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Binding Events (binding + event)
Selected AbstractsElectrochemically Induced Modulation of the Catalytic Activity of a Reversible Redoxsensitive RiboswitchELECTROANALYSIS, Issue 9 2008Denise Strohbach Abstract Over the past decade, RNA conformation has been shown to respond to external stimuli. Thus, dependent on the presence of a high affinity ligand, specifically designed ribozymes can be regulated in a classical allosteric way. In this scenario, a binding event in one part of the RNA structure induces conformational changes in a separated part, which constitutes the catalytic centre. As a result activity is switched on (positive regulation) or off (negative regulation). We have developed a hairpin aptazyme responding to flavine mononucleotide (FMN). Ribozyme activity is dependent on binding of FMN and thus is switched on in the presence of FMN in its oxidized form. Under reducing conditions, however, FMN changes its molecular geometry, which is associated with loss of binding and consequently down-regulation of ribozyme activity. While in previous experiments sodium dithionite was used for reduction of FMN, we now present an assay for electrochemically induced activity switching. We have developed an electrochemical microcell that allows for iterative cycles of reduction/oxidation of FMN in an oxygen free atmosphere and thus for reversible switching of ribozyme activity. The reaction proceeds in droplets of 3 to 10,,L at micro- to nanomolar concentrations of the reaction components. [source] Specific Ca2+ Fluorescent Sensor: Signaling by Conformationally Induced PET Suppression in a Bichromophoric AcridinedioneEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 34 2009Pichandi Ashokkumar Abstract A series of acridinedione-based bichromophoric podand systems 1a,c were synthesized and characterized. Among these, bichromophore 1c shows specific binding of Ca2+ in the presence of other biologically important metal ions like Na+, K+, Mg2+, and Zn2+. The selective complexation was proved by steady-state emission, time-resolved emission, and 1H NMR titration. Signaling of the binding event was achieved by Ca2+ -induced folding of the bichromophore, resulting in PET suppression in the acridinedione chromophore. Involvement of a PET process in the optical signaling was confirmed by comparing bichromophores 1a,c with non-PET compound 2 and monochromophore model compound 3. Non-PET compound 2 failed to give optical response upon Ca2+ binding as a result of the absence of a PET process in the Ca2+ -bound complex. Monochromophore 3 shows a similar optical response, which is the same as that in 1c. Titration of the metal-ion-bound complex of 1c with EDTA released the metal ion from the complex, thereby regaining the original photophysical properties of the bichromophore.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Synthesis of Functionalized Au Nanoparticles for Protein Detection,ADVANCED MATERIALS, Issue 3 2008R. Jana Aptamer and antibody functionalized Au nanoparticles are synthesized and used for protein detection (see figure). These particles are highly water soluble and as small as 10 nm. However, they are enlarged after a protein binding event to enhance signal sensitivity. A conventional western blot protocol is used to enable detection of the proteins with nanomolar sensitivity, with the naked eye. [source] Facile detection of specific RNA-polypeptide interactions by MALDI-TOF mass spectrometryJOURNAL OF PEPTIDE SCIENCE, Issue 8 2008Maki Sugaya Abstract A simple method for the detection of specific RNA-polypeptide interactions using MALDI-TOF mass spectroscopy is described. Instead of direct observation of the RNA-polypeptide complex, we attempted the indirect observation of the binding event by focusing on the disappearance of the free polypeptide signal upon interaction with RNA. As a result, specific binding of the Rev-response element (RRE) RNA of the HIV with two RRE-binding peptide aptamers, DLA and RLA peptides, as well as the bacteriophage , boxB RNA with the , N peptide was observed. We also show that specific RNA-binding peptides can be identified from a mixture of peptides with varying RNA-binding affinity, showing that the method could be applied to high-throughput screening from simple peptide libraries. The method described in this study provides a quick and simple method for detecting specific RNA,polypeptide interactions that avoids difficulties associated with direct observation of RNA and RNA,polypeptide complexes, which may find various applications in the analysis of RNA,polypeptide interactions and in the identification of novel RNA-binding polypeptides. