Screening of Peptides that Inhibit Bacterial Binding to Fibronectin using Combinatorial Peptide Libraries

Infective endocarditis is often caused by passage of oral endogenous bacteria into the blood stream. Such bacteremia occurs after tooth extraction, and occasionally even after brushing of the teeth. Abnormal or damaged heart valves, including artificial valves, show high risk of infection. Antibiotics are widely used to prevent this infection, however, frequent use of these have resulted in the generation of resistant mutants, which generate serious social problems. Thus, the development of more effective and safer drugs for the prevention of such infections is very desirable. The adhesion of bacteria to fibronectin, one of the major extracellular matrix (ECM) protein exposed on the wound endocardia, is considered critical for the infection. We have previously found a novel mode of interaction between endocarditis-causing bacteria and human fibronectin. The present study focuses on the discovery of candidate compounds that inhibit the association between microorganisms and fibronectin. Positional scanning libraries (PSL) with N-terminal biotinylated 6-mer peptides have been constructed and screened for binding to a monoclonal antibody for fibronectin that inhibits the bacterial fibronectin-binding. The consensus sequences derived from these experiments are expected to be structural mimetics of the local structure of fibronectin involved in the bacterial adhesion. Since individual synthetic 6-mer peptides did not show the desired action, discontinuous epitopes can be envisaged and therefore a 9-mer-PSL was constructed to reveal conformational epitopes. In the second library, several 9-mer peptides based on the screening were synthesized and gave improved results.Australian Peptide Conference Issue     

Ligand Binding by Fibroblast Growth Factor Receptors Investigated Using Chimeric Receptor Molecules

Abstract

In order to map in detail the ligand binding sites of fibroblast growth factor receptor 2 (FGFR2) and keratinocyte growth factor receptor (KGFR), we have generated receptor molecules that are chimeric within the membrane proximal sequence that varies between them. The chimeric molecules are found to bind aFGF with a greater than 5-fold difference in affinity, indicating that there is coupling between the chimeric regions with respect to aFGF binding. Further, binding of bFGF and KGF is abolished in the chimeras, showing that the binding site for these ligands requires the whole of the 48- or 50- amino acid variable sequence to be intact. Direct interactions between the different regions exchanged in the chimeras are most probably involved in forming KGF or bFGF binding sites.     

Mass Ligand Binding Screening for Receptor Antagonists: Prototype New Drugs and Blind Alleys

Abstract

The ligand binding assay is a powerful tool in the search for antagonists for novel receptors, and for identification of novel classes of antagonists for well-known receptors. Ligand binding mass screening can be adapted for very high throughput. In order for mass screening to be useful, it is necessary to strictly define the binding characteristics for a compound to be considered a putative receptor antagonist. In practice, we have found that synthetic pursuit of a compound with a K_i of ± 1 uM is likely to lead down a blind alley unless very good evidence for specificity is available. Even potent competitors for binding should be thoroughly evaluated in assays of biological activity before a synthetic program is initiated in earnest.     

A Screening Strategy Based on Differential Binding of Ligand to Receptor and to Binding Proteins: Screening for Compounds Interacting with Corticotrophin-Releasing Factor-Binding Protein

The ligand-receptor interaction has been commonly used in development of high throughput screening assays for new drugs. In some cases, an endogenous ligand interacts not only with membrane receptors but also with soluble binding proteins. Corticotrophin-releasing factor (CRF) is an important stress neurotransmitter/hormone involved in both the central and peripheral nervous systems. CRF exerts its function by interacting with CRFR1 and CRFR2 receptors. In addition, CRF-binding protein (CRF-BP) binds CRF with high affinity. Accordingly, CRF-BP has been suggested to play an important role in modulating CRF function. Based on the potential involvement of CRF-BP in many neurological disorders, it is desirable to develop a screening assay to look for drugs that either mimic or interfere with CRF binding to CRF-BP. An assay was developed to monitor the interactions of radiolabeled CRF with human/rat CRF-BP and the mouse CRFR1 (mCRFR1) receptor. By carefully examining the binding characteristics of radiolabeled CRF to mCRFR1, the assay was able to identify compounds that bind to CRF-BP with high affinity and have little or no affinity for mCRFR1 receptors. Based on a mathematical model, we have verified the screening system with several well-characterized CRF ligands that all have different affinities for CRF receptors and CRF-BP.     

