Is Protein Folding a Thermodynamically Unfavorable,Active, Energy-Dependent Process?

The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.     

Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences

The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an average number of substitutions per amino acid (x) from 0.6 to 5.6, a total of 81 sets. Comparison of the performance of sequence alignments constructed by MAHDS and previously developed algorithms using the CS and Z score criteria and the benchmark alignment database (BAliBASE) indicated that, although the quality of the alignments built with MAHDS was somewhat lower than that of the other algorithms, it was compensated by greater statistical significance. MAHDS could construct statistically significant alignments of artificial sequences with x ≤ 4.8, whereas the other algorithms (T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK) could not perform that at x > 2.4. The application of MAHDS to align 21 families of highly diverged proteins (identity < 20%) from Pfam and HOMSTRAD databases showed that it could calculate statistically significant alignments in cases when the other methods failed. Thus, MAHDS could be used to construct statistically significant multiple alignments of highly divergent protein sequences, which accumulated multiple mutations during evolution.     

Activity–Composition Relations of Chromium Oxide in Silicate Melts at 1500°C under Strongly Reducing Conditions

The solubility and activity–composition relations of chromium oxide in melts of the systems CaO–CrO _x –SiO₂ and CaO–Al₂O₃–CrO _x –SiO₂ have been determined at 1500°C by equilibrating melts with Pt–Cr alloys at known oxygen pressures. It is shown that the increase in the concentration of divalent chromium ions, as the oxygen pressure and the basicity of melt decrease, results in a dramatic increase in the solubility of chromium oxide in the liquid phase. An increase in the Al₂O₃ content of the melt leads to a decrease in the solubility of chromium oxide over the whole composition range studied. The activity coefficient of CrO has been found to increase with increasing melt basicity and decreasing oxygen pressure whereas the activity coefficient of CrO_1.5 decreases sharply with increasing melt basicity for siliceous melts but levels off at a basicity ratio (wt% CaO/wt% SiO₂) of about 0.7. An increase in the Al₂O₃ content of the melts results in an increase in the activity coefficient of CrO.     

Influence of corrosion and mechanical loads on advanced ceramic components

Advanced oxide ceramics are prospective materials for severe application conditions, including corrosion, particularly, in oxygen-rich environments, combined with the action of mechanical loads. The corrosion behavior and mechanical strength decrease of oxide ceramics, such as high alumina, alumina–mullite and zirconia-based ceramics, were studied in water steam supercritical conditions (elevated temperatures and pressures). The strength decrease under the action of the studied aggressive environment is mostly dealt with the glassy phase dissolution and intergranular corrosion for alumina–mullite and high alumina ceramics, while degradation of zirconia-based ceramics is also dealt with the phase transformation. The influence of structure defects related to processing of the ceramics on corrosion is considered.     

Stereoselective Formation of 1,4‐Anhydro‐2‐C‐carboxytetritols in the Degradation of 1,5‐Anhydroribitol and 1,5‐Anhydroxylitol with Oxygen in Aqueous Alkali

Abstract

In addition to other acid products, degradation of 1,5‐anhydroribitol (5) and 1,5‐anhydroxylitol (6) with oxygen in 1.25 M NaOH produced diastereomeric 1,4‐anhydro‐2‐C‐carboxy‐D‐erythritol (7) and 1,4‐anhydro‐2‐C‐carboxy‐D‐threitol (8) and their enantiomers as major products. However, the ratio of the diastereomers differed for the two reactants. Thus, their formation could not proceed solely by benzilic acid‐type rearrangements through α‐dicarbonyl intermediates as typically proposed for formation of alkyl C‐carboxyfuranosides from alkyl glycopyranosides in similar reactions. The α‐dicarbonyl species that can form from 5 and 6 are identical. Potential mechanisms to account for stereoselective formation of 7 and 8 are presented.     

Grafting of titanium dioxide microspheres with a temperature‐responsive polymer via surface‐initiated atom transfer radical polymerization without the use of silane coupling agents

Titania microspheres with narrow size distribution and diameters of about 1 µm were prepared and subsequently functionalized using surface‐initiated atom transfer radical polymerization (ATRP) of N‐isopropylacrylamide. The ATRP initiator was immobilized on the particle surface via acylation of surface hydroxyl groups with α‐bromoisobutyryl bromide. Subsequently, an established ATRP reaction system was used for the preparation of titania surface‐grafted poly(N‐isopropylacrylamide) (PNiPAAm). Characterization was performed with electron microscopies, X‐ray diffraction, infrared spectroscopy and dynamic light scattering. It was found that the particle size in aqueous dispersions changed reversibly with temperature as expected for a shell of PNiPAAm, a polymer with a lower critical solution temperature at 32 °C. This confirmed the successful preparation of functional, stimuli‐responsive TiO₂ microparticles via a straightforward controlled surface‐initiated polymerization method.     

