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Affinity Ligand (affinity + ligand)
Selected AbstractsSmall-Molecule Affinity Ligands for Protein Purification: Combined Computational Enrichment and Automated In-line Screening of an Optically Encoded Library,ANGEWANDTE CHEMIE, Issue 20 2010Jakob Hand in Hand: Eine vielseitige Methode zur Entwicklung niedermolekularer Affinitätsliganden wird beschrieben. Die Kombination aus Datenbankanreicherung mit automatisiertem Screening und Affinitätskartierung einer optisch codierten kombinatorischen Bibliothek ermöglichte die Identifizierung eines neuen Satzes von Liganden für die einstufige Aufreinigung des menschlichen Wachstumshormons (siehe Bild). [source] Electrochemically 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] Identification of calreticulin as a ligand of GABARAP by phage display screening of a peptide libraryFEBS JOURNAL, Issue 21 2007Jeannine Mohrlüder 4-Aminobutyrate type A (GABAA) receptor-associated protein (GABARAP) is a ubiquitin-like modifier implicated in the intracellular trafficking of GABAA receptors, and belongs to a family of proteins involved in intracellular vesicular transport processes, such as autophagy and intra-Golgi transport. In this article, it is demonstrated that calreticulin is a high affinity ligand of GABARAP. Calreticulin, although best known for its functions as a Ca2+ -dependent chaperone and a Ca2+ -buffering protein in the endoplasmic reticulum, is also localized to the cytosol and exerts a variety of extra-endoplasmic reticulum functions. By phage display screening of a randomized peptide library, peptides that specifically bind GABARAP were identified. Their amino acid sequences allowed us to identify calreticulin as a potential GABARAP binding protein. GABARAP binding to calreticulin was confirmed by pull-down experiments with brain lysate and colocalization studies in N2a cells. Calreticulin and GABARAP interact with a dissociation constant Kd = 64 nm and a mean lifetime of the complex of 20 min. Thus, the interaction between GABARAP and calreticulin is the strongest so far reported for each protein. [source] Biomimetic affinity purification of cardiotoxin and its pharmacological effects on the nervous system,JOURNAL OF MOLECULAR RECOGNITION, Issue 3 2008Dexian Dong Abstract Cobra venom is a very precious natural resource. The traditional method for purification of cardiotoxin from cobra venom is a multi-step, high cost, and low recovery procedure. By molecular modeling and docking with SYBYL software, we designed and synthesized an affinity ligand, m-aminobenzoic acid, for high efficiency purification of this therapeutically useful Chinese cobra venom cardiotoxin. The one-step recovery of cardiotoxin reached 64% and the purity reached 92% upon purification. The binding capacity of this synthetic ligand was 9.1,mg cardiotoxin/g moist weight gel and the affinity constant for cardiotoxin was 5.5,×,103,M,1. Unlike a natural affinity ligand, this synthetic ligand is highly stable, and has great potential for industrial scale production of cardiotoxin. In addition, we examined the effects of cardiotoxin on the nervous system in a mouse model. Results showed that cardiotoxin could maintain analgesic effects for 120,min with a dose of less than 0.06,mg/kg (2.8% of the LD50). Administration of 0.12,mg/kg cardiotoxin could improve scopolamine impairments of memory in mice. These results suggest that cardiotoxin may be a potential drug for nervous system diseases. Copyright © 2008 John Wiley & Sons, Ltd. [source] Competitive affinity capillary electrophoresis assay based on a "hybrid" pre-incubation/on-capillary mixing format using an enantioselective aptamer as affinity ligandJOURNAL OF SEPARATION SCIENCE, JSS, Issue 12 2008Josephine Ruta Abstract In this paper, we describe an aptamer-based competitive affinity CE (ACE) assay involving (i) the pre-incubation of the target (D-arginine) and the specific ligand (anti-D-arginine-L-RNA aptamer) before (ii) the competition with the labeled target (dansylated D-arginine) through an on-capillary mixing strategy. The effects of some critical operating parameters such as the applied voltage and the sample-aptamer mixture plug length on the assay sensitivity were investigated. The ACE assay appeared particularly dependent on the plug length of the pre-incubated sample-aptamer solution. It was shown that this "hybrid" strategy significantly improved the assay sensitivity relative to that obtained with a "full" on-capillary mixing approach. [source] High-resolution crystal structure of human Mapkap kinase 3 in complex with a high affinity ligandPROTEIN SCIENCE, Issue 1 2010Robert Cheng Abstract The Mapkap kinases 2 and 3 (MK2 and MK3) have been implicated in intracellular signaling pathways leading to the production of the pro-inflammatory cytokine tumor necrosis factor alpha. MK2 has been pursued by the biopharmaceutical industry for many years for the development of a small molecule anti-inflammatory treatment and drug-like inhibitors have been described. The development of some of these compounds, however, has been slowed by the absence of a high-resolution crystal structure of MK2. Herein we present a high-resolution (1.9 Å) crystal structure of the highly homologous MK3 in complex with a pharmaceutical lead compound. While all of the canonical features of Ser/Thr kinases in general and MK2 in particular are recapitulated in MK3, the detailed analysis of the binding