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] Endocytosis of plasma-derived factor V by megakaryocytes occurs via a clathrin-dependent, specific membrane binding eventJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 3 2005B. A. BOUCHARD Summary., Megakaryocytes were analyzed for their ability to endocytose factor V to define the cellular mechanisms regulating this process. In contrast to fibrinogen, factor V was endocytosed by megakaryocytes derived from CD34+ cells or megakaryocyte-like cell lines, but not by platelets. CD41+ex vivo -derived megakaryocytes endocytosed factor V, as did subpopulations of the megakaryocyte-like cells MEG-01, and CMK. Similar observations were made for fibrinogen. Phorbol diester-induced megakaryocytic differentiation of the cell lines resulted in a substantial increase in endocytosis of both proteins as compared to untreated cells that did not merely reflect their disparate plasma concentrations. Factor IX, which does not associate with platelets or megakaryocytes, was not endocytosed by any of the cells examined. Endocytosis of factor V by megakaryocytes proceeds through a specific and independent mechanism as CHRF-288 cells endocytosed fibrinogen but not factor V, and the presence of other plasma proteins had no effect on the endocytosis of factor V by MEG-01 cells. Furthermore, as the endocytosis of factor V was also demonstrated to occur through a clathrin-dependent mechanism, these combined data demonstrate that endocytosis of factor V by megakaryocytes occurs via a specific, independent, and most probably receptor-mediated, event. [source] Manipulation of Electrostatic and Saccharide Linker Interactions in the Design of Efficient Glycopolypeptide-Based Cholera Toxin InhibitorsMACROMOLECULAR BIOSCIENCE, Issue 1 2010Ronak Maheshwari Abstract Multivalent, glycopolymer inhibitors designed for the treatment of disease and pathogen infection have shown improvements in binding correlated with general changes in glycopolymer architecture and composition. We have previously demonstrated that control of glycopolypeptide backbone extension and ligand spacing significantly impacts the inhibition of the cholera toxin B subunit pentamer (CT B5) by these polymers. In the studies reported here, we elucidate the role of backbone charge and linker length in modulating the inhibition event. Peptides of the sequence AXPXG (where X is a positive, neutral or negative amino acid), equipped with the alkyne functionality of propargyl glycine, were designed and synthesized via solid-phase peptide synthetic methods and glycosylated via Cu(I)-catalyzed alkyne-azide cycloaddition reactions. The capacity of the glycopeptides to inhibit the binding of the B5 subunit of cholera toxin was evaluated. These studies indicated that glycopeptides with a negatively charged backbone show improved inhibition of the binding event relative to the other glycopeptides. In addition, variations in the length of the linker between the peptide and the saccharide ligand also affected the inhibition of CT by the glycopeptides. Our findings suggest that, apart from appropriate saccharide spacing and polypeptide chain extension, saccharide linker conformation and the systematic placement of charges on the polypeptide backbone are also significant variables that can be tuned to improve the inhibitory potencies of glycopolypeptide-based multivalent inhibitors. [source] Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: A molecular dynamics simulation studyBIOPOLYMERS, Issue 1 2009Rakina Yaneva Abstract Major histocompatibility (MHC) Class II cell surface proteins present antigenic peptides to the immune system. Class II structures in complex with peptides but not in the absence of peptide are known. Comparative molecular dynamics (MD) simulations of a Class II protein (HLA-DR3) with and without CLIP (invariant chain-associated protein) peptide were performed starting from the CLIP-bound crystal structure. Depending on the protonation of acidic residues in the P6 peptide-binding pocket the simulations stayed overall close to the start structure. The simulations without CLIP showed larger conformational fluctuations especially of ,-helices flanking the binding cleft. Largest fluctuations without CLIP were observed in a helical segment near the peptide C-terminus binding region matching a