Divergent responses of branched and straight-chain lipid membranes to butanol stress revealed by molecular dynamics simulation.

Blood banks around the world store blood components for several weeks ensuring its availability for transfusion medicine. Red blood cells (RBCs) are known to undergo compositional changes during storage, which may impact the cells’ function and eventually the recipients’ health. We extracted the RBC’s cytoplasmic membrane (RBCcm) to study the effect of storage on the membranes’ molecular structure and bending rigidity by a combination of X-ray diffraction (XRD), X-ray diffuse scattering (XDS) and coarse grained Molecular Dynamics (MD) simulations. Blood was stored in commercial blood bags for 2 and 5 weeks, respectively and compared to freshly drawn blood. Using mass spectrometry, we measured an increase of fatty acids together with a slight shift towards shorter tail lengths. We observe an increased fraction (6%) of liquid ordered (lo) domains in the RBCcms with storage time, and an increased lipid packing in these domains, leading to an increased membrane thickness and membrane order. The size of both, lo and liquid disordered (ld) lipid domains was found to decrease with increased storage time by up to 25%. XDS experiments reveal a storage dependent increase in the RBCcm’s bending modulus κ by a factor of 2.8, from 1.9 kBT to 5.3 kBT. MD simulations were conducted in the absence of proteins. The results show that the membrane composition has a small contribution to the increased bending rigidity and suggests additional protein-driven mechanisms.

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

The highly immunogenic properties of outer membrane vesicles (OMVs), small spherical nanoparticles commonly released by Gram-negative bacteria, led to their application as vaccine candidate. ClearColi™ is an engineered Escherichia coli strain, which does not produce endotoxic response in humans and is useful for production of OMV-based vaccines. Therefore, producing ClearColi™ OMVs with high yield attracts particular interest. As stresses can be removed by OMVs, they may affect OMVs release. We aimed to investigate the effects of culture temperature, chemical (NaCl, ethanol, EDTA, D-cycloserine, polymyxin B, 1-octanol, and H2O2) and thermal stresses on release of ClearColi™ OMVs. Herein, the growth rate of ClearColi™ was decreased in the presence of all chemical stresses with the exception of H2O2. The optimum temperature for OMVs production was 37℃ and their release was not increased under thermal shock. The highest and lowest OMVs release was obtained in the presence of NaCl and H2O2, respectively. Electron microscopy images confirmed that the bilayer spherical-shaped OMVs were isolated under different stresses. Furthermore, SEM and DLS analysis demonstrated that OMVs released under EDTA stress are smaller than those released from untreated cultures. It can be concluded that chemical stresses have influence on the level of ClearColi™ OMVs production. However, changes in their content should be further investigated.

The biooxidation capacity of an extremely thermoacidophilic archaeon Metallosphaera sedula (DSMZ 5348) was examined under bioenergetic challenges imparted by thermal or chemical stress in regard to its potential use in microbial bioleaching processes. Within the normal growth temperature range of M. sedula (70-79 degrees C) at pH 2.0, upward temperature shifts resulted in bioleaching rates that followed an Arrhenius-like dependence. When the cells were subjected to supraoptimal temperatures through gradual thermal acclimation at 81 degrees C (Han et al., 1997), cell densities were reduced but 3 to 5 times faster specific leaching rates (Fe3+ released from iron pyrite/cell/h) could be achieved by the stressed cells compared to cells at 79 degrees C and 73 degrees C, respectively. The respiration capacity of M. sedula growing at 74 degrees C was challenged by poisoning the cells with uncouplers to generate chemical stress. When the protonophore 2,4-dinitrophenol (5-10 μM) was added to a growing culture of M. sedula on iron pyrite, there was little effect on specific leaching rates compared to a culture with no protonophore at 74 degrees C; 25 μM levels proved to be toxic to M. sedula. However, a significant stimulation in specific rate was observed when the cells were subjected to 1 μM nigericin (+135%) and 2 μM (+63%); 5 μM levels of the ionophore completely arrested cell growth. The ionophore effect was further investigated in continuous culture growing on ferrous sulfate at 74 degrees C. When 1 μM nigericin was added as a pulse to a continuous culture, a 30% increase in specific iron oxidation rate was observed for short intervals, indicating a potential positive impact on leaching when periodic chemical stress is applied. This study suggests that biooxidation rates can be increased by strategic exposure of extreme thermoacidophiles to chemical or thermal stress, and this approach should be considered for improving process performance. Copyright 1998 John Wiley & Sons, Inc.

