intestinal immunity for the host defense, but to date, not much is known about the underlying mechanisms. The toll-like receptor (TLR) family plays an important role in host defense through recognizing bacterial pathogen-associated molecular patterns. Our recent research on the physiological function of food products has investigated the immunoregulatory effects of probiotic lactic acid bacteria (LAB) via TLR. Studies of swine, which often substitute for a human model, have demonstrated intestinal immunoregulation by the probiotic LAB mediated by TLR in the gut. On the basis of our study, efforts have also been made to develop a molecular immunoassay system for probiotic LAB and find novel immunostimulatory DNA sequences from probiotics and high potential immunobiotic LAB strains via TLR signaling. These findings may provide important clues at the molecular level on TLR signal transduction pathways and recognition mechanisms for the ligands. They also provide impetus to further delineate the activation mechanism of the innate immune response. In addition to identifying immunoregulatory factor immunogenics from LAB, a better understanding of intestinal immune regulation through cytokine networks holds out promise for basic food immunology research and the development of immunobiotic foods to prevent specific diseases. [source] Structure of macrophomate synthaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2004Toyoyuki Ose Macrophomate synthase (MPS) is an enzyme that catalyzes an extraordinarily complex conversion reaction, including two decarboxylations, two carbon,carbon bond formations and a dehydration, to form the benzoate analogue macrophomate from a 2-pyrone derivative and oxalacetate. Of these reactions, the two carbon,carbon bond formations are especially noteworthy because previous experiments have indicated that they proceed via a Diels,Alder reaction, one of the most widely used reactions in organic synthesis. The structural evidence that MPS catalyzes an intermolecular Diels,Alder reaction has been reported recently [Ose et al. (2003), Nature (London), 422, 185,189]. Interestingly, the tertiary structure as well as the quaternary structure of MPS are similar to those of 2-dehydro-3-deoxygalactarate (DDG) aldolase, a carbon,carbon bond-forming enzyme that catalyzes the reversible reaction of aldol condensation/cleavage. Here, the structure of MPS is described in detail and compared with that of DDG aldolase. Both enzymes have a (,/,)8 -barrel fold and are classified as belonging to the enolase superfamily based on their reaction strategy. The basic principles for carbon,carbon bond formation used by both MPS and DDG aldolase are the same with regard to trapping the enolate substrate and inducing subsequent reaction. The major differences in the active sites between these two enzymes are the recognition mechanisms of the second substrates, 2-pyrone and DDG, respectively. [source] Prenylflavonoids as Nonsteroidal Phytoestrogens and Related Structure,Activity RelationshipsCHEMMEDCHEM, Issue 4 2006Zhi-qiang Wang Abstract In the search for estrogen receptor (ER) modulators, a series of prenylflavonoids were found to be widely distributed amongst tonic herbal medicines and to possess estrogen-like activity in MCF-7/BOS cells, as evaluated by an estrogen-screening assay. Cell-cycle analysis revealed that the stimulatory effects of these compounds toward cell proliferation were elicited at the G1,S checkpoint and could significantly increase the S-phase population of MCF-7 cells under hormone-free conditions. ER-responsive gene (PS2, PgR) and protein (PgR) expression was also detected; mRNA and protein-expression levels for PS2 and PgR were up-regulated by the compounds in a dose-dependent manner. These effects could be inhibited by the pure ER antagonist ICI,182,780 ((7,-[9-{4,4,5,5,5-pentafluoropentyl}sulfinyl]nonyl)estra-1,3,5(10)-triene-3,17,-diol). It was therefore concluded that the estrogen-like effects of these prenylflavonoids were mediated primarily through ERs. Furthermore, to explore the structure,activity relationship based on the estrogen receptor and detailed molecular mechanisms among the prenylflavonoids, protein,ligand docking simulations were carried out by using the DS-MODELING software package. The binding affinity of each prenylflavonoid toward ER, was scored, and the receptor,ligand interaction was also analyzed to provide the simulation characteristics of virtual molecular recognition mechanisms. [source] Chiral recognition mechanisms with macrocyclic glycopeptide selectors,CHIRALITY, Issue 1 2009Alain Berthod Abstract Macrocyclic glycopeptide selectors are naturally occurring antibiotics produced by microorganisms. They were found to be excellent chiral selectors for a wide range of enantiomers, including amino acids. Four selectors are commercialized as chiral stationary phases (CSP) for chromatography. They are ristocetin, teicoplanin, vancomycin, and the teicoplanin aglycone (TAG). The key docking interaction for amino acid recognition was established to be a charge,charge interaction between the anionic carboxylate group of the amino acid and a cationic amine group of the macrocyclic peptidic selector basket. The carbohydrate units are responsible for secondary interactions. However, they hinder somewhat the charge,charge docking interaction. The TAG selector is more effective for amino acid enantioseparations than the other CSPs. The "sugar" units are however useful allowing for chiral recognitions of other analytes, e.g., ,-blockers, not possible with the aglycone. Thermodynamic studies established that normal phase and reversed phase enantioseparations were enthalpy-driven. With polar waterless mobile phases used in the polar ionic mode, some separations were enthalpy-driven and others were entropy-driven. The linear solvation energy method was tentatively used to gain knowledge about the chiral recognition mechanism. It appeared to be a viable approach with neutral molecules but it failed with ionizable solutes. With molecular solutes and the teicoplanin CSP, the study showed a significant role of the surface charge-induced dipole interaction and steric effects. The remarkable complementary enantioselectivity effect observed with the four CSPs is discussed. Chirality, 2009. © 2008 Wiley-Liss, Inc. [source] Novel cinchona carbamate selectors with complementary enantioseparation characteristics for N-acylated amino acidsCHIRALITY, Issue S1 2003Karl Heinz Krawinkler Abstract The synthesis and chromatographic evaluation of the enantiomer separation capabilities of covalently immobilized calix[4]arene-cinchona carbamate hybrid type receptors derived from quinine (QN) and its corresponding C9-epimer (eQN) in different solvents are reported. The receptors display complementary enantiomer separation profiles in terms of elution order, chiral substrate specificity, and mobile phase characteristics, indicating the existence of two distinct chiral recognition mechanisms. The QN-derived receptor binds the (S)-enantiomers of N-acylated amino acids more strongly, shows preferential recognition of open-chained amino acids, and superior enantioselectivity in polar media such as methanol/acetic acid. In contrast, the eQN congener preferentially recognizes the corresponding (R)-enantiomers, displays good enantioselectivity (, up to 1.74) for cyclic amino acids, and enhanced stereodiscriminating properties in apolar mobile phases, e.g., chloroform/acetic acid. A comparison of the enantiomer separation profiles with those of the corresponding QN and eQN tert -butyl carbamate congeners indicates no significant level of cooperativity between the calix[4]arene module and the cinchona units in terms of overall chiral recognition, most probably as a consequence of residual conformational flexibility of the calixarene module and the carbamate linkage. Chirality 15:S17,S29, 2003. © 2003 Wiley-Liss, Inc. [source] | |||||||||||||