Discretization orders for protein side chains

Proteins are important molecules that are widely studied in biology. Since their three-dimensional conformations can give clues about their function, an optimal methodology for the identification of such conformations has been researched for many years. Experiments of Nuclear Magnetic Resonance (NMR) are able to estimate distances between some pairs of atoms forming the protein, and the problem of identifying the possible conformations satisfying the available distance constraints is known in the scientific literature as the Molecular Distance Geometry Problem (MDGP). When some particular assumptions are satisfied, MDGP instances can be discretized, and solved by employing an ad-hoc algorithm, named the interval Branch & Prune. When dealing with molecules such as proteins, whose chemical structure is known, a priori information can be exploited for generating atomic orderings that allow for the discretization. In previous publications, we presented a handcrafted order for the protein backbones. In this work, we propose 20 new orders for the 20 side chains that can be present in proteins. Computational experiments on artificial and real instances from NMR show the usefulness of the proposed orders.     

Higher-Order Multilinear Poincaré and Sobolev Inequalities in Carnot Groups

The notions of higher-order weighted multilinear Poincaré and Sobolev inequalities in Carnot groups are introduced. As an application, weighted Leibniz-type rules in Campanato-Morrey spaces are established.     

Chromium(VI) oxide oxidation of non‐ethoxylated and ethoxylated alcohols for determination by electrospray ionization mass spectrometry

A new derivatization procedure to increase the sensitivity of electrospray ionization mass spectrometry (ESI‐MS) to non‐ethoxylated and ethoxylated alcohols was investigated. The analytes were oxidized with chromium(VI) oxide and the resulting carboxylic and ethoxy‐carboxylic acids were isolated by extraction with ethyl acetate; the extracts were alkalinized and infused into the ESI‐MS system working in the negative‐ion mode. The yields of the combined oxidation‐extraction were ca. 100% for non‐ethoxylated fatty alcohols dissolved in acetone and they decreased moderately in samples containing increasing amounts of water (e.g., a 75% yield was obtained with 50% water). Ethoxylated alcohols with more than two ethylene oxide units resulted in yields of ca. 60%. Low limits of detection (LODs) were obtained when the procedure was applied to the analysis of body‐care products and cosmetics containing fatty alcohols, e.g., in a varicose‐vein cream, the LODs were 25 µg cetyl alcohol and 7.5 µg stearyl alcohol (detected as palmitic acid and stearic acid, respectively) per gram of sample. High molecular mass alcohols were also detected in seawater after pre‐concentration by solid‐phase extraction. Thus, the proposed method is particularly valuable for use in industrial samples having complex matrices and in environmental samples and it is competitive with other methods for the analysis of trace amounts of fatty alcohols. Copyright © 2010 John Wiley & Sons, Ltd.     

Synthesis and biomimetic mineralization of l‐proline substituted polyphosphazenes as bulk and nanofiber

This work presents the synthesis of polyphosphazenes bearing L ‐proline methyl ester (ProOMe) and 4‐hydroxy‐l ‐proline methyl ester (HypOMe), aiming for new bioactive polymers for bone repair. The polymers were characterized by ¹H and ³¹P NMR, FTIR, DSC, and TGA. Electrospun fibers were prepared using poly[bis(l ‐proline methyl ester)phosphazene] (PProP), and their potential for biomimetic mineralization, as well as the bulk material, were tested in simulated body fluid (1×SBF). Samples were analyzed between 24 h and 3 weeks of incubation using SEM/EDS and FTIR. After 24 h, spherical and flower‐like shapes of calcium phosphates (CaP) were crystallized on the bulk samples. The nanofibers presented spherical CaP crystals attached to them after 48 h of incubation. The Ca/P molar ratio of the crystals varied from 1.5 to 1.6. According to this study, PProP presents bioactivity in vitro, and its fibers offer sites for CaP nucleation like the collagen fibers in bone. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2013 , 51, 1318–1327     

Determination of four acidic nonsteroidal anti‐inflammatory drugs in wastewater samples by dispersive liquid–liquid microextraction based on solidification of floating organic droplet and high‐performance liquid chromatography

A simple, environmentally friendly, and sensitive dispersive liquid–liquid microextraction based on solidification of floating organic droplet for the extraction of four acidic nonsteroidal anti‐inflammatory drugs (ketoprofen, naproxen, ibuprofen, and diclofenac) from wastewater samples subsequent by high‐performance liquid chromatography analysis was developed. The influence of extraction parameters such as pH, the effect of solution ionic strength, type of extraction solvent, disperser solvent, and extraction solvent volume were studied. High enrichment factors (283–302) were obtained through the developed method. The method provides good linearity (r > 0.999) in a concentration range of 1–100 μg/L, good intra‐ and inter‐day precision (relative standard deviation < 7%) and low limits of quantification. The relative recoveries of the selected compounds were situated over 80% both in synthetic and real water samples. The developed method has been successfully applied for the analysis of the selected compounds in wastewater samples.     

