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Recognition Events (recognition + event)
Kinds of Recognition Events Selected AbstractsNMR Investigation of the Bound Conformation of Natural and Synthetic Oligomannosides to Banana LectinEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2007Caroline Clavel Abstract The conformational behaviour of three mannose-containing oligosaccharides, namely, the ,1,3[,1,6] trisaccharide, a heptasaccharide with ,1,2, ,1,3 and ,1,6 linkages and a tetrasaccharide consisting of ,1,3 and ,1,2 linkages, when bound to banana lectin (BanLec) has been evaluated by trNOE NMR methods and docking calculations. It was found that the molecular recognition event involves a conformational selection process with only one of the conformations present in the free state of the sugar being recognised at the lectin binding site. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] The molecular mechanism of human group IIA phospholipase A2 inactivation by bolinaquinoneJOURNAL OF MOLECULAR RECOGNITION, Issue 6 2009Maria Chiara Monti Abstract The molecular basis of the human group IIA secretory phospholipase A2 inactivation by bolinaquinone (BLQ), a hydroxyquinone marine terpenoid, has been investigated for the comprehension of its relevant antiinflammatory properties, through the combination of spectroscopic techniques, biosensors analysis, mass spectrometry (MS) and molecular docking. Indeed, sPLA2s are well known to be implicated in the pathogenesis of inflammation such as rheumatoid arthritis, septic shock, psoriasis and asthma. Our results suggest a mechanism of competitive inhibition guided by a non-covalent molecular recognition event, disclosing the key role of the BLQ hydroxyl-quinone moiety in the chelation of the catalytic Ca2+ ion inside the enzyme active site. The understanding of the sPLA2 -IIA inactivation mechanism by BLQ could be useful for the development of a new chemical class of PLA2 inhibitors, able to specifically target the enzyme active site. Copyright © 2009 John Wiley & Sons, Ltd. [source] A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactionsJOURNAL OF MOLECULAR RECOGNITION, Issue 3 2007Matthew A. Cooper Abstract The widespread exploitation of biosensors in the analysis of molecular recognition has its origins in the mid-1990s following the release of commercial systems based on surface plasmon resonance (SPR). More recently, platforms based on piezoelectric acoustic sensors (principally ,bulk acoustic wave' (BAW), ,thickness shear mode' (TSM) sensors or ,quartz crystal microbalances' (QCM)), have been released that are driving the publication of a large number of papers analysing binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights salient theoretical and practical aspects of the technologies that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and lipidic and polymeric interfaces. Key differentiators between optical and acoustic sensing modalities are also reviewed. Copyright © 2007 John Wiley & Sons, Ltd. [source] Damage Detection and Base Flipping in Direct DNA Alkylation RepairCHEMBIOCHEM, Issue 3 2009Cai-Guang Yang Prof. Abstract The foreign lesion: The mechanistic questions for DNA base damage detection by repair proteins are discussed in this Minireview. Repair proteins could either probe and locate a weakened base pair that results from base damage, or passively capture an extrahelical base lesion in the first step of damage searching on double-stranded DNA. How some repair proteins, such as AGT (see figure), locate base lesions in DNA is still not fully understood. To remove a few damaged bases efficiently from the context of the entire genome, the DNA base repair proteins rely on remarkably specific detection mechanisms to locate base lesions. This efficient molecular recognition event inside cells has been extensively studied with various structural and biochemical tools. These studies suggest that DNA base damage can be located by repair proteins by using two mechanisms: a repair protein can probe and detect a weakened base pair that results from mutagenic or cytotoxic base damage; alternatively, a protein can passively capture and stabilize an extrahelical base lesion. Our chemical and structural studies on the direct DNA repair proteins hAGT, C-Ada and ABH2 suggest that these proteins search for weakened base pairs in their first step of damage searching. We have also discovered a very unique base-flipping mechanism used by the DNA repair protein AlkB. This protein distorts DNA and favors single stranded DNA (ssDNA) substrates over double-stranded (dsDNA) ones. Potentially, it locates base lesions in dsDNA by imposing a constraint that targets less rigid regions of the duplex DNA. The exact mechanism of how AlkB and related proteins search for damage in ssDNA and dsDNA still awaits further studies. [source] Extrahelical Damaged Base Recognition by DNA Glycosylase EnzymesCHEMISTRY - A EUROPEAN JOURNAL, Issue 3 2008James Abstract The efficient enzymatic detection of damaged bases concealed in the DNA double helix is an essential step during DNA repair in all cells. Emergent structural and mechanistic