High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models

Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/ . © 2013 Wiley Periodicals, Inc.     

Mixed Aggregates of 1-Methoxyallenyllithium with Lithium Chloride

A combined computational and ¹³C NMR study was used to investigate the formation of mixed aggregates of 1-methoxyallenyllithium and lithium chloride in tetrahydrofuran (THF) solution. The observed and calculated chemical shifts, as well as the calculated free energies of mixed aggregate formation (MP2/6-31+G(d)), are consistent with the formation of a mixed dimer as the major species in solution. Free energies of mixed dimer, trimer, and tetramer formation were calculated by using the B3LYP and MP2 methods and the 6-31+G(d) basis set. The two methods generated different predictions of which mixed aggregates will be formed, with B3LYP/6-31+G(d) favoring mixed trimers and tetramers in THF solution, and MP2/6-31+G(d) favoring mixed dimers. Formation of the sterically unhindered mixed dimers is also consistent with the enhanced reactivity of these compounds in the presence of lithium chloride. The spectra are also consistent with some residual 1-methoxyallenyllithium tetramer, as well as small amounts of higher mixed aggregates. Although neither computational method is perfect, for this particular system, the calculated free energies derived using the MP2 method are in better agreement with experimental data than those derived using the B3LYP method.     

Revealing Phosphorus Nitrides up to the Megabar Regime: Synthesis of α′-P3N5, δ-P3N5 and PN2

Non-metal nitrides are an exciting field of chemistry, featuring a significant number of compounds that can possess outstanding material properties. These properties mainly rely on maximizing the number of strong covalent bonds, with crosslinked XN₆ octahedra frameworks being particularly attractive. In this study, the phosphorus–nitrogen system was studied up to 137 GPa in laser-heated diamond anvil cells, and three previously unobserved phases were synthesized and characterized by single-crystal X-ray diffraction, Raman spectroscopy measurements and density functional theory calculations. δ-P₃N₅ and PN₂ were found to form at 72 and 134 GPa, respectively, and both feature dense 3D networks of the so far elusive PN₆ units. The two compounds are ultra-incompressible, having a bulk modulus of K₀=322 GPa for δ-P₃N₅ and 339 GPa for PN₂. Upon decompression below 7 GPa, δ-P₃N₅ undergoes a transformation into a novel α′-P₃N₅ solid, stable at ambient conditions, that has a unique structure type based on PN₄ tetrahedra. The formation of α′-P₃N₅ underlines that a phase space otherwise inaccessible can be explored through materials formed under high pressure.     

Characterization of a highly stable zwitterionic hydrophilic interaction chromatography stationary phase based on hybrid organic–inorganic particles

We have characterized a sulfobetaine stationary phase based on 1.7 μm ethylene-bridged hybrid organic–inorganic particles, which is intended for use in hydrophilic interaction chromatography. The efficiency of a column packed with this material was determined as a function of flow rate, demonstrating a minimum reduced plate height of 2.4. The batch-to-batch reproducibility was assessed using the separation of a mixture of acids, bases, and neutrals. We compared the retention and selectivity of the hybrid sulfobetaine stationary phase to that of several benchmark materials. The hybrid sulfobetaine material gave strong retention for polar neutrals and high selectivity for methyl groups, hydroxy groups, and configurational isomers. Large differences in cation and anion retention were observed among the columns. We characterized the acid and base stability of the hybrid sulfobetaine stationary phase, using accelerated tests at pH 1.3 and 11.0, both at 70°C. The results support a recommended pH range of 2–10. We also investigated the performance of columns packed with this material for metal-sensitive analytes, comparing conventional stainless steel column hardware to hardware that incorporates hybrid surface technology to mitigate interactions with metal surfaces. Compared to the conventional columns, the hybrid surface technology columns showed a greatly improved peak shape.     

Intra- and Inter-molecular Sulf- hydryl Hydrogen Bonding: Facilitating Proton Transfer Events for Determination of pH in Sea Water

This work presents the electrochemical response of a 2-(methylthio)phenol glassy carbon based electrode for a promising voltammetric pH sensor in both buffered and low-buffered solutions. Electropolymerization of the redox species was performed with the resulting polymer presenting a Nernstian response in buffered media, with a sensitivity of 51 mV/pH unit. The effectiveness of the sulfhydryl bond to facilitate proton transfer from the bulk solution to the phenol molecules has been confirmed, providing an accurate pH measurement of 8.28 in sea water media, compared to that measured with a calibrated glass pH probe of 8.30.     

Excitation dependent quenching of luminescence in LED phosphors

Droop, the decrease of efficiency with increased power density, became a major topic with InGaN LEDs, after its introduction in 2007. This paper provides insight into droop in localized center luminescence phosphors, exemplified here by Eu²⁺ doped materials. This topic is of increasing importance, as high brightness blue LEDs have reached outputs >1 W/mm². The nonlinearities in phosphor quantum efficiency result in drive‐dependent color point shift and reduction of overall efficiency of phosphor converted white LEDs which utilize Eu²⁺ activated phosphors. The efficiency quenching can be traced back to two processes, well‐known in laser physics, excited state absorption or/and cross relaxation by Foerster/Dexter transfer. Both processes lead to reduction in phosphor efficiency, but they can be differentiated. Understanding the root cause of efficiency quenching opens ways to minimize the practical consequences. (© 2016 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Investigating microcrystalline cellulose crystallinity using Raman spectroscopy

Cellulose - Microcrystalline cellulose (MCC) is a semi-crystalline material with inherent variable crystallinity due to raw material source and variable manufacturing conditions. MCC crystallinity...     

A flow system for hydrogen peroxide production at reticulated vitreous carbon via electroreduction of oxygen

In this work, a reticulated vitreous carbon electrode (RVCE, 96.5 % porosity, 24 cm^?1) was modified with 2-anthraquinonyl groups to electrocatalytically reduce dissolved oxygen in neutral aqueous solution (0.1 M phosphate buffer solution supported with 3 M potassium chloride, pH of 6.7) to hydrogen peroxide (H₂O₂) at 25 °C under atmospheric pressure. The obtained current density was ca. 3 mA cm^?2. For the first time, the oxygen reduction was investigated on a novelly designed RVCE housed in a gravity-feed flow system. Fractional current conversions obtained on the RVC flow cell were compared and contrasted with those on a two-dimensional electrode, viz. a tubular flow electrode. The modified-on catalyst has the benefit in terms of easy separation of the product from the catalyst. The in situ generated low concentration of H₂O₂ provides potential applications to water purification processes and disinfection for water and food.     

Long‐Wavelength Fluorescent Reporters for Monitoring Protein Kinase Activity

In vivo optical imaging must contend with the limitations imposed by the optical window of tissue (600–1000 nm). Although a wide array of fluorophores are available that are visualized in the red and near‐IR region of the spectrum, with the exception of proteases, there are few long wavelength probes for enzymes. This situation poses a particular challenge for studying the intracellular biochemistry of erythrocytes, the high hemoglobin content of which optically obscures subcellular monitoring at wavelengths less than 600 nm. To address this, tunable fluorescent reporters for protein kinase activity were developed. The probing wavelength is preprogrammed by using readily available fluorophores, thereby enabling detection within the optical window of tissue, specifically in the far‐red and near‐IR region. These agents were used to monitor endogenous cAMP‐dependent protein kinase activity in erythrocyte lysates and in intact erythrocytes when using a light‐activatable reporter.