Effects of liquid crystalline and shear alignment on the optical properties of cellulose nanocrystal films

Rheo-optics, microspectrophotometry, and optical contrast measurements were used to gain new insights into the interrelated effects of liquid crystalline phase behavior, flow alignment, and microstructural relaxation on cellulose nanocrystal (CNC) films’ alignment and optical properties. Optical contrast measurements were found to be an effective and facile way of determining changes in anisotropy directly from cross-polarized microscopy images. This method was used to continuously measure microstructural relaxation after the cessation of shear as well as the anisotropy of dried CNC films. Aqueous liquid crystalline CNC dispersions showed greater alignment after shear than isotropic or biphasic dispersions. However, CNC gels exhibited lower alignment at equivalent shear rates. The combination of greater initial alignment and slower relaxation of sheared liquid crystalline dispersions resulted in the most optically anisotropic films. Depending on their thickness, the CNC films were optically transparent in the visible regime or exhibited tunable interference colors. The results of this work highlight the tunability of CNC dispersion processing for producing color filters and other optical materials with controlled properties.     

Towards quantitative catalytic lignin depolymerization

The products of base-catalyzed liquid-phase hydrolysis of lignin depend markedly on the operating conditions. By varying temperature, pressure, catalyst concentration, and residence time, the yield of monomers and oligomers from depolymerized lignin can be adjusted. It is shown that monomers of phenolic derivatives are the only primary products of base-catalyzed hydrolysis and that oligomers form as secondary products. Oligomerization and polymerization of these highly reactive products, however, limit the amount of obtainable product oil containing low-molecular-weight phenolic products. Therefore, inhibition of concurrent oligomerization and polymerization reactions during hydrothermal lignin depolymerization is important to enhance product yields. Applying boric acid as a capping agent to suppress addition and condensation reactions of initially formed products is presented as a successful approach in this direction. Combination of base-catalyzed lignin hydrolysis with addition of boric acid protecting agent shifts the product distribution to lower molecular weight compounds and increases product yields beyond 85%.     

Ion Mobility-Mass Spectrometry Study of Folded Ubiquitin Conformers Induced By Treatment with <Emphasis Type="Italic">cis</Emphasis>-[Pd(en)(H<Subscript>2</Subscript>O)<Subscript>2</Subscript>]<Superscript>2+</Superscript>

Ion mobility-mass spectrometry is used to study the new conformers of bovine ubiquitin (Ub) and the palladium(II) binding sites after the incubation with cis-[Pd(en)(H₂O)₂]²⁺ where en = ethylenediamine. Palladium(II) complexes are potentially useful proteomic reagents because they selectively bind to the side groups of methionine and histidine and hydrolytically cleave the peptide bond. Incubating 1.0 mM solution of Ub with 10.0 molar excess of cis-[Pd(en)(H₂O)₂]²⁺ results with one to four Pd²⁺ or Pd(en)²⁺ being attached to intact Ub and two conformer families at each of the 4+ to 11+ charge states. The 4+ and 5+ species exhibit a compact form, which is also observed in untreated Ub, and a new highly folded conformer. The 6+ to 10+ exhibit an elongated form, also observed in Ub, and a new partially folded conformer. The new conformers are shown to be more stable if they contain at least one Pd²⁺, rather than all Pd(en)²⁺. IM-MS/MS of [UbPd₂en+5H]⁹⁺ shows that both the partially folded and elongated conformers first lose the en ligand, followed by dissociating into product ions that indicate that Met1, Glu51/Asp52, His68, and Glu16 are binding sites for Pd²⁺. These results suggest that Pd²⁺ is simultaneously binding to multiple side groups across different regions of Ub. This type of sequestering of Pd²⁺ probably reduces the efficiency of Pd²⁺ ions to selectively cleave Ub because it prevents Pd²⁺ anchoring to only Met or His and to an adjacent backbone amide nitrogen and forming the “activated complex” necessary for specific peptide bond cleavage.     

Minimizing the probability of lifetime ruin under stochastic volatility

We assume that an individual invests in a financial market with one riskless and one risky asset, with the latter’s price following a diffusion with stochastic volatility. Given the rate of consumption, we find the optimal investment strategy for the individual who wishes to minimize the probability of going bankrupt. To solve this minimization problem, we use techniques from stochastic optimal control.