Numerical Simulation of Anisotropic Shrinkage in a 2D Compact of Elongated Particles

Microstructural evolution during simple solid-state sintering of two-dimensional compacts of elongated particles packed in different arrangements was simulated using a kinetic, Monte Carlo model. The model used simulates curvature-driven grain growth, pore migration by surface diffusion, vacancy formation, diffusion along grain boundaries, and annihilation. Only the shape of the particles was anisotropic; all other extensive thermodynamic and kinetic properties such as surface energies and diffusivities were isotropic. We verified our model by simulating sintering in the analytically tractable cases of simple-packed and close-packed, elongated particles and comparing the shrinkage rate anisotropies with those predicted analytically. Once our model was verified, we used it to simulate sintering in a powder compact of aligned, elongated particles of arbitrary size and shape to gain an understanding of differential shrinkage. Anisotropic shrinkage occurred in all compacts with aligned, elongated particles. However, the direction of higher shrinkage was in some cases along the direction of elongation and in other cases in the perpendicular direction, depending on the details of the powder compact. In compacts of simple-packed, mono-sized, elongated particles, shrinkage was higher in the direction of elongation. In compacts of close-packed, mono-sized, elongated particles and of elongated particles with a size and shape distribution, the shrinkage was lower in the direction of elongation. The results of these simulations are analyzed, and the implication of these results is discussed.     

(<Emphasis Type="Italic">Z,Z</Emphasis>)-6,9-Heneicosadien-11-One: Major Sex Pheromone Component Of Painted Apple Moth, <Emphasis Type="Italic">Teia anartoides</Emphasis>

(Z, Z)-6,9-Heneicosadien-11-one (Z6Z9-11-one-21Hy) was identified as the major sex pheromone component of the painted apple moth (PAM), Teia anartoides (Lepidoptera: Lymantriidae), on the basis of (1) comparative gas chromatographic-electroantennographic detection (GC-EAD) analyses, GC-mass spectrometry (MS), high-performance liquid chromatography (HPLC)-MS, and HPLC-UV/visible spectroscopy of pheromone gland extracts and authentic standards; (2) GC-EAD analyses of effluvia of calling females; and (3) wind tunnel and field trapping experiments with a synthetic standard. In field experiments in Australia, synthetic Z6Z9-11-one-21Hy as a single component attracted male moths. Wind tunnel experiments suggested that a 4-component blend consisting of Z6Z9-11-one-21Hy, (6Z,9R,10S)-cis-9,10-epoxy-heneicosene (Z6-9R10S-epo-21Hy), (E, E)-7,9-heneicosadien-6,11-dione (E7E9-6,11-dione-21Hy), and 6-hydroxy-(E, E)-7,9-heneicosadien-11-one (E7E9-6-ol-11-one-21Hy) (all present in pheromone gland extracts) might induce more males to orient toward, approach, and contact the source than did Z6Z9-11-one-21Hy as a single component. Additional experiments are needed to determine conclusively whether or not Z6-9R10S-epo-21Hy, E7E9-6,11-dione-21Hy, and E7E9-6-ol-11-one-21Hy might be minor sex pheromone components of PAM. Moreover, attractiveness of synthetic pheromone and virgin PAM females needs to be compared to determine whether synthetic pheromone could replace PAM females as trap baits in the program to monitor eradication of exotic PAM in New Zealand.     

AICAR Protects Vascular Endothelial Cells from Oxidative Injury Induced by the Long-Term Palmitate Excess

Hyperlipidemia manifested by high blood levels of free fatty acids (FFA) and lipoprotein triglycerides is critical for the progression of type 2 diabetes (T2D) and its cardiovascular complications via vascular endothelial dysfunction. However, attempts to assess high FFA effects in endothelial culture often result in early cell apoptosis that poorly recapitulates a much slower pace of vascular deterioration in vivo and does not provide for the longer-term studies of endothelial lipotoxicity in vitro. Here, we report that palmitate (PA), a typical FFA, does not impair, by itself, endothelial barrier and insulin signaling in human umbilical vein endothelial cells (HUVEC), but increases NO release, reactive oxygen species (ROS) generation, and protein labeling by malondialdehyde (MDA) hallmarking oxidative stress and increased lipid peroxidation. This PA-induced stress eventually resulted in the loss of cell viability coincident with loss of insulin signaling. Supplementation with 5-aminoimidazole-4-carboxamide-riboside (AICAR) increased endothelial AMP-activated protein kinase (AMPK) activity, supported insulin signaling, and prevented the PA-induced increases in NO, ROS, and MDA, thus allowing to maintain HUVEC viability and barrier, and providing the means to study the long-term effects of high FFA levels in endothelial cultures. An upgraded cell-based model reproduces FFA-induced insulin resistance by demonstrating decreased NO production by vascular endothelium.