Polyelemental,Multicomponent Perovskite Semiconductor Libraries through Combinatorial Screening

Recently, perovskites with multiple cations, metals, and anions have shown very high efficiencies and stabilities for perovskite solar cells. The novel materials frequently exhibit unexpected and beneficial properties, outperforming simpler counterparts. The trend of increasing material complexity requires a systematic strategy to explore polyelemental “multicomponent engineering.” Here, a combinatorial approach is introduced to generate all possible, unique combinations within a set of available components. Thus, with each new component, the combinatorial framework can generate the full theoretical parameter space. Based on reported components, the experimental parameter space can then be identified. The exceptional material versatility of perovskites is suited for high‐throughput screening, machine‐learning, or data mining, laying the foundation for a “perovskite genome project” that thoroughly catalogues the entire material family for desired properties. This can provide the framework for theoretical simulations toward understanding the fundamental working principles of perovskite materials enabling the “next big thing” after perovskites. Finally, informed by literature, a promising candidate list for future material exploration is presented including novel organic‐free, Pb‐free, and all‐inorganic perovskites. These compounds are primary contenders toward stable, high efficiency, and reproducible materials for rapid industrialization of perovskite solar cells, lasers, light‐emitting diodes, photo detectors, or particle detectors.     

Endogenous Inhibitor of Ligand Binding to the Muscarinic Acetylcholine Receptor

An endogenous inhibitor of L-[3H]quinuclinidinyl benzilate binding to the brain muscarinic acetylcholine receptor was identified. [3H]Quinuclinidinyl benzilate binding to rat brain synaptosomes was measured using a filtration assay. The inhibitor was prepared from several calf tissues and was found in highest specific activity in thymus. The loss of binding activity was slow, requiring a 30-40 min preincubation of the synaptosomes with the inhibitor, and reversed by removing the inhibitor by washing the membranes. Scatchard analysis of the binding data showed that the inhibition was noncompetitive resulting from both a decrease in affinity and a decrease in the number of binding sites. Zn2+ was required in low concentrations for this effect. Muscarinic acetylcholine receptor in synaptic membranes and in membranes free of most peripheral membrane proteins was still sensitive to inhibition. Preliminary characterization of the inhibitory molecule showed that it is of low molecular weight, moderately heat-stable, and acidic. The inhibitor was inactivated by reagents that are nonspecific for nucleophiles, but not by reagents specific for primary amine or thiol groups.     

From Combinatorial Libraries to MHC Ligand Motifs, T-cell Superagonists and Antagonists

Complete experimental data sets of HLA-ligand motifs and T-cell recognition patterns can be derived from combinatorial peptide libraries. These data provide the exact molecular basis for a fast development of synthetic vaccines, T-cell superagonists and non-peptide antagonists. Patient-specific peptides, peptidomimetics and vaccines of highest reactivity can be derived directly from the data sets via our prediction programme EPIPREDICT. The resulting lead structures may be developed into valuable diagnostics and therapeutic tools for the treatment of viral infections, autoimmune diseases and tumors. As one example, antibody and T cell recognition in the intestinal auto-immune disease, coeliac disease was investigated in more detail concerning the deamidation of gamma-gliadin peptides by tissue transglutaminase 9tTG) leading to autoreactive peptides specific for HLA-DQA1*0501, DQB1*0201.     