Regarding their resistance five sealants were tested in vitro after experiencing mechanical, thermal and chemical stress. Included for testing were two fluoride varnishes: Fluor Protector [FP] (Ivoclar Vivadent) and Protecto CaF2 Nano One-Step Seal [PN] (BonaDent) and three fluoride-composite filled sealants (with acid etch technique): Clinpro XT Varnish [CP] (3 M Espe), Pro Seal [PS] & Light Bond [LB] (Reliance Orthodontic Products) and a positive control group [CG] Tetric EvoFlow (Ivoclar Vivadent). The sealants were applied on 180 bovine teeth (n = 10/ sealer) in a standardized manner after bracket bonding. Mechanical pressure and its effect by simulating different time points and standardized electric cleaning protocol was tested first. Followed by thermal burden due to varying thermal stress and thirdly change in pH stress imitating chemical exposure were examined separately. A digital microscope and a grid incisal and apical to the brackets (n = 32 fields) was used to standardize the optical analysis. Material loss due to mechanical stress compared to CG (score 0.00) was CP (1.2%), FP (21.5%), LB (22.2%) and PN (81.1%). No significant difference to CG presented PS. Material loss due to thermal stress was CP (0.5%), PS (2%), FP (2.6%), LB (3.1%) and PN (39.9%). Material loss due to chemical stress was FP (1.8%), PS (2.1%), LB (5.5%) and PN (39.6%). No significant difference to CG presented CP. Only PS and CP had optically provable, good resiliance to mechanical, thermal and chemical stress. Significantly poorer outcomes in particular showed PN.

Author response: Working strokes produced by curling protofilaments at disassembling microtubule tips can be biochemically tuned and vary with species

Aromatic residues forming tyrosine corners within Greek key motifs are critical for the folding, stability, and order of βγ-crystallins and thus lens transparency. To delineate how a double amino acid substitution in an N-terminal-domain tyrosine corner of the CRYGS mutant p.F10_Y11delinsLN causes juvenile autosomal dominant cortical lamellar cataracts, human γS-crystallin c-DNA was cloned into pET-20b (+) and a p.F10_Y11delinsLN mutant was generated via site-directed mutagenesis, overexpressed, and purified using ion-exchange and size-exclusion chromatography. Structure, stability, and aggregation properties in solution under thermal and chemical stress were determined using spectrofluorimetry and circular dichroism. In benign conditions, the p.F10_Y11delinsLN mutation does not affect the protein backbone but alters its tryptophan microenvironment slightly. The mutant is less stable to thermal and GuHCl-induced stress, undergoing a two-state transition with a midpoint of 60.4 °C (wild type 73.1 °C) under thermal stress and exhibiting a three-state transition with midpoints of 1.25 and 2.59 M GuHCl (wild type: two-state transition with Cm = 2.72 M GuHCl). The mutant self-aggregates upon heating at 60 °C, which is inhibited by α-crystallin and reducing agents. Thus, the F10_Y11delinsLN mutation in human γS-crystallin impairs the protein's tryptophan microenvironment, weakening its stability under thermal and chemical stress, resulting in self-aggregation, lens opacification, and cataract.

Understand relations between mechanical/thermal/chemical stresses and attrition of oxygen carrier in chemical looping process

Microsecond-Resolution Recording of T4 Lysozyme Observes a Brownian Ratchet

3-Fluted orthopaedic drills exhibit superior bending stiffness to their 2-fluted rivals: Clinical implications for targeting ability and the incidence of drill-bit failure

