First-principle study of interfacial properties between γ-TiAl and TiC,VN

The adhesion, wettability, atomic bonding and electronic structure of γ-TiAl(110)/TiC(100) and γ-TiAl(110)/VN(100) interfaces were performed and investigated using first-principle calculations. Surface energy of γ-TiAl, TiC and VN with low crystal indices was calculated and compared, respectively. The three Al-terminated γ-TiAl(110)/ceramic(100) interface models were investigated to illustrate the interfacial bonding nature. The structure of Al atom placed on the top of the metalloid C and N atoms at the interface is the preferred interfacial structure with the larger work of adhesion. The electronic structure results show that the structure with metalloid site exists with the stronger polar covalent bonding between the interfacial Al and metalloid atom. The interfacial structure with metal site exhibits a mixture of the metallic features with some degree of covalent features. The simulation results are in agreement with the experimental results, in which the γ-TiAl/TiC interface exhibits the better wettability and stronger bonding than the γ-TiAl/VN interface.     

Stabilization of β-glucosidase by polyhydric alcohols

Thermal stability of β-glucosidase in Thermomonospora curvata lysed cell extracts, culture solids and lyophilized cells was increased 9–16-fold by polyhydric alcohols. Sorbitol, the most soluble of these alcohols, doubled the recovery of β-glucosidase during preliminary purification procedures.     

A comparison of the interfacial interactions of the apoprotein from high density lipoprotein and β-casein with phospholipids

The conformations adopted by β-casein and the total apoprotein from serum high density lipoprotein when spread at the air-water interface are compared; the monolayer data are consistent with the apoprotein being α-helical and the β-casein being disordered with segments distributed in loops and trains. The penetration of these hydrophobic proteins into phosphatidylcholine monolayers in different physical states was investigated. More protein can penetrate into monolayers when they are in the liquid-expanded state; for penetration at constant total surface area the lateral compressibility of the lipid is an important factor. The charge and conformation of the polar group of the phospholipid does not have a major influence on the interaction. The mixed films of lipid and protein have a mosaic structure; probably the β-casein is in a compressed state whereas the apoprotein is extended as α-helices in the plane of the interface. The chain-length dependences of the interaction of the apoprotein with phosphatidylcholine monolayers and bilayers are different; when the apoprotein binds to bilayers of shorter-chain phosphatidylcholines it alters the shape of the lipid-water interface whereas with monolayers the interface remains planar throughout.     

Production of nikkomycin by immobilized Streptomyces cells — Physiological properties

Summary The antibiotic nikkomycin can be produced by calcium alginate immobilized mycelium of Streptomyces tendae Tü 901 in batch and continuous culture.Scanning electron micrographs show the porous structure of the matrix and the distribution of the cells in the gel.Some physiological properties of free and immobilized mycelia were compared. Immobilization does not change the relative amounts of nikkomycin compounds in the culture broth. DNA and protein content were the same in free and immobilized cells. The specific activity of fructosediphosphate aldolase dropped during fermentation and was lower for entrapped than for free cells. The specific activity of mannitol dehydrogenase increased up to the end of the fermentation and was the same for free and immobilized mycelium.In continuous culture the relative amount of mannitol consumed decreased with increasing flow rate. When the medium was supplemented with amino acids mannitol consumption increased significantly.Dedicated to Prof. Dr. L. Acker on the occasion of his 70th birthday     

A determination of liquid–vapour interfacial properties for methanol using a linear-combination-based isotropic periodic sum

We performed molecular dynamics simulations of the methanol liquid–vapour interfacial systems for a wide temperature range of 200–350 K. The linear-combination-based isotropic periodic sum (LIPS) method was used for estimating Coulombic interactions of the systems. The temperature dependence of the liquid and vapour phase densities, surface thickness and surface tension using the LIPS method was almost equal to that of the Ewald sum method. The temperature dependence of the electrostatic potential profile using the LIPS method was very similar to that of the Ewald sum method. We conclude that the LIPS method provides a reasonable accuracy in determining the liquid–vapour interfacial properties of polar molecules for many temperature conditions.     