approaches have provided glimpses into this enigmatic molecular recognition event in several systems. A ubiquitous feature of these essential reactions is the binding of the damaged base in an extrahelical binding mode. The reaction pathway by which this remarkable extrahelical state is achieved is of great interest and even more debate. [source] The capsid protein of human immunodeficiency virus: intersubunit interactions during virus assemblyFEBS JOURNAL, Issue 21 2009Mauricio G. Mateu The capsid protein (CA) of HIV-1 is composed of two domains, the N-terminal domain (NTD) and the C-terminal domain (CTD). During the assembly of the immature HIV-1 particle, both CA domains constitute a part of the Gag polyprotein, which forms a spherical capsid comprising up to 5000 radially arranged, extended subunits. Gag,Gag interactions in the immature capsid are mediated in large part by interactions between CA domains, which are involved in the formation of a lattice of connected Gag hexamers. After Gag proteolysis during virus maturation, the CA protein is released, and approximately 1000,1500 free CA subunits self-assemble into a truncated cone-shaped capsid. In the mature capsid, NTD,NTD and NTD,CTD interfaces are involved in the formation of CA hexamers, and CTD,CTD interfaces connect neighboring hexamers through homodimerization. The CA,CA interfaces involved in the assembly of the immature capsid and those forming the mature capsid are different, at least in part. CA appears to have evolved an extraordinary conformational plasticity, which allows the creation of multiple CA,CA interfaces and the occurrence of CA conformational switches. This minireview focuses on recent structure,function studies of the diverse CA,CA interactions and interfaces involved in HIV-1 assembly. Those studies are leading to a better understanding of molecular recognition events during virus morphogenesis, and are also relevant for the development of anti-HIV drugs that are able to interfere with capsid assembly or disassembly. [source] The helix nucleation site and propensity of the synthetic mitochondrial presequence of ornithine carbamoyltransferaseFEBS JOURNAL, Issue 18 2000Harmen H. J. De Jongh This study describes the helix nucleation site and helix propagation of the amphiphilic helical structure of the mitochondrial presequence of rat ornithine carbamoyltransferase. We investigated this property of the 32-residue synthetic presequence using CD and 2D-HR NMR techniques by determining the structure as a function of the concentration of trifluoroethanol. It was found that the hydrophobic cluster Ile7-Leu8-Leu9 forms the helix nucleation site, expanding to include residues Asn4 to Lys16 when the concentration of trifluoroethanol is increased from 10 to 30%. At higher trifluoroethanol concentrations an increased ,stiffening' of the polypeptide backbone (to Arg26) is observed. In addition, by recording CD spectra at different trifluoroethanol concentrations as a function of temperature, it was found that the equilibrium constant between helix and random coil formation for this peptide exhibits a strong temperature dependence with maximum values between 20 and 30 °C. Comparison of these equilibrium constants with those of homopolymers stressed the unique character of the mitochondrial presequence. The findings are discussed in relation to the molecular recognition events at different stages of the transport process of this protein into mitochondria. [source] A Graphene Nanoprobe for Rapid, Sensitive, and Multicolor Fluorescent DNA AnalysisADVANCED FUNCTIONAL MATERIALS, Issue 3 2010Shijiang He Abstract Coupling nanomaterials with biomolecular recognition events represents a new direction in nanotechnology toward the development of novel molecular diagnostic tools. Here a graphene oxide (GO)-based multicolor fluorescent DNA nanoprobe that allows rapid, sensitive, and selective detection of DNA targets in homogeneous solution by exploiting interactions between GO and DNA molecules is reported. Because of the extraordinarily high quenching efficiency of GO, the fluorescent ssDNA probe exhibits minimal background fluorescence, while strong emission is observed when it forms a double helix with the specific targets, leading to a high signal-to-background ratio. Importantly, the large planar surface of GO allows simultaneous quenching of multiple DNA probes labeled with different dyes, leading to a multicolor sensor for the detection of multiple DNA targets in the same solution. It is also demonstrated that this GO-based sensing platform is suitable for the detection of a range of analytes when complemented with the use of functional DNA structures. [source] Dry-reagent disposable biosensor for visual genotyping of single nucleotide polymorphisms by oligonucleotide ligation reaction: application to pharmacogenetic analysis,HUMAN MUTATION, Issue 8 2008Dimitra K. Toubanaki Abstract Most genotyping methods for known single-nucleotide polymorphisms (SNPs) are based on hybridization with allele-specific probes, oligonucleotide ligation reaction (OLR), primer extension or invasive cleavage. OLR offers superior specificity because