segment recognized by antibodies specific for empty Class II proteins. Simulations on a Val86Tyr mutation that fills the peptide N-terminus binding P1 pocket or of a complex with a CLIP fragment (dipeptide) bound to P1 showed an unexpected long range effect. In both simulations the mobility not only of P1 but also of the entire binding cleft was reduced compared to simulations without CLIP. It correlates with the experimental finding that the CLIP fragment binding to P1 is sufficient to prevent antibody recognition specific for the empty form at a site distant from P1. The results suggest a mechanism how a local binding event of small peptides or of an exchange factor near P1 may promote peptide binding and exchange through a long range stabilization of the whole binding cleft in a receptive (near bound) conformation. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 14,27, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Multivalent Carbohydrate Recognition on a Glycodendrimer-Functionalized Flow-Through ChipCHEMBIOCHEM, Issue 11 2008Hilbert M. Branderhorst Abstract Dendrimers were fitted out with up to eight mannose moieties by "click" chemistry. They were subsequently attached to aluminum oxide chips via a spacer that was linked to the dendrimer core; this resulted in a microarray of glycodendrimers. Binding of the glycodendrimers to the fluorescent lectins ConA and GNA was observable in real time. In a single experiment it was possible to observe the multivalency enhancement or cluster effect in the binding event. This effect was small for ConA, in agreement with its widely spaced binding sites, whereas it was large for GNA, with its twelve much more closely spaced binding sites. The dendrimer-fitted chip represents a valuable screening tool for multivalency effects. Furthermore kinetic and thermodynamic data on binding events can be deduced. Inhibition experiments are also possible with the system as was shown for ConA with ,-methyl mannose as the inhibitor. [source] Synthesis of Benzaldehyde-Functionalized Glycans: A Novel Approach Towards Glyco-SAMs as a Tool for Surface Plasmon Resonance StudiesCHEMISTRY - A EUROPEAN JOURNAL, Issue 23 2010Sebastian Kopitzki Dipl.-Chem. Abstract In recent years the interest in tools for investigating carbohydrate,protein (CPI) and carbohydrate-carbohydrate interactions (CCI) has increased significantly. For the investigation of CPI and CCI, several techniques employing different linking methods are available. Surface plasmon resonance (SPR) imaging is a most appropriate tool for analyzing the formation of self-assembled monolayers (SAM) of carbohydrate derivatives, which can mimic the glycocalyx. In contrast to the SPR imaging methods used previously to analyze CPI and CCI, the novel approach reported herein allows a facile and rapid synthesis of linker spacers and carbohydrate derivatives and enhances the binding event by controlling the amount and orientation of ligand. For immobilization on biorepulsive amino-functionalized SPR chips by reductive amination, diverse aldehyde-functionalized glycan structures (glucose, galactose, mannose, glucosamine, cellobiose, lactose, and lactosamine) have been synthesized in several facile steps that include olefin metathesis. Effective immobilization and the first binding studies are presented for the lectin concanavalin A. [source] Insights into the structure of plant ,-type phospholipase DFEBS JOURNAL, Issue 10 2007Susanne Stumpe Phospholipases D play an important role in the regulation of cellular processes in plants and mammals. Moreover, they are an essential tool in the synthesis of phospholipids and phospholipid analogs. Knowledge of phospholipase D structures, however, is widely restricted to sequence data. The only known tertiary structure of a microbial phospholipase D cannot be generalized to eukaryotic phospholipases D. In this study, the isoenzyme form of phospholipase D from white cabbage (PLD,2), which is the most widely used plant phospholipase D in biocatalytic applications, has been characterized by small-angle X-ray scattering, UV-absorption, CD and fluorescence spectroscopy to yield the first insights into its secondary and tertiary structure. The structural model derived from small-angle X-ray scattering measurements reveals a barrel-shaped monomer with loosely structured tops. The far-UV CD-spectroscopic data indicate the presence of ,-helical as well as ,-structural elements, with the latter being dominant. The fluorescence and near-UV CD spectra point to