Binding motifs of silver in prion octarepeat model peptides: a joint ion mobility, IR and UV spectroscopies, and theoretical approach

Transition metal-ion complexation is essential to the function and structural stability of many proteins. We studied silver complexation with the octarepeat motif ProHisGlyGlyGlyTrpGlyGln of the prion protein, which shows competitive sites for metal chelation including amide, indole and imidazole groups. This octapeptide is known as a favourable transition metal binding site in prion protein. We used ion mobility spectrometry (IMS), infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory calculations (DFT) to identify the binding motifs of a silver cation on HisGlyGlyGlyTrp peptide as well as on peptide subsequences. Ultra-violet photodissociation (UVPD) and collision induced dissociation mass spectrometry together with the time-dependent density functional method was then exploited to study the influence of binding sites on optical properties and on the ground and excited states reactivity of the peptide. We show that the metal cation is bound to the π-system of the indole group and a nitrogen atom of the imidazole group and that charge transfers from the indole group to the silver cation occur in excited electronic states.     

Fixed-rank matrix factorizations and Riemannian low-rank optimization

Motivated by the problem of learning a linear regression model whose parameter is a large fixed-rank non-symmetric matrix, we consider the optimization of a smooth cost function defined on the set of fixed-rank matrices. We adopt the geometric framework of optimization on Riemannian quotient manifolds. We study the underlying geometries of several well-known fixed-rank matrix factorizations and then exploit the Riemannian quotient geometry of the search space in the design of a class of gradient descent and trust-region algorithms. The proposed algorithms generalize our previous results on fixed-rank symmetric positive semidefinite matrices, apply to a broad range of applications, scale to high-dimensional problems, and confer a geometric basis to recent contributions on the learning of fixed-rank non-symmetric matrices. We make connections with existing algorithms in the context of low-rank matrix completion and discuss the usefulness of the proposed framework. Numerical experiments suggest that the proposed algorithms compete with state-of-the-art algorithms and that manifold optimization offers an effective and versatile framework for the design of machine learning algorithms that learn a fixed-rank matrix.     

Double-structured ultrasonic high frequency reactor using an optimised slant bottom

The present work has been carried out in order to design a new type of ultrasonic reactor consisting of a double-structured tank. The inner working compartment is built with a slant bottom to allow a better ultrasonic transmission. This paper reports the effect of the inclination angle on acoustic efficiency for several different plates, e.g. two plates made of glass (2 mm and 3 mm thickness) and one made of PVC (3 mm thickness). The acoustic efficiency was determined as the ratio of the signal measured by a hydrophone in the presence of the plate to that signal in the absence of the plate. Having optimised the system, the ultrasonic powers in the inner and the outer compartments of the slant bottom reactor were determined by hydrogen peroxide dosimetry.     

Borrowing hydrogen: a catalytic route to C-C bond formation from alcohols

Ruthenium complexes have been shown to perform efficient transfer hydrogenation reactions between alcohols and alkenes; in combination with an in situ Wittig reaction, indirect formation of C-C bonds has been achieved from alcohols.     

Radical Anions of Oxidized vs. Reduced Oxytocin: Influence of Disulfide Bridges on CID and Vacuum UV Photo-Fragmentation

The nonapeptide oxytocin (OT) is used as a model sulfur-containing peptide to study the damage induced by vacuum UV (VUV) radiations. In particular, the effect of the presence (or absence in reduced OT) of oxytocin’s internal disulfide bridge is evaluated in terms of photo-fragmentation yield and nature of the photo-fragments. Intact, as well as reduced, OT is studied as dianions and radical anions. Radical anions are prepared and photo-fragmented in two-color experiments (UV?+?VUV) in a linear ion trap. VUV photo-fragmentation patterns are analyzed and compared, and radical-induced mechanisms are proposed. The effect of VUV is principally to ionize but secondary fragmentation is also observed. This secondary fragmentation seems to be considerably enabled by the initial position of the radical on the molecule. In particular, the possibility to form a radical on free cysteines seems to increase the susceptibility to VUV fragmentation. Interestingly, disulfide bridges, which are fundamental for protein structure, could also be responsible for an increased resistance to ionizing radiations.

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Transesterification catalysts to improve clay exfoliation in synthetic biodegradable polyester nanocomposites

We report here on the melt intercalation preparation of polymer/clay nanocomposites based on three commercial synthetic biodegradable polyesters: EastarBio Ultra, Ecoflex, and Bionolle, respectively. The montmorillonite clay addition is performed either by direct dispersion of Cloisite 30B in the polyester matrix or by dispersing a “PCL-grafted Cloisite 30B” masterbatch in the biodegradable polyesters. All obtained nanocomposites display an intercalated morphology as attested by X-ray diffraction measurements. The various analyses clearly show that the Bionolle (BIO) matrix gives the best results. Morphological characterization and mechanical properties of these nanocomposites also show that the “masterbatch route” leads to poor results as a consequence of the very low compatibility between the poly(ε-caprolactone) (PCL) of the masterbatch and the three other polyester matrices. In a second part, nanocomposites based on the BIO matrix are prepared by direct dispersion of the organo-clay in the presence of three different metal-based catalysts with the aim to promote transesterification reactions between the nanocomposite constituents. The mechanical properties and morphological characterization of these nanocomposites show that the tin-based catalyst (Sn) is the more efficient. Indeed, the effectiveness of transesterification reactions taking place between the ester functions of the BIO matrix and the hydroxyl groups of the organo-clay and the resulting “grafting” of BIO chains on the organo-clay surface are confirmed by thermogravimetric analyses performed after the extraction procedure. TEM observations show that this catalyst enhances the clay platelets exfoliation within the BIO matrix as a consequence of the transesterification reactions. Nanocomposites prepared in presence of Sn show better clay dispersion and enhanced stiffness with a 60% increase in Young’s modulus.     

Entropic stabilization of isolated beta-sheets

Temperature-dependent electric deflection measurements have been performed for a series of unsolvated alanine-based peptides (Ac-WA(n)-NH(2), where Ac = acetyl, W = tryptophan, A = alanine, and n = 3, 5, 10, 13, and 15). The measurements are interpreted using Monte Carlo simulations performed with a parallel tempering algorithm. Despite alanine's high helix propensity in solution, the results suggest that unsolvated Ac-WA(n)-NH(2) peptides with n > 10 adopt beta-sheet conformations at room temperature. Previous studies have shown that protonated alanine-based peptides adopt helical or globular conformations in the gas phase, depending on the location of the charge. Thus, the charge more than anything else controls the structure.