Dynamics of the Ligand Binding Domain Layer during AMPA Receptor Activation

Ionotropic glutamate receptors are postsynaptic tetrameric ligand-gated channels whose activity mediates fast excitatory transmission. Glutamate binding to clamshell-shaped ligand binding domains (LBDs) triggers opening of the integral ion channel, but how the four LBDs orchestrate receptor activation is unknown. Here, we present a high-resolution x-ray crystal structure displaying two tetrameric LBD arrangements fully bound to glutamate. Using a series of engineered metal ion trapping mutants, we showed that the more compact of the two assemblies corresponds to an arrangement populated during activation of full-length receptors. State-dependent cross-linking of the mutants identified zinc bridges between the canonical active LBD dimers that formed when the tetramer was either fully or partially bound by glutamate. These bridges also stabilized the resting state, consistent with the recently published full-length apo structure. Our results provide insight into the activation mechanism of glutamate receptors and the complex conformational space that the LBD layer can sample.     

Ligand Based Virtual Screening Using Self-organizing Maps

The Protein Journal - Conventional drug discovery methods rely primarily on in-vitro experiments with a target molecule and an extensive set of small molecules to choose the suitable ligand. The...     

Anions Mediate Ligand Binding in Adineta vaga Glutamate Receptor Ion Channels

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Highlights? The AvGluR1 LBD is a hybrid structure with iGluR prokaryotic and eukaryotic features ? AvGluR1 binds hydrophobic amino acids as well as glutamate ? Chloride ions acts as surrogate ligand atoms in the Ala, Ser, and Met complexes ? The AvGluR1 LBD assembles as a dimer but with very low affinity     

褪黑激素受体基因的研究进展

褪黑激素通过与药理学特异性的高亲和性G-蛋白耦联受体相结合来发挥其生物学功能。本文介绍了褪黑激素受体的结构、功能与调控、褪黑激素受体基因的克隆及基因结构、褪黑激素受体基因的发育性表达与作用、褪黑激素受体基因的定位与多态性分析,并讨论了该基因与繁殖季节性的关系。 Abstract:Melatonin exerts its biological effects through pharmacological specific,high affinity G protein-coupled receptors.This review introduced the structure,function,and regulation of melatonin receptor,the cloning and structure,developmental expression,mapping and polymorphism of melatonin receptor gene.The relationship between melatonin receptor gene and reproductive seasonality was also discussed.     

A Method for Dissecting Two Site Receptor Interactions in Ligand Binding Studies

Abstract

A general model has been developed describing the relationship between the measured (IC₅₀) and absolute affinities (K_I), observed in radioligand binding studies when two ligands, one radioactive, interact with two receptors or binding sites. The model shows the dependence of the IC₅₀'s upon the concentration of radioligand for any combinations of the absolute affinities of the radioligand (K_d's) and the displacing ligand (K_I's). By constraining the affinities of the two ligands for the sites, five special cases of the general model can be described that model all possible 'selectivities' the ligands may have for the sites. The properties of these five cases can be exploited experimentally to probe the nature of the ligand/site interactions by the simple expedient of constructing a number of displacement curves at different radioligand concentrations. The method has been tested experimentally in three situations where two ligand/two site interactions occur, and is shown to be a useful technique to qualitatively examine the underlying binding reactions.     

High-resolution Structures of the Ligand Binding Domain of the Wild-type Bacterial Aspartate Receptor