tight packing of the aromatic residues in the core of the protein. From the near-UV CD signals and activity data as a function of the calcium ion concentration, two binding events characterized by dissociation constants in the ranges of 0.1 mm and 10,20 mm can be confirmed. The stability of PLD,2 proved to be substantially reduced in the presence of calcium ions, with salt-induced aggregation being the main reason for irreversible inactivation. [source] Tuning Specific Biomolecular Interactions Using Electro-Switchable Oligopeptide SurfacesADVANCED FUNCTIONAL MATERIALS, Issue 16 2010Chun L. Yeung Abstract The ability to regulate biomolecular interactions on surfaces driven by an external stimuli is of great theoretical interest and practical impact in the biomedical and biotechnology fields. Herein, a new class of responsive surfaces that rely on electro-switchable peptides to control biomolecular interactions on gold surfaces is presented. This system is based upon the conformational switching of positively charged oligolysine peptides that are tethered to a gold surface, such that bioactive molecular moieties (biotin) incorporated on the oligolysines can be reversibly exposed (bio-active state) or concealed (bio-inactive state) on demand, as a function of surface potential. The dynamics of switching the biological properties is studied by observing the binding events between biotin and fluorescently labeled NeutrAvidin. Fluorescence microscope images and surface plasmon resonance spectral data clearly reveal opposite binding behaviors when +0.3 V or ,0.4 V vs. SCE are applied to the surface. High fluorescence intensities are observed for an applied positive potential, while minimal fluorescence is detected for an applied negative potential. Surface plasmon resonance spectroscopy (SPR) results provided further evidence that NeutrAvidin binding to the surface is controlled by the applied potential. A large SPR response is observed when a positive potential is applied on the surface, while a negative applied potential induces over 90% reduction in NeutrAvidin binding. [source] Construction and Characterization of Porous SiO2/Hydrogel Hybrids as Optical Biosensors for Rapid Detection of BacteriaADVANCED FUNCTIONAL MATERIALS, Issue 14 2010Naama Massad-Ivanir Abstract The use of a new class of hybrid nanomaterials as label-free optical biosensors for bacteria detection (E. coli K12 as a model system) is demonstrated. The hybrids combine a porous SiO2 (PSiO2) optical nanostructure (a Fabry,Pérot thin film) used as the optical transducer element and a hydrogel. The hydrogel, polyacrylamide, is synthesized in situ within the nanostructure inorganic host and conjugated with specific monoclonal antibodies (IgGs) to provide the active component of the biosensor. The immobilization of the IgGs onto the hydrogel via a biotin-streptavidin system is confirmed by fluorescent labeling experiments and reflective interferometric Fourier transform spectroscopy (RIFTS). Additionally, the immobilized IgGs maintain their immunoactivity and specificity when attached to the sensor surface. Exposure of these modified-hybrids to the target bacteria results in "direct cell capture" onto the biosensor surface. These specific binding events induce predictable changes in the thin-film optical interference spectrum of the hybrid. Preliminary studies demonstrate the applicability of these biosensors for the detection of low bacterial concentrations in the range of 103,105 cell mL,1 within minutes. [source] Highly Stable Au Nanoparticles with Tunable Spacing and Their Potential Application in Surface Plasmon Resonance BiosensorsADVANCED FUNCTIONAL MATERIALS, Issue 1 2010Shuyan Gao Abstract Colloidal Au-amplified surface plasmon resonance (SPR), like traditional SPR, is typically used to detect binding events on a thin noble metal film. The two major concerns in developing colloidal Au-amplified SPR lie in 1) the instability, manifested as a change in morphology following immersion in organic solvents and aqueous solutions, and 2) the uncontrollable interparticle distance, determining probe spacing and inducing steric hindrance between neighboring probe molecules. This may introduce uncertainties into such detecting techniques, degrade the sensitivity, and become the barricade hampering colloidal Au-based transducers from applications in sensing. In this paper, colloidal Au-amplified SPR transducers are produced by using ultrathin Au/Al2O3 nanocomposite films via a radio frequency magnetron