This research contributes to the study of prickle sensation in terms of single fiber bending modulus and flexural rigidity, which are important factors for fabric-evoked prickle for garment tactile comfort. In this study, a novel technique was used to study the flexural buckling behavior of single fibers using an axial fiber-compression-bending analyzer (FICBA). The bending behavior and bending equivalent modulus of different single fibers were measured and analyzed. The bending properties of single fibers were quantified by calculating the equivalent bending modulus, and the flexural rigidity via measurement of the protruding length ( l), diameter ( d) of single fiber, and its critical force ( Pcr), obtained from the peak point of the force–displacement curve. The experimental results indicate that ramie single fiber has the highest bending modulus, while cotton has the lowest bending modulus. However, hemp, jute, wool, flax, and cashmere fiber have bending modulus values lower than ramie but higher than cotton. On the other hand, the flexural rigidity of jute fiber is higher than that of wool followed by ramie, hemp, flax, cashmere, and cotton consecutively. Therefore, jute, wool, and ramie are stiffer than the other fibers, especially jute fiber. Thus, jute, wool, and ramie are uncomfortable single fibers because the fabric-evoked prickle, which is caused by short, coarse, and stiff fibers protruding from the fabric surface, generate sufficient force to evoke a low level of activity on a human nociceptors, but insufficient to penetrate the human skin so as to cause itchiness.

Molecular and chemical chaperones are key components of the two main mechanisms that ensure structural stability and activity under environmental stresses. Yet, chemical chaperones are often regarded only as osmolytes and their role beyond osmotic regulation is not fully understood. Here, we systematically studied a large group of chemical chaperones, representatives of diverse chemical families, for their protective influence under either thermal or chemical stresses. Consistent with previous studies, we observed that in spite of the structural similarity between sugars and sugar alcohols, they have an apparent difference in their protective potential. Our results support the notion that the protective activity is mediated by the solvent and the presence of water is essential. In the current work we revealed that i) polyols and sugars have a completely different profile of protective activity toward trifluoroethanol and thermal stress; ii) minor changes in solvent composition that do not affect enzyme activity, yet have a great effect on the ability of osmolytes to act as protectants and iii) increasing the number of active groups of carbohydrates makes them better protectants while increasing the number of active groups of methylamines does not, as revealed by attempts to synthesize de novo designed methylamines with multiple functional groups.

BRAF kinase is an essential target for anti-cancer drug development. Emergence of the β3-αC loop deletion mutation (ΔNVTAP) in BRAF kinase frequently occurred in human cancers seriously compromises the therapeutic efficacy of some BRAF kinase inhibitors, such as dabrafenib and vemurafenib. However, the mechanism of this resistance is still not well understood. In this study, the influence of the β3-αC deletion mutation on the binding profiles of three BRAF kinase inhibitors (AZ628, dabrafenib, and vemurafenib) with BRAFV600E or BRAFΔNVTAP was explored by conventional molecular dynamics (MD) simulations and binding free energy calculations. The simulation results indicated that the β3-αC deletion mutation enhances the flexibility of the αC helix and alters their conformations, which amplify the conformational entropy change (-TΔS) and weaken the interactions between the inhibitors and BRAF. The further per-residue binding free energy decomposition analysis revealed that the ΔNVTAP mutation changed the contributions of a few key residues to the bindings of dabrafenib or vemurafenib, such as L57, L66, W83, C84, F135, G145, and F147, but did not have obvious impact on the contributions of these residues to AZ628. Our results provide valuable clues to understand the mechanisms of drug resistance conferred by the β3-αC deletion mutation.

Differential gene expression in juvenile polyps of the coral Acropora tenuis exposed to thermal and chemical stresses

In reversed-phase liquid chromatography (RPLC), retained analytes can diffuse faster along the hydrophobic surface of the stationary phase than when dissolved in the water (W)–acetonitrile (ACN) mobile phase. We investigate the surface diffusion of four typical aromatic hydrocarbon analytes in RPLC through molecular dynamics simulations in a slit-pore RPLC model consisting of a silica-supported, end-capped, C18 stationary phase and a 70/30 (v/v) W/ACN mobile phase. Our data show that the lateral (surface-parallel) diffusive mobility of the analytes goes through a maximum in the ACN ditch, an ACN-rich border layer around the terminal part of the bonded-phase chains, because the solvent composition there is more conducive to analyte mobility than the W-rich mobile phase. At their lateral mobility maximum, analytes have contacts with 12–15 bonded-phase groups, 5–6 ACN and 1–2 W molecules. The lateral mobility gain from surface diffusion decreases with analyte polarity first and size second (like and unlike r...