Understanding the Selectivity Mechanism of the Human Asialoglycoprotein Receptor (ASGP-R) toward Gal- and Man-type Ligands for Predicting Interactions with Exogenous Sugars

A practical approach for addressing the computer simulation of protein-carbohydrate interactions is described here. An articulated computational protocol was set up and validated by checking its ability to predict experimental data, available in the literature, and concerning the selectivity shown by the Carbohydrate Recognition Domain (CRD) of the human asialoglycoprotein receptor (ASGP-R) toward Gal-type ligands. Some required features responsible for the interactions were identified. Subsequently the same protocol was applied to monomer sugar molecules that constitute the building blocks for alginates and ulvans. Such sugar polymers may supply a low-cost source of rare sugars with a potential impact on several industrial applications, from pharmaceutical to fine chemical industry. An example of their applicative exploitation could be given by their use in developing biomaterial with adhesion properties toward hepatocytes, through interaction with the ASGP-R. Such a receptor has been already proposed as a target for exogenous molecules, specifically in the case of hepatocytes, for diagnostic and therapeutic purposes. The DOCK5.2 program was used to search optimal locations of the above ligands of interest into CRD binding site and to roughly estimate interaction energies. Finally, the binding ΔG of theoretical protein-ligand complexes was estimated by using the DelPhi program in which the solvation free energy is accounted for with a continuum solvent model, by solving the Poisson-Boltzmann equation. The structure analysis of the obtained complexes and their ΔG values suggest that one of the sugar monomers of interest shows the desired characteristics.     

Chemical Biology for Understanding Matrix Metalloproteinase Function

The matrix metalloproteinase (MMP) family has long been associated with normal physiological processes such as embryonic implantation, tissue remodeling, organ development, and wound healing, as well as multiple aspects of cancer initiation and progression, osteoarthritis, inflammatory and vascular diseases, and neurodegenerative diseases. The development of chemically designed MMP probes has advanced our understanding of the roles of MMPs in disease in addition to shedding considerable light on the mechanisms of MMP action. The first generation of protease‐activated agents has demonstrated proof of principle as well as providing impetus for in vivo applications. One common problem has been a lack of agent stability at nontargeted tissues and organs due to activation by multiple proteases. The present review considers how chemical biology has impacted the progress made in understanding the roles of MMPs in disease and the basic mechanisms of MMP action.     

Effect of the degree of branching on the glass transition temperature of polyesters

Glass transition temperature dependence on the branching degree can be empirically estimated by excluding additional effects on this parameter as molecular weight distribution, end group interactions or crystallization. In this communication aliphatic–aromatic polyesters with a well defined degree of branching between 0% (linear) and 50% (hyperbranched) are investigated by differential scanning calorimetry. The hydrogen bonding effect of the OH-terminal groups was successfully extracted from the pure branching effect by protection of the end-functionalities. Fractionation of samples with variation of the branching degree and end-functionalities led to series of narrowly distributed molar masses. The dependence of the molecular weight on the glass transition temperature for different branching degrees was calculated and compared for polar and non-polar end groups.     

Studies of the antenna effect in polymer molecules. 29. Synthesis and properties of poly[sodium styrene sulfonate-co-(4-acryolyloxyphenyl)-10,15,20-tritolylporphyrin] in aqueous solution

The novel water soluble antenna polyelectrolyte: poly[sodium styrene sulfonate-co-(4-acryolyloxyphenyl)-10,15,20-tritolylporphyrin] (PSSS-Po) was synthesised, and its photophysical and photochemical properties were studied. Solubilisation of the various molecular probes such as pyrene or perylene in aqueous solution of the PSSS-Po proved that the polymer chain adopts the compact conformation. The interior of the polymer pseudomicelle is significantly less polar than water. The effective quenching of polymeric porphyrin fluorescence by sulfopropyl viologen (SPV) can be explained considering the possibility of electron transfer from the singlet-excited state of Po to SPV. This has been supported by measuring an absorption spectrum for PSSS-Po/SPV system after selective irradiation of Po chromophores. The formation of the new absorption bands characteristic for SPV⁻ radical anion indicated that the charge separation was achieved in that system.     

Dispersing Behavior of Hydroxyapatite Powders Produced by Wet-Chemical Synthesis

Three hydroxyapatite powders with different surface properties were produced by wet-chemical synthesis and characterized. The electrokinetic properties of powders dispersed in water were investigated by electroacoustic spectroscopy measurements. The different surface reactivity (pH_iep and ζ potential versus pH curves) was related to the interplay of dissolution and adsorption of Ca²⁺ ions. With a view toward the preparation of porous bodies by sponge impregnation, the behavior of powder suspensions was studied. Four deflocculants were tested, and the optimum dispersing conditions for each powder were found. Anionic polyelectrolytes resulted in the best effective dispersing agent, with different optimum amounts added to the suspensions.     