The high-resolution structures of the wild-type periplasmic domain of the bacterial aspartate receptor have been determined in the absence and presence of bound aspartate to 1.85 and 2.2 Å resolution, respectively. As we reported earlier, in the refined structure of the complexed form of the crosslinked cysteine mutant receptor, the binding of the aspartate at the first site was mediated through four bridging water molecules while the second site showed an occupant electron density that best fit a sulfate group, which was present in the crystallization solution at high concentration. In the wild-type periplasmic domain structure two aspartate residues are bound per dimer, but with different occupancies. There exists a “strong” aspartate-binding site whose binding is again mediated by four water molecules while the second site contains aspartate whoseB-factor is about 10% higher, signifying weaker binding. The interaction between the second, “weaker” aspartate with the three ligand-binding arginine side-chains is slightly different from the first site. The major difference is that there are three water molecules mediating the binding of aspartate at the second site, whereas in the first site there are four bridging water molecules. The fact that aspartate-complexed crystals of the wild-type were grown with a large excess aspartate while the cross-linked crystals were grown with equal molar aspartate may explain the difference in the stoichiometry observed. The conservation of the four bridging water molecules in the strong aspartate site of both the cross-linked and wild-type periplasmic domain may reflect an important binding motif.The periplasmic domain in the apo form is a symmetrical dimer, in which each of the subunits is equivalent, and the two aspartate binding sites are identical. Upon the binding of aspartate, the subunits are no longer symmetrical. The main difference between the aspartate-bound and unbound forms is in a small, rigid-body rotation between the subunits within a dimer. The rotation is similar in both direction and magnitude in the crosslinked and wild-type periplasmic domains. The presence of the second aspartate in the wild-type structure does not make any additional rotation compared to the single-site binding. The conservation of the small angular changein vitrosuggests that the inter-subunit rotation may have relevance to the understanding of the mechanism of transmembrane signal transductionin vivo.     

Dimerization of Corticotropin-Releasing Factor Receptor Type 1 Is Not Coupled to Ligand Binding

As described previously, receptor dimerization of G protein-coupled receptors may influence signaling, trafficking, and regulation in vivo. Up to now, most studies aiming at the possible role of receptor dimerization in receptor activation and signal transduction are focused on class A GPCRs. In the present work, the dimerization behavior of the corticotropin-releasing factor receptor type 1 (CRF₁R), which belongs to class B of GPCRs and plays an important role in coordination of the immune response, stress, and learning behavior, was investigated by using fluorescence resonance energy transfer (FRET). For this purpose, we generated fusion proteins of CRF₁R tagged at their C-terminus to a cyan or yellow fluorescent protein, which can be used as a FRET pair. Binding studies verified that the receptor constructs were able to bind their natural ligands in a manner comparable with the wild-type receptor, whereas cAMP accumulation proved the functionality of the constructs. In microscopic studies, a dimerization of the CRF₁R was observed, but the addition of either CRF-related agonists or antagonists did not show any dose-related increase of the observed FRET signal, indicating that the dimer-monomer ratio is not changed on addition of ligand.     

Characterization of Ligand Binding to the Cannabinoid Receptor of Rat Brain Membranes Using a Novel Method: Application to Anandamide

Abstract: Ligand binding to the cannabinoid receptor of brain membranes has been characterized using [³H]CP 55,940 and the Multiscreen Filtration System. Binding of [³H]CP 55,940 is saturable and reaches equilibrium by 45 min at room temperature. At a concentration of 10 µg of membrane protein/well, the K _D for [³H]CP 55,940 is 461 p M and the B _max is 860 fmol/mg of protein. The apparent K _D of [³H]CP 55,940 is dependent upon tissue protein concentration, increasing to 2,450 p M at 100 µg of membrane protein. Binding of [³H]CP 55,940 is dependent upon the concentration of bovine serum albumin in the buffer; the highest ratio of specific to nonspecific binding occurs between 0.5 and 1.0 mg/ml. The K _i of anandamide, a putative endogenous ligand of the cannabinoid receptor, is 1.3 µ M in buffer alone and 143 n M in the presence of 0.15 m M phenylmethylsulfonyl fluoride. When [¹⁴C]anandamide is incubated with rat forebrain membranes at room temperature, it is degraded to arachidonic acid; the hydrolysis is inhibited by 0.15 m M phenylmethylsulfonyl fluoride. These results support the hypothesis that anandamide is a high-affinity ligand of the cannabinoid receptor and that it is rapidly degraded by membrane fractions.