co-sputtering method. Deposited Au/Al2O3 nanocomposite films exhibit superior stability, and average interparticle distances between Au nanoparticles with similar average sizes can be tuned by changing surface coverage. These characteristics are ascribed to the spacer function and rim confinement of dielectric Al2O3 and highlight their advantages for application in optimal nanoparticle-amplified SPR, especially when the probe size is smaller than the target molecule size. This importance is demonstrated here for the binding of protein (streptavidin) targets to the probe (biotin) surface. In this case, the dielectric matrix Al2O3 is a main contributor, behaving as a spacer, tuning the concentration of Au nanoparticles, and manipulating the average interparticle distance, and thus guaranteeing an appropriate number of biotin molecules and expected near-field coupling to obtain optimal sensing performance. [source] Decorating Liquid Crystal Surfaces with Proteins for Real-Time Detection of Specific Protein,Protein BindingADVANCED FUNCTIONAL MATERIALS, Issue 22 2009Deny Hartono Abstract Here, a novel method of immobilizing proteins with well-defined orientation directly on liquid crystal surfaces that allow subsequent real-time imaging of specific protein,protein binding events on these surfaces is reported. Self-assembly of nitrilotriacetic acid terminated amphiphiles loaded with Ni2+ ions at aqueous-liquid crystal interface creates a surface capable of immobilizing histidine-tagged ubiquitin through complex formation between Ni2+ and histidine. When these surfaces containing immobilized histidine-tagged ubiquitin are exposed to anti-ubiquitin antibody, the spatial and temporal of specific protein,protein binding events trigger orientational transitions of liquid crystals. As a result, sharp liquid crystal optical switching from dark to bright can readily be observed under polarized lighting. The protein,protein binding can be observed within seconds and only requires nanogram quantities of proteins. This work demonstrates a simple strategy to immobilize proteins with well-defined orientation on liquid crystal surfaces for real-time and label-free detection of specific protein,protein binding events, which may find use in biomedical diagnostics. [source] Functional Nanostructured Plasmonic MaterialsADVANCED MATERIALS, Issue 10 2010Jimin Yao Abstract Plasmonic crystals fabricated with precisely controlled arrays of subwavelength metal nanostructures provide a promising platform for sensing and imaging of surface binding events with micrometer spatial resolution over large areas. Soft nanoimprint lithography provides a robust, cost-effective method for producing highly uniform plasmonic crystals of this type with predictable optical properties. The tunable multimode plasmonic resonances of these crystals and their ability for integration into lab-on-a-chip microfluidic systems can both be harnessed to achieve exceptionally high analytical sensitivities down to submonolayer levels using even a common optical microscope, circumventing numerous technical limitations of more conventional surface plasmon resonance techniques. In this article, we highlight some recent advances in this field with an emphasis on the fabrication and characterization of these integrated devices and their demonstrated applications. [source] Exploring Optical Properties of Liquid Crystals for Developing Label-Free and High-Throughput Microfluidic Immunoassays,ADVANCED MATERIALS, Issue 2 2009Chang-Ying Xue The orientational transition of liquid crystals (LCs) is used as a label-free detection mechanism for immunoassays developed in microfluidic systems. LCs only show bright optical textures (visible to the naked eye) in the line-line intersections in which label-free antibodies bind to their surface-immobilized antigens, suggesting the feasibility of using LCs to detect specific antigen-antibody binding events in a high-throughput and multiplexed manner. [source] DNA-Based Self-Sorting of Nanoparticles on Gold Surfaces,ADVANCED MATERIALS, Issue 15 2007U. Plutowski Site-selective deposition of nanoparticles onto surfaces is desirable for the fabrication of nanoscale devices. For nanoparticles with vastly different numbers of DNA chains on their surfaces, multivalent binding of short-sequence motifs and nonspecific adsorption complicate sequence-specific immobilization from mixtures. A new nanoparticle coating method that suppresses salt-induced aggregation and undesirable binding events is