Electrochemical preparation and redox/ion exchange properties of polypyrrole in aqueous sodium hexafluoroaluminate

Electrodeposition and redox switching performance of polypyrrole in aqueous solution of sodium hexafluoroaluminate are described. An incorporation of NaAlF₆²⁻ into the polymer phase is indicated by the EQCM analysis of electrodeposition. A SEM micrograph shows a characteristic morphology of the polymer layer. A mechanism of the redox process of polypyrrole is discussed based on CV and EQCM results involving the measurements performed as a function of a time scale of the redox cycle and a life time of the electrode. Structure determining interactions between polymer sites and counterions are indicated. Participations of ion-pair counterion, co-ion, salt, water, oxygen in the redox process of polypyrrole are discussed. A slow irreversible rearrangement in the structure/composition, inducing a change in the mechanism of the reversible redox process, is postulated to occur during the reduction process of the virgin anion-exchanging polypyrrole. Long time scale processes were observed to result in cation exchange properties accompanied by a substantial decrease in redox activity and/or CV currents of the polypyrrole electrode. The performance of the primary hexafluoroaluminate counterion electrode, prepared in aqueous solution of sodium hexafluoroaluminate, is compared to the secondary hexafluoroaluminate counterion electrode, prepared in a presence of the sodium chloride solution. In general, the CV and EQCM characteristics of the two system are similar due to pronounced contribution of the bathing electrolyte to the performance of the polymer electrode.     

Rational design and selection of bivalent peptide ligands of thrombin incorporating P4-P1 tetrapeptide sequences: from good substrates to potent inhibitors

The tetrapeptide Phe-Asn-Pro-Arg is a structurally optimized sequence for binding to the active site of thrombin. By conjugating this tetrapeptide or some variants to a C-terminal fragment of hirudin, we were able to generate a series of new bivalent inhibitors of thrombin containing only genetically encodable natural amino acids. We found that synergistic binding to both the active site and an exosite of thrombin can be enhanced through substitutions of amino acid residues at the P3 and P3' sites of the active-site directed sequence, Phe(P4)-Xaa(P3)-Pro(P2)-Arg(P1)-Pro(P1')-Gln(P2')-Yaa(P3'). Complementary to rational design, a phage library was constructed to explore further the residue requirements at the P4, P3 and P3' sites for bivalent and optimized two-site binding. Very significantly, panning of the phage library has led to thrombin-inhibitory peptides possessing strong anti-clotting activities in the low nanomolar range and yet interfering only partially the catalytic active site of thrombin. Modes of action of the newly discovered bivalent inhibitors are rationalized in light of the allosteric properties of thrombin, especially the interplay between the proteolytic action and regulatory binding occurring at thrombin surfaces remote from the catalytic active site.     

Multimerization of a chimeric anti-CD20 single-chain Fv-Fc fusion protein is mediated through variable domain exchange

A series of single-chain anti-CD20 antibodies was produced byfusing single-chain Fv (scFv) with human IgG1 hinge and Fc regions,designated scFv-Fc. The initial scFv-Fc construct was assembledusing an 18 amino acid (aa) linker between the antibody light-and heavy-chain variable regions, with the Cys residue in theupper hinge region (Kabat 233) mutagenized to Ser. Anti-CD20scFv-Fc retained specific binding to CD20-positive cells andwas active in mediating complement-dependent cytolysis. Size-exclusionHPLC analysis revealed that the purified scFv-Fc included multimericas well as monomeric components. Variant scFv-Fcs were constructedincorporating four different hinges between the scFv and Fcregions, or three different linkers in the scFv domain. Allformed multimers, with the highest level of multimerizationfound in the scFv-Fc with the shortest linker (8 aa). Eliminationof an unusual salt bridge between residues L38 and H89 in theV_L-V_H domain interface failed to reduce the formation of higherorder forms. Structural analysis of the scFv-Fc constructedwith 18 or 8 aa linkers by pepsin or papain cleavage suggestedthe proteins contained a form in which scFv units had cross-pairedto form a `diabody'. Thus, domain exchange or cross-pairingappears to be the basis of the observed multimerization.     

Micro RNA-124a Regulates Lipolysis via Adipose Triglyceride Lipase and Comparative Gene Identification 58

Lipolysis is the biochemical pathway responsible for the catabolism of cellular triacylglycerol (TG). Lipolytic TG breakdown is a central metabolic process leading to the generation of free fatty acids (FA) and glycerol, thereby regulating lipid, as well as energy homeostasis. The precise tuning of lipolysis is imperative to prevent lipotoxicity, obesity, diabetes and other related metabolic disorders. Here, we present our finding that miR-124a attenuates RNA and protein expression of the major TG hydrolase, adipose triglyceride lipase (ATGL/PNPLA2) and its co-activator comparative gene identification 58 (CGI-58/ABHD5). Ectopic expression of miR-124a in adipocytes leads to reduced lipolysis and increased cellular TG accumulation. This phenotype, however, can be rescued by overexpression of truncated Atgl lacking its 3''UTR, which harbors the identified miR-124a target site. In addition, we observe a strong negative correlation between miR-124a and Atgl expression in various murine tissues. Moreover, miR-124a regulates the expression of Atgl and Cgi-58 in murine white adipose tissue during fasting as well as the expression of Atgl in murine liver, during fasting and re-feeding. Together, these results point to an instrumental role of miR-124a in the regulation of TG catabolism. Therefore, we suggest that miR-124a may be involved in the regulation of several cellular and organismal metabolic parameters, including lipid storage and plasma FA concentration.