it involves two recognition events; namely, the hybridization of an allele-specific probe and a common probe to adjacent positions on target DNA. OLR products can be detected by microtiter well-based colorimetric, time-resolved fluorimetric or chemiluminometric assays, electrophoresis, microarrays, microspheres, and homogeneous fluorimetric or colorimetric assays. We have developed a simple, robust, and low-cost disposable biosensor in dry-reagent format, which allows visual genotyping with no need for instrumentation. The OLR mixture contains a biotinylated common probe and an allele-specific probe with a (dA)20 segment at the 3,-end. OLR products are denatured and applied to the biosensor next to gold nanoparticles that are decorated with oligo(dT) strands. The sensor is immersed in the appropriate buffer and all components migrate by capillary action. The OLR product is captured by immobilized streptavidin at the test zone (TZ) of the sensor and hybridizes with the oligo(dT) strands of the nanoparticles. A characteristic red line is generated due to the accumulation of nanoparticles. The excess nanoparticles are captured by immobilized oligo(dA) at the control zone of the strip, giving a second red line. We have applied successfully the proposed OLR-dipstick assay to the genotyping of four SNPs in the drug-metabolizing enzyme genes CYP2D6 (*3 and *4) and CYP2C19 (*2 and *3). The results were in agreement with direct sequencing. Hum Mutat 0,1,8, 2008. © 2008 Wiley-Liss, Inc. [source] Microarray-based survey of a subset of putative olfactory genes in the mosquito Anopheles gambiaeINSECT MOLECULAR BIOLOGY, Issue 6 2005H. Biessmann Abstract Female Anopheles gambiae mosquitoes respond to odours emitted from humans in order to find a blood meal, while males are nectar feeders. This complex behaviour is controlled at several levels, but is probably initiated by the interaction of various molecules in the antennal sensilla. Important molecules in the early odour recognition events include odourant binding proteins (OBPs), which may be involved in odour molecule transport, odourant receptors (ORs) that are expressed in the chemosensory neurones and odour degrading enzymes (ODEs). To obtain a better understanding of the expression patterns of genes that may be involved in host odour reception in females, we generated a custom microarray to study their steady state mRNA levels in chemosensory tissues, antennae and palps. These results were supported by quantitative RT PCR. Our study detected several OBPs that are expressed at significantly higher levels in antennae and palps of females vs. males, while others showed the opposite expression pattern. Most OBPs are slightly down-regulated 24 h after blood feeding, but some, especially those with higher expression levels in males, are up-regulated in blood-fed females, suggesting a shift in blood-fed females from human host seeking to nectar feeding. [source] Integrins, cations and ligands: making the connectionJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 7 2003J-P. Xiong Summary., Integrins are cell adhesion receptors that couple extracellular divalent cation-dependent recognition events with intracellular mechanical and biochemical responses and vice versa, thus affecting every function of nucleated cells. The structural basis of this bidirectional signaling and its dependency on cations has been the focus of intensive study over the past three decades. Significant progress made recently in elucidating the three-dimensional structure of the extracellular and cytoplasmic segments of integrins is giving valuable new insights into the tertiary and quaternary changes that underlie activation, ligand recognition and signaling by these receptors. [source] Macromolecular helicity inversion of poly(phenylacetylene) derivatives induced by various external stimuliMACROMOLECULAR SYMPOSIA, Issue 1 2003Katsuhiro Maeda Abstract Unique macromolecular helicity inversion of stereoregular, optically active poly(phenylacetylene) derivatives induced by external achiral and chiral stimuli is briefly reviewed. Stereoregular, cis-transoidal poly(phenylacetylene)s bearing an optically active substituent, such as (1R,2S)-norephedrine (poly- 1) and , -cyclodextrin residues (poly- 2), show an induced circular dichroism (ICD) in the UV-visible region of the polymer backbone in solution due to a predominantly one-handed helical conformation of the polymers. However, poly- 1 undergoes a helix-helix transition upon complexation with chiral acids having an R configuration, and the complexes exhibit a dramatic change in the ICD of poly- 1. Poly- 2 also shows the inversion of macromolecular helicity responding to molecular and chiral recognition events that occurred at the remote cyclodextrin residues from the polymer backbone; the helicity inversion is accompanied by a visible color change. A similar helix-helix transition of poly((R)- or (S)-(4-((1-(1-naphthyl)ethyl)carbamoyl)phenyl)acetylene) is also briefly described. [source] NMR spectroscopic characterization of the membrane affinity of polyolsMAGNETIC RESONANCE IN CHEMISTRY, Issue 11 2005Daniela Fischer Abstract