reported. Size-selective sorting of gold nanoparticles up to 60,nm diameter onto nanopatterned surfaces is shown (see figure). [source] PDK1 and PKB/Akt: Ideal Targets for Development of New Strategies to Structure-Based Drug DesignIUBMB LIFE, Issue 3 2003Thomas Harris Abstract Growth factor binding events to receptor tyrosine kinases result in activation of phosphatidylinositol 3-kinase (PI3K), and activated PI3K generates the membrane-bound second messengers phosphatidylinositol 3,4-diphosphate [PI(3,4)P2] and PI(3,4,5)P3, which mediate membrane translocation of the phosphoinositide-dependent kinase-1 (PDK1) and protein kinase B (PKB, also known as Akt). In addition to the kinase domain, PDK1 and PKB contain a pleckstrin homology (PH) domain that binds to the second messenger, resulting in the phosphorylation and activation of PKB by PDK1. Recent evidence indicates that constitutive activation of PKB contributes to cancer progression by promoting proliferation and increased cell survival. The indicating of PDK1 and PKB as primary targets for discovery of anticancer drugs, together with the observations that both PDK1 and PKB contain small-molecule regulatory binding sites that may be in proximity to the kinase active site, make PDK1 and PKB ideal targets for the development of new strategies to structure-based drug design. While X-ray structures have been reported for the kinase domains of PDK1 and PKB, no suitable crystals have been obtained for either PDK1 or PKB with their PH domains intact. In this regard, a novel structure-based strategy is proposed, which utilizes segmental isotopic labeling of the PH domain in combination with site-directed spin labeling of the kinase active site. Then, long-range distance restraints between the 15N-labeled backbone amide groups of the PH domain and the unpaired electron of the active site spin label can be determined from magnetic resonance studies of the enhancement effect that the paramagnetic spin label has on the nuclear relaxation rates of the amide protons. The determination of the structure and position of the PH domain with respect to the known X-ray structure of the kinase active site could be useful in the rational design of potent and selective inhibitors of PDK1 and PKB by 'linking' the free energies of binding of substrate (ATP) analogs with analogs of the inositol polar head group of the phospholipid second messenger. The combined use of X-ray crystallography, segmental isotopic and spin labeling, and magnetic resonance studies can be further extended to the study of other dynamic multidomain proteins and targets for structure-based drug design. IUBMB Life, 55: 117-126, 2003 [source] Probing DNA,peptide interaction forces at the single-molecule levelJOURNAL OF PEPTIDE SCIENCE, Issue 12 2006Norbert Sewald Abstract The versatility of chemical peptide synthesis combined with the high sensitivity of AFM single-molecule force spectroscopy allows us to investigate, quantify, and control molecular recognition processes (molecular nanotechnology), offering a tremendous potential in chemical biology. Single-molecule force spectroscopy experiments are able to detect fast intermediate transition states, details of the energy landscape, and structural changes, while avoiding multiple binding events that can occur under ensemble conditions. Dynamic force spectroscopy (DFS) is even able to provide data on the complex lifetime. This minireview outlines the biophysical methodology, discusses different experimental set-ups, and presents representative results in the form of two case studies, both dealing with DNA-binding peptides. They may serve as model systems, e.g., for transcription factors or gene transfection agents. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd. [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] A new generation of protein display scaffolds for molecular recognitionPROTEIN SCIENCE, Issue 1 2006Ralf J. Hosse Abstract Engineered antibodies and their fragments are invaluable tools for a vast range of biotechnological and pharmaceutical applications. However, they are facing increasing competition from a new generation of protein display scaffolds, specifically selected for binding virtually any target. Some of them have already entered clinical trials. Most of these nonimmunoglobulin proteins are involved in natural binding events and have amazingly diverse origins, frameworks, and functions, including even intrinsic enzyme activity. In many respects, they are superior over antibody-derived affinity