interaction of the drug-like ligand within the adenine binding pocket allows relevant conclusions to be drawn for the further design of potent and selective drug candidates. [source] Affinity-enhanced protein partitioning in decyl ,- D -glucopyranoside two-phase aqueous micellar systemsBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2005Henry Lam Abstract Liquid,liquid extraction in two-phase aqueous complex-fluid systems has been proposed as a scalable, versatile, and cost-effective purification method for the downstream processing of biotechnological products. In the case of two-phase aqueous micellar systems, careful choices of the phase-forming surfactants or surfactant mixtures allow these systems to separate biomolecules based on size, hydrophobicity, charge, or specific affinity. In this article, we investigate the affinity-enhanced partitioning of a model affinity-tagged protein,green fluorescent protein fused to a family 9 carbohydrate-binding module (CBM9-GFP),in a two-phase aqueous micellar system generated from the nonionic surfactant n -decyl ,- D -glucopyranoside (C10G1), which acts simultaneously as the phase-former and the affinity ligand. In this simple system, CBM9-GFP was extracted preferentially into the micelle-rich phase, despite the opposing tendency of the steric, excluded-volume interactions operating between the protein and the micelles. We obtained more than a sixfold increase (from 0.47 to 3.1) in the protein partition coefficient (Kp), as compared to a control case where the affinity interactions were "turned off" by the addition of a competitive inhibitor (glucose). It was demonstrated conclusively that the observed increase in Kp can be attributed to the specific affinity between the CBM9 domain and the affinity surfactant C10G1, suggesting that the method can be generally applied to any CBM9-tagged protein. To rationalize the observed phenomenon of affinity-enhanced partitioning in two-phase aqueous micellar systems, we formulated a theoretical framework to model the protein partition coefficient. The modeling approach accounts for both the excluded-volume interactions and the affinity interactions between the protein and the surfactants, and considers the contributions from the monomeric and the micellar surfactants separately. The model was shown to be consistent with the experimental data, as well as with our current understanding of the CBM9 domain. © 2005 Wiley Periodicals, Inc. [source] Expression of Functional Recombinant Mussel Adhesive Protein Type 3A in Escherichia coliBIOTECHNOLOGY PROGRESS, Issue 3 2005Dong Soo Hwang Mussel adhesive proteins, including the 20-plus variants of foot protein type 3 (fp-3), have been suggested as potential environmentally friendly adhesives for use in aqueous conditions and in medicine. Here we report the novel production of a recombinant Mytilus galloprovincialis foot protein type 3 variant A (Mgfp-3A) fused with a hexahistidine affinity ligand in Escherichia coli and its ,99% purification with affinity chromatography. Recombinant Mgfp-3A showed a superior purification yield and better apparent solubility in 5% acetic acid (prerequisites for large-scale production and practical use) compared to those of the previously reported recombinant M. galloprovincialis foot protein type 5 (Mgfp-5). The adsorption abilities and adhesion forces of purified recombinant Mgfp-3A were compared with those of Cell-Tak (a commercial mussel extract adhesive) and recombinant Mgfp-5 using quartz crystal microbalance analysis and modified atomic force microscopy, respectively. These assays showed that the adhesive ability of recombinant Mgfp-3A was comparable to that of Cell-Tak but lower than that of recombinant Mgfp-5. Collectively, these results indicate that recombinant Mgfp-3A may be useful as a commercial bioadhesive or an adhesive ingredient in medical or underwater environments. [source] Affinity Ligand Selection from a Library of Small Molecules: Assay Development, Screening, and ApplicationBIOTECHNOLOGY PROGRESS, Issue 1 2005Lakshmi D. Saraswat A facile and cost-effective process for screening synthetic libraries for an affinity ligand is described. A high throughput 96-well plate filtration method was designed to screen both discrete compounds and mixtures of compounds attached to a solid support. Human serum albumin (HSA) was used as a target protein to demonstrate the proof of concept. Detection and quantitation by fluorescence was accomplished with the use of fluorescamine to conjugate the protein in the filtrate. It is found that mixtures demonstrating low average binding reflect an overall lower hit rate of the components, whereas deconvolution of mixtures with high protein binding consistently provides a high hit rate. This differs from many of the previous experiences screening solid-phase mixtures in which high false positive rates are noted to occur. A total of 100K compounds were tested: 25K as discrete samples and 75K as mixtures. An overall hit rate of 8% was observed. Secondary screening of compounds measured specificity, recovery, and dynamic binding capacity. The effectiveness of the method is illustrated using an affinity column made with a representative lead compound. A similar purity was achieved in a single-step purification of HSA from serum as compared to that obtained by two steps of ion-exchange chromatography. The process for primary screening of a large number of compounds is simple, inexpensive, and applicable