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.     

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.     

Intrinsic second-order nonlinearity in chalcogenide glasses containing HgI2

Frequency conversion using nonlinear optical (NLO) crystals is widely used in advanced photonic technologies to produce coherent light in the spectral regions where the available laser sources are missing. Isotropic glasses usually do not show second order nonlinear processes like second harmonic or difference frequency generation (SHG, DFG) except for temporarily induced anisotropy under external stimuli. Here, we show that a HgI₂–Ga₂S₃–GeS₂ homogeneous glass exhibits a strong intrinsic SHG response comparable with that of the well-known NLO single crystal LiNbO₃. The origin of this extremely rare phenomenon seems to be noncentrosymmetric bent HgI₂ molecules embedded in a sulfide glassy host. Taking into account the unique properties of chalcogenide glasses (wide IR transmission, low phonon density, unlimited ability to be modified changing the appropriate glass properties, fiber drawing and thin layer design), the observed phenomenon opens up the possibility of creating fundamentally new devices for mid-IR photonics.     

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.     

Cr(VI) removal from aqueous solution by activated carbon coated with quaternized poly(4-vinylpyridine)

A composite sorbent (GAC-QPVP) was prepared by coating poly(4-vinylpyridine) onto a granular activated carbon, followed by cross-linking and quaternization processes. The sorbent was characterized by scanning electron microscopy, point of zero charge measurement, and BET analysis. Batch experiments with variable pH, ionic strength, and concentrations of Cr(VI), sorbent, and competing anions were conducted to evaluate the selective sorption of Cr(VI) from aqueous solutions. The results showed that Cr(VI) sorption rates could be described by a reversible second-order kinetics, and equilibrium uptake of Cr(VI) increased with decreasing pH, decreasing ionic strength, and increasing sorbent concentration. The estimated maximum equilibrium uptake of chromium was 53.7 mg/g at pH = 2.25, 30.7 mg/g at pH = 3.65, and 18.9 mg/g at pH = 6.03, much higher than the maximum capacity of PVP-coated silica gel, an adsorbent for Cr examined previously. When compared with the untreated granular activated carbon, sorption onto GAC-QPVP resulted in much less Cr(VI) reduction and subsequent release of Cr(III). The effect of phosphate, sulfate, and nitrate was minor on the selective sorption of Cr(VI). An ion exchange model that was linked with aqueous speciation chemistry described Cr(VI) sorption reasonably well as a function of pH, ionic strength, and Cr(VI) concentration. Model simulations suggested that sorbed Cr(VI) was partially reduced to Cr(III) on the sorbent when pH was less than 4. The presence of Cr(III) on the sorbent was confirmed by the X-ray photoelectron spectroscopic analysis. Overall, the study has demonstrated that GAC-QPVP can effectively remove Cr(VI) from aqueous solutions under a wide range of experimental conditions, without significant Cr(III) release associated with the virgin GAC treatment.     

Interior-architectured ZnO nanostructure for enhanced electrical conductivity via stepwise fabrication process

Fabrication of ZnO nanostructure via direct patterning based on sol-gel process has advantages of low-cost, vacuum-free, and rapid process and producibility on flexible or non-uniform substrates. Recently, it has been applied in light-emitting devices and advanced nanopatterning. However, application as an electrically conducting layer processed at low temperature has been limited by its high resistivity due to interior structure. In this paper, we report interior-architecturing of sol-gel-based ZnO nanostructure for the enhanced electrical conductivity. Stepwise fabrication process combining the nanoimprint lithography (NIL) process with an additional growth process was newly applied. Changes in morphology, interior structure, and electrical characteristics of the fabricated ZnO nanolines were analyzed. It was shown that filling structural voids in ZnO nanolines with nanocrystalline ZnO contributed to reducing electrical resistivity. Both rigid and flexible substrates were adopted for the device implementation, and the robustness of ZnO nanostructure on flexible substrate was verified. Interior-architecturing of ZnO nanostructure lends itself well to the tunability of morphological, electrical, and optical characteristics of nanopatterned inorganic materials with the large-area, low-cost, and low-temperature producibility.     

