Structural modeling of high-affinity thyroid receptor-ligand complexes

Understanding the molecular basis of the binding modes of natural and synthetic ligands to nuclear receptors is fundamental to our comprehension of the activation mechanism of this important class of hormone regulated transcription factors and to the development of new ligands. Thyroid hormone receptors (TR) are particularly important targets for pharmaceuticals development because TRs are associated with the regulation of metabolic rates, body weight, and circulating levels of cholesterol and triglycerides in humans. While several high-affinity ligands are known, structural information is only partially available. In this work we obtain structural models of several TR-ligand complexes with unknown structure by docking high affinity ligands to the receptors` ligand binding domain with subsequent relaxation by molecular dynamics simulations. The binding modes of these ligands are discussed providing novel insights into the development of TR ligands. The experimental binding free energies are reasonably well-reproduced from the proposed models using a simple linear interaction energy free-energy calculation scheme.

Pharmacophore-based 3D QSAR studies on a series of high affinity 5-HT(1A) receptor ligands

5-HT(1A) receptor antagonists have been employed to treat depression, but the lack of structural information on this receptor hampers the design of specific and selective ligands. In this study, we have performed CoMFA studies on a training set of arylpiperazines (high affinity 5-HT(1A) receptor ligands) and to produce an effective alignment of the data set, a pharmacophore model was produced using Galahad. A statistically significant model was obtained, indicating a good internal consistency and predictive ability for untested compounds. The information gathered from our receptor-independent pharmacophore hypothesis is in good agreement with results from independent studies using different approaches. Therefore, this work provides important insights on the chemical and structural basis involved in the molecular recognition of these compounds. (C) 2010 Elsevier Masson SAS. All rights reserved.

Cathepsin X cleaves the beta 2 cytoplasmic tail of LFA-1 inducing the intermediate affinity form of LFA-1 and alpha-actinin-1 binding

The motility of T cells depends on the dynamic spatial regulation of integrin-mediated adhesion and de-adhesion. Cathepsin X, a cysteine protease, has been shown to regulate T-cell migration by interaction with lymphocyte function associated antigen-1 (LFA-1). LFA-1 adhesion to the ICAM-1 is controlled by the association of actin-binding proteins with the cytoplasmic tail of the beta(2) chain of LFA-1. Cleavage by cathepsin X of the amino acid residues S(769), E(768) and A(767) from the C-terminal of the beta(2) cytoplasmic tail of LFA-1 is shown to promote binding of the actin-binding protein alpha-actinin-1. Furthermore, cathepsin X overexpression reduced LFA-1 clustering and induced an intermediate affinity LFA-1 conformation that is known to associate with a-actinin-1. increased levels of intermediate affinity LFA-1 resulted in augmented cell spreading due to reduced attachment of T cells to the ICAM-1-coated surface. Gradual cleavage of LFA-1 by cathepsin X enables the transition between intermediate and high affinity LFA-1, an event that is crucial for effective T-cell migration.

Under flow impedimetric measurements using magnetic particles for label-free detection affinity target

The necessity to adapt sensors based on electrochemical techniques for high throughput analysis control increases the interest to develop new analytical systems able to perform measurements under buffer now. In this report we explored the possibility of employing a new system to make impedimetric measurements to detect the interaction between proteins and small molecules. The well-known biotin-streptavidin interaction was adopted to evaluate the proposed assembly. This system allows us to perform experiments under flow. Magnetic beads functionalized with streptavidin were used and first characterized using AFM and FTIR. Non-faradic impedance spectroscopy allowed the detection of the biotin-streptavidin interaction. Using our new system and under a flow of PBS buffer, 5 10-5 M of biotin was detected with a stable signal. (c) 2007 Elsevier B.V. All rights reserved.