Residual dipolar couplings (RDCs) are applied here for the analysis of weak, transient binding events between phosphatidylcholine bilayers and polyols. Large signal responses are observed even for low percentages of ,ligand-receptor complexes,' making RDCs a sensitive tool for the analysis of molecular recognition events. The different degree of alignment in solution can be compared as a result of the calculation of the alignment tensor elements. By varying polarity and/or charge of the molecules under investigation, nonspecific hydrophobic effects can be excluded. Copyright © 2005 John Wiley & Sons, Ltd. [source] MAMPs and MIMPs: proposed classifications for inducers of innate immunityMOLECULAR MICROBIOLOGY, Issue 6 2006David Mackey Summary Plants encode a sophisticated innate immune system. Resistance against potential pathogens often relies on active responses. Prerequisite to the induction of defences is recognition of the pathogenic threat. Significant advances have been made in our understanding of the non-self molecules that are recognized by plants and the means by which plants perceive them. Established terms describing these recognition events, including microbe-associated molecular pattern (MAMP), MAMP-receptor, effector, and resistance (R) protein, need clarification to represent our current knowledge adequately. In this review we propose criteria to classify inducers of plant defence as either MAMPs or microbe-induced molecular patterns (MIMPs). We refine the definition of MAMP to mean a molecular sequence or structure in ANY pathogen-derived molecule that is perceived via direct interaction with a host defence receptor. MIMPs are modifications of host-derived molecules that are induced by an intrinsic activity of a pathogen-derived effector and are perceived by a host defence receptor. MAMP-receptors have previously been classified separately from R-proteins as a discrete class of surveillance molecules. However, MAMP-receptors and R-proteins cannot be distinguished on the basis of their protein structures or their induced responses. We propose that MAMP-receptors and MIMP-receptors are each a subset of R-proteins. Although our review is based on examples from plant pathogens and plants, the principles discussed might prove applicable to other organisms. [source] Peptide microarrays for the characterization of antigenic regions of human chromogranin,APROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 14 2005Marcella Chiari Abstract Microarraying peptides is a powerful proteomics technique for studying molecular recognition events. Since peptides have small molecular mass, they are not easily accessible when adsorbed onto solid supports. Moreover, peptides can lack a well-defined three-dimensional structure, and therefore a correct orientation is essential to promote the interaction with their target. In this work, we investigated the suitability as a peptide array substrate of a glass slide coated with a copolymer of N,N -dimethylacrylamide, N,N -acryloyloxysuccinimide, and [3-(methacryloyl-oxy)propyl]trimethoxysilyl. This polymeric surface was used as substrate for peptides in the characterization of linear antigenic sites of human chromogranin,A, a useful tissue and serum marker for neuroendocrine tumors and a precursor of many biologically active peptides. The microarray support provided sufficient accessibility of the ligand, with no need for a spacer, as the polymer chains prevent interaction of immobilized peptides with substrate. In addition, the polymeric surface constitutes an aqueous micro-environment in which linear epitopes are freely exposed despite peptide random orientation. The results reported in this article are in accordance with those obtained in conventional ELISA assays using biotinylated and non-biotinylated peptides. [source] Non-Covalent Polyvalent Ligands by Self-Assembly of Small Glycodendrimers: A Novel Concept for the Inhibition of Polyvalent Carbohydrate,Protein Interactions In Vitro and In VivoCHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2006Gebhard Thoma Dr. Abstract Polyvalent carbohydrate,protein interactions occur frequently in biology, particularly in recognition events on cellular membranes. Collectively, they can be much stronger than corresponding monovalent interactions, rendering it difficult to control them with individual small molecules. Artificial macromolecules have been used as polyvalent ligands to inhibit polyvalent processes; however, both reproducible synthesis and appropriate characterization of such complex entities is demanding. Herein, we present an alternative concept avoiding conventional macromolecules. Small glycodendrimers which fulfill single molecule entity criteria self-assemble to form non-covalent nanoparticles. These particles,not the individual molecules,function as polyvalent ligands, efficiently inhibiting polyvalent processes both in vitro and in vivo. The synthesis and characterization of these glycodendrimers is described in detail. Furthermore, we report on the characterization of the non-covalent nanoparticles formed and on their biological evaluation. [source] | ||||||||||||||||