Synthesis of single-walled carbon nanotubes using hemoglobin-based iron catalyst

Hemoglobin (Hb) was used as a catalyst for the growth of single-walled carbon nanotubes (SWCNTs). Hb was deposited onto a hydrophilic treated substrate by spin coating method. After oxidation at 800 °C, protein chains were decomposed and iron oxide nanoparticles remained with an average diameter of 2.29 nm. High quality SWCNTs were synthesized with an average diameter of 1.22 nm. The protein chains prevent iron atoms aggregation and so the size of the nanoparticles is smaller than that from ferritin-like proteins.     

Liquid salt cooled flexible conversion ratio fast reactor: Neutronic design

This paper presents the neutronic design of a liquid salt cooled fast reactor with flexible conversion ratio. The main objective of the design is to accommodate interchangeably within the same reactor core alternative transuranic actinides management strategies ranging from pure burning to self-sustainable breeding. Two, the most limiting, core design options with unity and zero conversion ratios are described. Ternary, NaCl-KCl-MgCl₂ salt was chosen as a coolant after a rigorous screening process, due to a combination of favourable neutronic and heat transport properties. Large positive coolant temperature reactivity coefficient was identified as the most significant design challenge. A wide range of strategies aiming at the reduction of the coolant temperature coefficient to assure self-controllability of the core in the most limiting unprotected accidents were explored. However, none of the strategies resulted in sufficient reduction of the coolant temperature coefficient without significantly compromising the core performance characteristics such as power density or cycle length. Therefore, reactivity control devices known as lithium thermal expansion modules were employed instead. This allowed achieving all the design goals for both zero and unity conversion ratio cores. The neutronic feasibility of both designs was demonstrated through calculation of reactivity control and fuel loading requirements, fluence limits, power peaking factors, and reactivity feedback coefficients.     

Infinite-horizon Scheduling Algorithms for Optimal Search for Hidden Objects

This paper considers discrete search problems in which a decision-maker has to find objects lost or hidden in a given set of locations so as to minimize the expected losses incurred. Given a chance to look for a hidden object in the same location infinitely many times, this type of problem, in contrast to standard scheduling problems, has an infinite sequence as its solution. Thus we are concerned to find an algorithm that yields an optimal solution, rather than the optimal sequence itself. Using combinatorial techniques, fast optimal algorithms for solving the problems are obtained, and optimality conditions are presented for search criteria, under which the local-search algorithms yield the global optimum.     

Interferon-β Activity Is Affected by S100B Protein

Interferon-β (IFN-β) is a pleiotropic cytokine secreted in response to various pathological conditions and is clinically used for therapy of multiple sclerosis. Its application for treatment of cancer, infections and pulmonary diseases is limited by incomplete understanding of regulatory mechanisms of its functioning. Recently, we reported that IFN-β activity is affected by interactions with S100A1, S100A4, S100A6, and S100P proteins, which are members of the S100 protein family of multifunctional Ca²⁺-binding proteins possessing cytokine-like activities (Int J Mol Sci. 2020;21(24):9473). Here we show that IFN-β interacts with one more representative of the S100 protein family, the S100B protein, involved in numerous oncological and neurological diseases. The use of chemical crosslinking, intrinsic fluorescence, and surface plasmon resonance spectroscopy revealed IFN-β binding to Ca²⁺-loaded dimeric and monomeric forms of the S100B protein. Calcium depletion blocks the S100B–IFN-β interaction. S100B monomerization increases its affinity to IFN-β by 2.7 orders of magnitude (equilibrium dissociation constant of the complex reaches 47 pM). Crystal violet assay demonstrated that combined application of IFN-β and S100B (5–25 nM) eliminates their inhibitory effects on MCF-7 cell viability. Bioinformatics analysis showed that the direct modulation of IFN-β activity by the S100B protein described here could be relevant to progression of multiple oncological and neurological diseases.