molecules and offer an ever-extending arsenal of tools for, e.g., affinity purification, protein microarray technology, bioimaging, enzyme inhibition, and potential drug delivery. As excellent supporting frameworks for the presentation of polypeptide libraries, they can be subjected to powerful in vitro or in vivo selection and evolution strategies, enabling the isolation of high-affinity binding reagents. This article reviews the generation of these novel binding reagents, describing validated and advanced alternative scaffolds as well as the most recent nonimmunoglobulin libraries. Characteristics of these protein scaffolds in terms of structural stability, tolerance to multiple substitutions, ease of expression, and subsequent applications as specific targeting molecules are discussed. Furthermore, this review shows the close linkage between these novel protein tools and the constantly developing display, selection, and evolution strategies using phage display, ribosome display, mRNA display, cell surface display, or IVC (in vitro compartmentalization). Here, we predict the important role of these novel binding reagents as a toolkit for biotechnological and biomedical applications. [source] Surface plasmon resonance label-free monitoring of antibody antigen interactions in real timeBIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 1 2007Asta Kausaite Abstract Detection of biologically active compounds is one of the most important topics in molecular biology and biochemistry. One of the most promising detection methods is based on the application of surface plasmon resonance for label-free detection of biologically active compounds. This method allows one to monitor binding events in real time without labeling. The system can therefore be used to determine both affinity and rate constants for interactions between various types of molecules. Here, we describe the application of a surface plasmon resonance biosensor for label-free investigation of the interaction between an immobilized antigen bovine serum albumin (BSA) and antibody rabbit anti-cow albumin IgG1 (anti-BSA). The formation of a self-assembled monolayer (SAM) over a gold surface is introduced into this laboratory training protocol as an effective immobilization method, which is very promising in biosensing systems based on detection of affinity interactions. In the next step, covalent attachment via artificially formed amide bonds is applied for the immobilization of proteins on the formed SAM surface. These experiments provide suitable experience for postgraduate students to help them understand immobilization of biologically active materials via SAMs, fundamentals of surface plasmon resonance biosensor applications, and determination of non-covalent biomolecular interactions. The experiment is designed for master and/or Ph.D. students. In some particular cases, this protocol might be adoptable for bachelor students that already have completed an extended biochemistry program that included a background in immunology. [source] Potent Fluoro-oligosaccharide Probes of Adhesion in ToxoplasmosisCHEMBIOCHEM, Issue 15 2009Sarah A. Allman Abstract Unnatural, NMR- and MRI-active fluorinated sugar probes, designed and synthesised to bind to the pathogenic protein TgMIC1 from Toxoplasma gondii, were found to display binding potency equal to and above that of the natural ligand. Dissection of the binding mechanism and modes, including the first X-ray crystal structures of a fluoro-oligosaccharide bound to a lectin, demonstrate that it is possible to create effective fluorinated probe ligands for the study of, and perhaps intervention in, sugar,protein binding events. [source] Multivalent Carbohydrate Recognition on a Glycodendrimer-Functionalized Flow-Through ChipCHEMBIOCHEM, Issue 11 2008Hilbert M. Branderhorst Abstract Dendrimers were fitted out with up to eight mannose moieties by "click" chemistry. They were subsequently attached to aluminum oxide chips via a spacer that was linked to the dendrimer core; this resulted in a microarray of glycodendrimers. Binding of the glycodendrimers to the fluorescent lectins ConA and GNA was observable in real time. In a single experiment it was possible to observe the multivalency enhancement or cluster effect in the binding event. This effect was small for ConA, in agreement with its widely spaced binding sites, whereas it was large for GNA, with its twelve much more closely spaced binding sites. The dendrimer-fitted chip represents a valuable screening tool for