Templated assembly of organic-inorganic materials using the core shell structure of the P22 bacteriophage

Biomimetic chemistry offers new approaches to supramolecular materials synthesis and assembly. We have demonstrated that an assembled viral protein cage, comprising an organic core-shell structure, can be used as a template for the size constrained synthesis of Fe(2)O(3). Particle nucleation is directed by the inner scaffold protein layer, while the size constraints are determined by the outer capsid layer.     

Site-directed coordination chemistry with P22 virus-like particles

Protein cage nanoparticles (PCNs) are attractive platforms for developing functional nanomaterials using biomimetic approaches for functionalization and cargo encapsulation. Many strategies have been employed to direct the loading of molecular cargos inside a wide range of PCN architectures. Here we demonstrate the exploitation of a metal-ligand coordination bond with respect to the direct packing of guest molecules on the interior interface of a virus-like PCN derived from Salmonella typhimurium bacteriophage P22. The incorporation of these guest species was assessed using mass spectrometry, multiangle laser light scattering, and analytical ultracentrifugation. In addition to small-molecule encapsulation, this approach was also effective for the directed synthesis of a large macromolecular coordination polymer packed inside of the P22 capsid and initiated on the interior surface. A wide range of metals and ligands with different thermodynamic affinities and kinetic stabilities are potentially available for this approach, highlighting the potential for metal-ligand coordination chemistry to direct the site-specific incorporation of cargo molecules for a variety of applications.     

Hydrogen/deuterium exchange on protein solutions containing nucleic acids: utility of protamine sulfate

Obtaining global hydrogen/deuterium (H/D) exchange data on proteins is an important first step in amide proton exchange experiments. Important information such as the mode of exchange, the cooperativity of folding/unfolding reactions, and the effects of ligand binding can be readily obtained in global exchange experiments. Many interesting biological systems are complexes containing both proteins and nucleic acids. The low pH conditions required to quench H/D exchange reactions result in the formation of stable protein/nucleic acid precipitates which interfere with the liquid chromatography step of the experiment and preclude obtaining mass spectrometric data. In this work we show that the precipitation of proteins and nucleic acids is electrostatic in nature and can be prevented by high ionic strength and by removing nucleic acids by protamine sulfate. Using protamine sulfate in quenching solution, we were able to obtain global H/D data with protein samples containing large amounts of DNA or RNA.     

Mapping of protein:protein contact surfaces by hydrogen/deuterium exchange,followed by on-line high-performance liquid chromatography-electrospray ionization Fourier-transform ion-cyclotron-resonance mass analysis

Furfural contents in adapted and follow-up infant formulas were measured by RP-HPLC. The evolution of furfural compound contents during storage (a year at 20 and 37 degrees C) was studied. 2-Furylmethylketone and 5-methyl-2-furaldehyde were not detectable in analysed samples. The differences in the furfural compounds at point zero between both infant formulas has to be ascribed to the differences in protein and iron contents. An increase in free 5-hydroxymethyl-2-furfuraldehyde (HMF), 2-furaldehyde (F) and HMF+F contents was observed in all samples, although the differences were not statistically significant. The storage temperature affected the total HMF content and the storage time affected the total HMF and F contents.     

Synthesis of biotin‐tagged chemical cross‐linkers and their applications for mass spectrometry

Chemical cross‐linking combined with mass spectrometry (MS) has been used to elucidate protein structures and protein‐protein interactions. However, heterogeneity of the samples and the relatively low abundance of cross‐linked peptides make this approach challenging. As an effort to overcome this hurdle, we have synthesized lysine‐reactive homobifunctional cross‐linkers with the biotin in the middle of the linker and used them to enrich cross‐linked peptides. The reaction of biotin‐tagged cross‐linkers with purified HIV‐1 CA resulted in the formation of hanging and intramolecular cross‐links. The peptides modified with biotinylated cross‐linkers were effectively enriched and recovered using a streptavidin‐coated plate and MS‐friendly buffers. The enrichment of modified peptides and removal of the dominantly unmodified peptides simplify mass spectra and their analyses. The combination of the high mass accuracy of Fourier transform ion cyclotron resonance (FT‐ICR) MS and the tandem mass spectrometric (MS/MS) capability of the linear ion trap allows us to unambiguously identify the cross‐linking sites and additional modification, such as oxidation. Copyright © 2009 John Wiley & Sons, Ltd.     

HARVESTING ECONOMIC MODELS AND CATCH‐TO‐BIOMASS DEPENDENCE: THE CASE OF SMALL PELAGIC FISH

Abstract In the case of small pelagic fish, it seems reasonable to consider harvest functions depending nonlinearly on fishing effort and fish stock. Indeed, empirical evidence about these fish species suggests that marginal catch does not necessarily react in a linear way neither to changes in fishing effort nor in fish stock levels. This is in contradiction with traditional fishery economic models where catch‐to‐input marginal productivities are normally assumed to be constant. While allowing for nonlinearities in both catch‐to‐effort and catch‐to‐stock parameters, this paper extends the traditional single‐stock harvesting economic model by focusing on the dependence of the stationary solutions upon the nonlinear catch‐to‐stock parameter. Thus, we analyze equilibrium responses to changes in this parameter, which in turn may be triggered either by climatic or technological change. Given the focus in this study on the case of small pelagic fish, the analysis considers positive but small values for the catch‐to‐stock parameter.