Crystal structure of an antiviral ankyrin targeting the HIV-1 capsid and molecular modeling of the ankyrin-capsid complex

Ankyrins are cellular repeat proteins, which can be genetically modified to randomize amino-acid residues located at defined positions in each repeat unit, and thus create a potential binding surface adaptable to macromolecular ligands. From a phage-display library of artificial ankyrins, we have isolated Ank^GAG1D4, a trimodular ankyrin which binds to the HIV-1 capsid protein N-terminal domain (NTD^CA) and has an antiviral effect at the late steps of the virus life cycle. In this study, the determinants of the Ank^GAG1D4-NTD^CA interaction were analyzed using peptide scanning in competition ELISA, capsid mutagenesis, ankyrin crystallography and molecular modeling. We determined the Ank^GAG1D4 structure at 2.2 Å resolution, and used the crystal structure in molecular docking with a homology model of HIV-1 capsid. Our results indicated that NTD^CA alpha-helices H1 and H7 could mediate the formation of the capsid-Ank^GAG1D4 binary complex, but the interaction involving H7 was predicted to be more stable than with H1. Arginine-18 (R18) in H1, and R132 and R143 in H7 were found to be the key players of the Ank^GAG1D4-NTD^CA interaction. This was confirmed by R-to-A mutagenesis of NTD^CA, and by sequence analysis of trimodular ankyrins negative for capsid binding. In Ank^GAG1D4, major interactors common to H1 and H7 were found to be S45, Y56, R89, K122 and K123. Collectively, our ankyrin-capsid binding analysis implied a significant degree of flexibility within the NTD^CA domain of the HIV-1 capsid protein, and provided some clues for the design of new antivirals targeting the capsid protein and viral assembly.     

Amperometric bienzyme electrode for l-carnitine

An electrochemical sensor with two soluble enzymes allows assay of 0.1–10 mM, l- carnitine with an accuracy of 2%. The assay takes about 2 min. The first enzyme, carnitine dehydrogenase, catalyzes the oxidation of l-carnitine by NAD⁺. The NADH formed is oxidized by hexacyanoferrate(III) in a reaction catalyzed by diaphorase, and the hexacyanoferrate(II) produced is oxidized by electrolysis at 0.3 V. The sensor can be used for several days.     

Slow flows of yield stress fluids: yielding liquids or flowing solids?

Yield stress fluids (YSF) exhibit strongly non-linear rheological characteristics. As a consequence, they develop original flow features (as compared to simple fluids) under various boundary conditions. This paper reviews and analyzes the characteristics of a series of slow flows (just beyond yielding) under more or less complex conditions (simple shear flow, flow through a cavity, dip-coating, blade-coating, Rayleigh-Taylor instability, Saffman-Taylor instability) and highlights some of their common original characteristics: (i) a transition from a solid regime to a flowing regime which does not correspond to a true “liquid state,” the flow in this regime may rather be seen as a succession of solid states during very large deformation; (ii) a strong tendency to localization of the yielded regions in some small region of the material while the rest of the material undergoes some deformation in its solid state; (iii) the deformation of YSF interface with another fluid, in the form of fingers tending to penetrate the material via a local liquefaction process. Finally, these observations suggest that slow flows of YSF are a kind of extension of plastic flows for very large deformations and without irreversible changes of the structure. This suggests that the field of plasticity and the field of slow flows of YSF could benefit from each other.     

<Emphasis Type="Italic">Q</Emphasis>-systems as Cluster Algebras II: Cartan Matrix of Finite Type and the Polynomial Property

We define the cluster algebra associated with the Q-system for the Kirillov–Reshetikhin characters of the quantum affine algebra \({U_q(\widehat{\mathfrak {g}})}\) for any simple Lie algebra \({\mathfrak {g}}\), generalizing the simply-laced case treated in (Kedem in Q-systems as cluster algebras. arXiv:0712.2695 [math.RT], 2007). We describe some special properties of this cluster algebra, and explain its relation to the deformed Q-systems which appeared on our proof of the combinatorial-KR conjecture. We prove that the polynomiality of the cluster variables in terms of the “initial cluster seeds”, including solutions of the Q-system, is a consequence of the Laurent phenomenon and the boundary conditions. We also define the cluster algebra associated with T-systems, or general systems which take the form of T-systems in the bipartite case. Such systems describe the recursion relations satisfied by the q-characters of Kirillov–Reshetikhin modules and also appear in the categorification picture in terms of preprojective algebras of Geiss, Leclerc and Schröer. We give a formulation of both Q-systems and generalized T-systems as cluster algebras with coefficients. This provides a proof of the polynomiality of solutions of all such “generalized T-systems” with appropriate boundary conditions.     

Inorganic solid Li ion conductors: An overview

This short review presents the state-of-the-art knowledge on crystalline, composite and amorphous inorganic solid lithium ion conductors, which are of interest as potential solid electrolytes in lithium batteries and might replace the currently used polymeric lithium ion conductors. The discussion of crystalline Li ion conductors includes perovskite-type Lithium Lanthanum Titanates, NASICON-type, LiSICON- and Thio-LiSICON-type Li ion conductors, as well as garnet-type Li ion conducting oxides. The part on composite Li ion conductors discusses materials containing oxides and mesoporous oxides. In the amorphous Li ion conductor part, mechanical attrition of Li compounds, oxide and sulfide-based glasses as well as LIPON and related systems are presented.     

Silylated Melamine and Cyanuric Acid as Precursors for Imprinted and Hybrid Silica Materials with Molecular Recognition Properties

Imprinted materials : Monosilylated derivatives of melamine and cyanuric acid are used in the preparation of hybrid silica. The assembly of the melamine and cyanuric acid moieties through molecular recognition properties is the key factor in building a bridged silsesquioxane and an imprinted hybrid silica (see picture).