multivalency effects. Furthermore kinetic and thermodynamic data on binding events can be deduced. Inhibition experiments are also possible with the system as was shown for ConA with ,-methyl mannose as the inhibitor. [source] Design and Characterisation of an Artificial DNA-Binding CytochromeCHEMBIOCHEM, Issue 7 2004D. Dafydd Jones Dr. Abstract We aim to design novel proteins that link specific biochemical binding events, such as DNA recognition, with electron transfer functionality. We want these proteins to form the basis of new molecules that can be used for templated assembly of conducting cofactors or for thermodynamically linking DNA binding with cofactor chemistry for nanodevice applications. The first examples of our new proteins recruit the DNA-binding basic helix region of the leucine zipper protein GCN4. This basic helix region was attached to the N and C termini of cytochrome b562(cyt b562) to produce new, monomeric, multifunctional polypeptides. We have fully characterised the DNA and haem-binding properties of these proteins, which is a prerequisite for future application of the new molecules. Attachment of a single basic helix of GCN4 to either the N or C terminus of the cytochrome does not result in specific DNA binding but the presence of DNA-binding domains at both termini converts the cytochrome into a specific DNA-binding protein. Upon binding haem, this chimeric protein attains the spectral characteristics of wild-type cyt b562. The three forms of the protein, apo, oxidised holo and reduced holo, all bind the designed (ATGAcgATGA) target DNA sequence with a dissociation constant, KD, of approximately 90 nM. The protein has a lower affinity (KDca. 370 nM) for the wild-type GCN4 recognition sequence (ATGAcTCAT). The presence of only half the consensus DNA sequence (ATGAcgGGCC) shifts the KDvalue to more than 2500 nM and the chimera does not bind specifically to DNA sequences with no target recognition sites. Ultracentrifugation revealed that the holoprotein,DNA complex is formed with a 1:1 stoichiometry, which indicates that a higher-order protein aggregate is not responsible for DNA binding. Mutagenesis of a loop linking helices 2 and 3 of the cytochrome results in a chimera with a haem-dependent DNA binding affinity. This is the first demonstration that binding of a haem group to a designed monomeric protein can allosterically modulate the DNA binding affinity. [source] Thermodynamic Analysis of Receptors Based on Guanidinium/Boronic Acid Groups for the Complexation of Carboxylates, ,-Hydroxycarboxylates, and Diols: Driving Force for Binding and CooperativityCHEMISTRY - A EUROPEAN JOURNAL, Issue 15 2004Sheryl L. Wiskur Dr. Abstract The thermodynamics of guanidinium and boronic acid interactions with carboxylates, ,-hydroxycarboxylates, and diols were studied by determination of the binding constants of a variety of different guests to four different hosts (7,10). Each host contains a different combination of guanidinium groups and boronic acids. The guests included molecules with carboxylate and/or diol moieties, such as citrate, tartrate, and fructose, among others. The Gibbs free energies of binding were determined by UV/Vis absorption spectroscopy, by use of indicator displacement assays. The receptor based on three guanidinium groups (7) was selective for the tricarboxylate guest. The receptors that incorporated boronic acids (8,10) had higher affinities for guests that included ,-hydroxycarboxylate and catechol moieties over guests containing only carboxylates or alkanediols. Isothermal titration calorimetry revealed the enthalpic and entropic contributions to the Gibbs free energies of binding. The binding of citrate and tartrate was investigated with hosts 7,10, for which all the binding events were exothermic, with positive entropy. Because of the selectivity of hosts 8,10, a simple boronic acid (14) was also investigated and determined to be selective for ,-hydroxycarboxylates and catechols over amino acids and alkanediols. Further, the cooperativity of 8 and 9 in binding tartrate was also investigated, revealing little or no cooperativity with 8, but negative cooperativity with 9. A linear entropy/enthalpy compensation relationship for all the hosts 7,10, 14, and the carboxylate-/diol-containing guests was also obtained. This relationship indicates that increasing enthalpy of binding is offset by similar losses in entropy for molecular recognition involving guanidinium and boronic acid groups. [source] | |||||||||||||||||||||||||