to any soluble target protein of known or unknown function from crude mixtures and may have additional utility as a generic chemical affinity tool for the functional characterization of novel proteins emerging from proteomics work. [source] Affinity-Based Protein Surface Pattern Formation by Ligand Self-Selection from Mixed Protein SolutionsADVANCED FUNCTIONAL MATERIALS, Issue 19 2009Manish Dubey Abstract Photolithographically prepared surface patterns of two affinity ligands (biotin and chloroalkane) specific for two proteins (streptavidin and HaloTag, respectively) are used to spontaneously form high-fidelity surface patterns of the two proteins from their mixed solution. High affinity protein-surface self-selection onto patterned ligands on surfaces exhibiting low non-specific adsorption rapidly yields the patterned protein surfaces. Fluorescence images after protein immobilization show high specificity of the target proteins to their respective surface patterned ligands. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging further supports the chemical specificity of streptavidin and HaloTag for their surface patterned ligands from mixed protein solutions. However, ToF-SIMS did detect some non-specific adsorption of bovine serum albumin, a masking protein present in excess in the adsorbing solutions, on the patterned surfaces. Protein amino acid composition, surface coverage, density, and orientation are important parameters that determine the relative ToF-SIMS fragmentation pattern yields. ToF-SIMS amino acid-derived ion fragment yields summed to produce surface images can reliably determine which patterned surface regions contain bound proteins, but do not readily discriminate between different co-planar protein regions. Principal component analysis (PCA) of these ToF-SIMS data, however, improves discrimination of ions specific to each protein, facilitating surface protein pattern identification and image contrast. [source] Utilizing a library of synthetic affinity ligands for the enrichment, depletion and one-step purification of leech proteinsJOURNAL OF MOLECULAR RECOGNITION, Issue 3 2008Dexian Dong Abstract Although the concept of affinity purification using synthetic ligands had been utilized for many years, there are few articles related to this research area, and they focus only on the affinity purification of specific protein by a defined library of synthetic ligands. This study presents the design and construction of a 700-member library of synthetic ligands in detail. We selected 297 ligand columns from a 700-member library of synthetic ligands to screen leech protein extract. Of the 297, 154 columns had an enrichment effect, 83 columns had a depletion effect, 36 columns had a one-step purification effect, and 58 columns had a one-step purification via flowthrough effect. The experimental results achieved by this large library of affinity ligands provide solid convincing data for the theory that affinity chromatography could be used for the enrichment of proteins that are present in low abundance, the depletion of high abundance proteins, and one-step purification of special proteins. Copyright © 2008 John Wiley & Sons, Ltd. [source] Binding properties of peptidic affinity ligands for plasmid DNA capture and detectionAICHE JOURNAL, Issue 2 2009Ying Han Abstract Peptides constructed from ,-helical subunits of the Lac repressor protein (LacI) were designed then tailored to achieve particular binding kinetics and dissociation constants for plasmid DNA purification and detection. Surface plasmon resonance was employed for quantification and characterization of the binding of double stranded Escherichia coli plasmid DNA (pUC19) via the lac operon (lacO) to "biomimics" of the DNA binding domain of LacI. Equilibrium dissociation constants (KD), association (ka), and dissociation rates (kd) for the interaction between a suite of peptide sequences and pUC19 were determined. KD values measured for the binding of pUC19 to the 47mer, 27mer, 16mer, and 14mer peptides were 8.8 ± 1.3 × 10,10 M, 7.2 ± 0.6 × 10,10 M, 4.5 ± 0.5 × 10,8 M, and 6.2 ± 0.9 × 10,6 M, respectively. These findings show that affinity peptides, composed of subunits from a naturally occurring operon,repressor interaction, can be designed to achieve binding characteristics suitable for affinity chromatography and biosensor devices. © 2008 American Institute of Chemical Engineers AIChE J, 2009 [source] Isatin-binding proteins of rat and mouse brain: Proteomic identification and optical biosensor validationPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 1 2010Olga Buneeva Abstract Isatin (indole-2,3-dione) is an endogenous indole that has a distinct and discontinuous distribution in the brain and in other mammalian tissues and body fluids. Its output is increased under conditions of stress and anxiety. Isatin itself and its analogues exhibit a wide range of pharmacological activities but its specific biological targets still are not well characterized. Affinity chromatography of Triton X-100 lysates of soluble and particulate fractions of mouse and rat whole brain homogenates on 5-aminocaproyl-isatin-Sepharose followed by subsequent proteomic analysis resulted in identification of 65 and 64 individual proteins, respectively. Isatin-binding capacity of some of the identified proteins has been validated in an optical biosensor study using a Biacore 3000 optical biosensor, 5-aminocarproyl-isatin, and 5-aminoisatin as the