Immobilized analogues of sunflower trypsin inhibitor-1 constitute a versatile group of affinity sorbents for selective isolation of serine proteases

Sunflower trypsin inhibitor-1 (SFI-1), a natural 14-residue cyclic peptide, and some of its synthetic acyclic variants are potent protease inhibitors displaying peculiar inhibitory profiles. Here we describe the synthesis and use of affinity sorbents prepared by coupling SFTI-1 analogues to agarose resin. Chymotrypsinand trypsin-like proteases could then be selectively isolated from pancreatin; similarly, other proteases were obtained from distinct biological sources. The binding capacity of [Lys5]-SFTI-1-agarose for trypsin was estimated at over 10 mg/mL of packed gel. SFTI-1-based resins could find application either to improve the performance of current purification protocols or as novel protease-discovery tools in different areas of biological investigation. (C) 2009 Elsevier B.V. All rights reserved.

Specificity and affinity motifs for Grb2 SH2-ligand interactions

Protein–protein interactions are often mediated by the recognition of short continuous amino acid stretches on target proteins by specific binding domains. Affinity-based selection strategies have successfully been used to define recognition motifs for a large series of such protein domains. However, in many biological systems specificity of interaction may be of equal or greater importance than affinity. To address this issue we have developed a peptide library screening technology that can be used to directly define ligands for protein domains based on both affinity and specificity of interaction. We demonstrate the value of this approach by the selection of peptide ligands that are either highly specific for the Grb2 Src homology 2 (SH2) domain or that are cross-reactive between a group of related SH2 domains. Examination of previously identified physiological ligands for the Grb2 SH2 domain suggests that for these ligands regulation of the specificity of interaction may be an important factor for in vivo ligand selection.

Exploiting affinity propagation for energy-efficient information discovery in sensor networks

Wireless sensor networks (WSN) are attractive for information gathering in large-scale data rich environments. Emerging WSN applications require dissemination of information to interested clients within the network requiring support for differing traffic patterns. Further, in-network query processing capabilities are required for autonomic information discovery. In this paper, we formulate the information discovery problem as a load-balancing problem, with the combined aim being to maximize network lifetime and minimize query processing delay. We propose novel methods for data dissemination, information discovery and data aggregation that are designed to provide significant QoS benefits. We make use of affinity propagation to group "similar" sensors and have developed efficient mechanisms that can resolve both ALL-type and ANY-type queries in-network with improved energy-efficiency and query resolution time. Simulation results prove the proposed method(s) of information discovery offer significant QoS benefits for ALL-type and ANY-type queries in comparison to previous approaches.

Ni2+-based immobilized metal ion affinity chromatography of lactose operon repressor protein from Escherichia coli

A two-step chromatographic sequence is described for the purification of native lactose operon repressor protein from Escherichia coli cells. The first step involves Ni2+-based immobilized metal ion affinity chromatography of the soluble cytoplasmic extract. This method provides superior speed, resolution and yield than the established phosphocellulose cation-exchange chromatographic procedure. Anion-exchange chromatography is used for further purification to >95% purity. The identity and purity of the lactose repressor protein were demonstrated using sodium dodecylsulphate polyacrylamide electrophoresis, crystallization, tryptic finger-printing mass spectrometry, and inducer binding assays. The purified lac repressor exhibited inducer sensitivity for operator DNA binding and undergoes a conformational change upon inducer binding. By all these extensive biochemical criteria, the purified protein behaves exactly as that described for the Escherichia coli lactose operon repressor.

Apparent in vivo Δ-6 desaturase activity, efficiency, and affinity are affected by total dietary C18 PUFA in the freshwater fish Murray cod

Dietary fatty acids are known to modulate fatty acid metabolism in fish. However, the innate capability of fish to bioconvert short chain fatty acids to health promoting long chain fatty acids (LCPUFA) is insufficient to compensate for a reduced dietary intake. While many studies have focused on the dietary regulation of the fatty acid bioconversion pathways, there is little known regarding the effects of the dietary levels of C18 polyunsaturated fatty acids (PUFA) on fatty acid metabolism. Here, we show a greater degree of apparent enzyme activity (Δ-6 desaturase) in fish fed a diet with higher amounts of dietary C18 PUFA. In particular, fish receiving high amounts of dietary C18 PUFA had a greater amount of Δ-6 desaturase activity acting on 18:3n-3 than 18:2n-6. However, with the gradual reduction of dietary C18 PUFA there was a shift in substrate preference of Δ-6 desaturase from 18:3n-3 to 18:2n-6. This information will provide valuable insight for the implementation of low fish oil diets, which permit the maintenance of n-3 LCPUFA levels in farmed Murray cod.