affinity ligands. The Kd values (of 0.1,20,,M) obtained during the optical biosensor experiments were consistent with the range of Kd values recently reported for [3H]isatin binding to brain sections. Although the number of isatin-binding proteins identified in the mouse and rat brain was similar, only 21 proteins (about one-third) were identical in the two species. This may be one reason for the differences in isatin effects in rats and mice reported in the literature. [source] Antibodies and Genetically Engineered Related Molecules: Production and PurificationBIOTECHNOLOGY PROGRESS, Issue 3 2004A. Cecília A. Roque Antibodies and antibody derivatives constitute 20 % of biopharmaceutical products currently in development, and despite early failures of murine products, chimeric and humanized monoclonal antibodies are now viable therapeutics. A number of genetically engineered antibody constructions have emerged, including molecular hybrids or chimeras that can deliver a powerful toxin to a target such as a tumor cell. However, the general use in clinical practice of antibody therapeutics is dependent not only on the availability of products with required efficacy but also on the costs of therapy. As a rule, a significant percentage (50,80%) of the total manufacturing cost of a therapeutic antibody is incurred during downstream processing. The critical challenges posed by the production of novel antibody therapeutics include improving process economics and efficiency, to reduce costs, and fulfilling increasingly demanding quality criteria for Food and Drug Administration (FDA) approval. It is anticipated that novel affinity-based separations will emerge from the development of synthetic ligands tailored to specific biotechnological needs. These synthetic affinity ligands include peptides obtained by synthesis and screening of peptide combinatorial libraries and artificial non-peptidic ligands generated by a de novo process design and synthesis. The exceptional stability, improved selectivity, and low cost of these ligands can lead to more efficient, less expensive, and safer procedures for antibody purification at manufacturing scales. This review aims to highlight the current trends in the design and construction of genetically engineered antibodies and related molecules, the recombinant systems used for their production, and the development of novel affinity-based strategies for antibody recovery and purification. [source] Cellulose and Glass Fiber Affinity Membranes for the Chromatographic Separation of BiomoleculesBIOTECHNOLOGY PROGRESS, Issue 1 2004Eli Ruckenstein Macroporous cellulose and glass membranes were prepared from filter paper and glass fiber filter, respectively. To enhance their stability, the cellulose membranes were crosslinked with epichlorohydrin, and the glass membranes were crosslinked with glutaraldehyde or organic bifunctional silanes. Several pathways for the modification, activation, and ligand immobilization were used and compared. For cellulose membranes, the diazotization method provided the best results, whereas the glutaraldehyde method provided the best performance for glass membranes, regarding both their stability and ligand immobilization capacity. The characterization of the membranes was made by using a triazine dye, bovine serum albumin, and trypsin as test ligands. The membrane morphologies and the uniformities of ligand distribution across the membrane cartridges were investigated. Numerous affinity ligands were immobilized onto the membranes, and the prepared affinity membranes have been used to separate or purify concanavalin A, peroxidase, protease inhibitors, globulin, fibronectin, and other biomolecules. [source] An Integrated Process for Mammalian Cell Perfusion Cultivation and Product Purification Using a Dynamic FilterBIOTECHNOLOGY PROGRESS, Issue 4 2002Leda R. Castilho In the present work, a dynamic filter was employed to develop an integrated perfusion/purification process. A recombinant CHO cell line producing a human anti-HIV IgG was employed in the experiments. In the first part of this work, the dynamic filter was fitted with conventional microfiltration membranes and tested as a new external cell retention device for perfusion cultivations. The filter was connected to a running perfusion bioreactor and operated for approximately 400 h at an average cell concentration of 10 million cells mL,1, whereby cell viability remained above 90% and no problems of sterility were experienced. In the second part of this work, the dynamic filter was employed to simultaneously carry out cell separation and product purification, using membrane adsorbers containing Protein A affinity ligands. An automated system was built, which integrated the features of an automated perfusion bioreactor and of a liquid chromatography system. The IgG was continuously adsorbed onto the affinity membranes and was periodically recovered through elution cycles. After connection of the filter, the system was operated for approximately 300 h, whereby three elution cycles were carried out. No progressive increase in transmembrane pressure was observed, indicating no membrane fouling problems, and the IgG was recovered practically free of contaminants in a 14-fold concentrated form, indicating that the integrated, one-step perfusion/purification process developed during this work is a promising alternative for the production of biologicals derived from mammalian cells. [source] | |||||||||||||