Brand affinity and consumer repurchase behaviour : an empirical analysis

This research established a construct termed brand affinity, comprising the measures of anticipation of usage, social attraction, commitment, loyalty, and trust. In the context of a highly uncertain, intermittently available service, it was found that brand affinity had greater influence over consumers' repurchase intentions than the typical antecedents of overall and attribute level satisfaction.

Unification of the copper(I) binding affinities of the metallo-chaperones Atx1, Atox1, and related proteins : Detection probes and affinity standards

Literature estimates of metal-protein affinities are widely scattered for many systems, as highlighted by the class of metallo-chaperone proteins, which includes human Atox1. The discrepancies may be attributed to unreliable detection probes and/or inconsistent affinity standards. In this study, application of the four CuI ligand probes bicinchoninate, bathocuproine disulfonate, dithiothreitol (Dtt), and glutathione (GSH) is reviewed, and their CuI affinities are re-estimated and unified. Excess bicinchoninate or bathocuproine disulfonate reacts with CuI to yield distinct 1:2 chromatophoric complexes [CuIL2] 3- with formation constants β2 = 1017.2 and 1019.8 M-2, respectively. These constants do not depend on proton concentration for pH ≥7.0. Consequently, they are a pair of complementary and stable probes capable of detecting free Cu+ concentrations from 10-12 to 10-19 M. Dtt binds CuI with KD∼10-15 M at pH 7, but it is air-sensitive, and its CuI affinity varies with pH. The CuI binding properties of Atox1 and related proteins (including the fifth and sixth domains at the N terminus of the Wilson protein ATP7B) were assessed with these probes. The results demonstrate the following: (i) their use permits the stoichiometry of high affinity CuI binding and the individual quantitative affinities (KD values) to be determined reliably via noncompetitive and competitive reactions, respectively; (ii) the scattered literature values are unified by using reliable probes on a unified scale; and (iii) Atox1-type proteins bind CuI with sub-femtomolar affinities, consistent with tight control of labile Cu+ concentrations in living cells.

Overcoming interfacial affinity issues in natural fiber reinforced polylactide biocomposites by surface adsorption of amphiphilic block copolymers

This work demonstrates that the interfacial properties in a natural fiber reinforced polylactide biocomposite can be tailored through surface adsorption of amphiphilic and biodegradable poly (ethylene glycol)-b-poly-(L-lactide) (PEG-PLLA) block copolymers. The deposition from solvent solution of PEG-PLLA copolymers onto the fibrous substrate induced distinct mechanisms of molecular organization at the cellulosic interface, which are correlated to the hydrophobic/hydrophilic ratios and the type of solvent used. The findings of the study evidenced that the performance of the corresponding biocomposites with polylactide were effectively enhanced by using these copolymers as interfacial coupling agents. During the fabrication stage, diffusion of the polylactide in the melt induced a change in the environment surrounding block copolymers which became hydrophobic. It is proposed that molecular reorganization of the block copolymers at the interface occurred, which favored the interactions with both the hydrophilic fibers and hydrophobic polylactide matrix. The strong interactions such as intra- and intermolecular hydrogen bonds formed across the fiber−matrix interface can be accounted for the enhancement in properties displayed by the biocomposites. Although the results reported here are confined, this concept is unique as it shows that by tuning the amphiphilicity and the type of building blocks, it is possible to control the surface properties of the substrate by self-assembly and disassembly of the amphiphiles for functional materials.