Single-molecule atomic force microscopy force spectroscopy study of Aβ-40 interactions

Misfolding and aggregation of amyloid β-40 (Aβ-40) peptide play key roles in the development of Alzheimer's disease (AD). However, very little is known about the molecular mechanisms underlying these molecular processes. We developed a novel experimental approach that can directly probe aggregation-prone states of proteins and their interactions. In this approach, the proteins are anchored to the surface of the atomic force microscopy substrate (mica) and the probe, and the interaction between anchored molecules is measured in the approach-retraction cycles. We used dynamic force spectroscopy (DFS) to measure the stability of transiently formed dimers. One of the major findings from DFS analysis of α-synuclein (α-Syn) is that dimeric complexes formed by misfolded α-Syn protein are very stable and dissociate over a range of seconds. This differs markedly from the dynamics of monomers, which occurs on a microsecond to nanosecond time scale. Here we applied the same approach to quantitatively characterize interactions of Aβ-40 peptides over a broad range of pH values. These studies showed that misfolded dimers are characterized by lifetimes in the range of seconds. This value depends on pH and varies between 2.7 s for pH 2.7 and 0.1 s for pH 7, indicating that the aggregation properties of Aβ-40 are modulated by the environmental conditions. The analysis of the contour lengths revealed the existence of various pathways for dimer dissociation, suggesting that dimers with different conformations are formed. These structural variations result in different aggregation pathways, leading to different types of oligomers and higher-order aggregates, including fibrils.     

Influence of 7α-hydroxycholesterol on sphingomyelin and sphingomyelin/phosphatidylcholine films - The Langmuir monolayer study complemented with theoretical calculations

Under pathological conditions, cholesterol oxidation products (oxysterols) appear in enhanced concentration in blood and cerebrospinal fluid, which leads to cytotoxic effect, especially in central nervous system. However, the mode of action of oxysterols on the membrane level has not been fully resolved. In this paper we have investigated the interaction between 7α- hydroxycholesterol, 7α-OH (one of the most abundant oxysterol in human body) and two major membrane lipids: sphingomyelin, SM (basic component of lipid rafts and nerve membrane) and 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine, POPC (main phospholipid of mammalian cell membranes). 7α-OH/SM mixtures may mimic pathologically changed lipid raft (ordered phase, L_O) while the SM/POPC system can model its surrounding (liquid-disordered phase, L_α). For our study, the Langmuir monolayer technique (based on registration of the surface pressure/area, π/A isotherms), complemented with surface visualization technique (Brewster angle microscopy, BAM) and theoretical calculations, have been employed. The observed affinity of 7α-OH to SM, which appears to be stronger than in cholesterol/SM system, indicates that cholesterol might be partially replaced in lipid rafts by its oxidized derivative. Its incorporation significantly increases rigidity of the system in relation to normal (cholesterol-containing) raft, which can disturb its proper functioning. On the other hand, the poor effect of this oxysterol on the raft's environment was observed.     

Modulation of the activity of cytosolic phospholipase A2�� (cPLA2��) by cellular sphingolipids and inhibition of cPLA2�� by sphingomyelin

We examined the effect of the cellular sphingolipid level on the release of arachidonic acid (AA) and activity of cytosolic phospholipase A2α (cPLA2α) using two Chinese hamster ovary (CHO)-K1-derived mutants deficient in sphingolipid synthesis: LY-B cells defective in the LCB1 subunit of serine palmitoyltransferase for de novo synthesis of sphingolipid species, and LY-A cells defective in the ceramide transfer protein CERT for SM synthesis. When LY-B and LY-A cells were cultured in Nutridoma medium and the sphingolipid level was reduced, the release of AA stimulated by the Ca²⁺ ionophore {"type":"entrez-nucleotide","attrs":{"text":"A23187","term_id":"833253","term_text":"A23187"}}A23187 increased 2-fold and 1.7-fold, respectively, compared with that from control cells. The enhancement in LY-B cells was decreased by adding sphingosine and treatment with the cPLA2α inhibitor. When CHO cells were treated with an acid sphingomyelinase inhibitor to increase the cellular SM level, the release of AA induced by {"type":"entrez-nucleotide","attrs":{"text":"A23187","term_id":"833253","term_text":"A23187"}}A23187 or PAF was decreased. In vitro studies were then conducted to test whether SM interacts directly with cPLA2α. Phosphatidylcholine vesicles containing SM reduced cPLA2α activity. Furthermore, SM disturbed the binding of cPLA2α to glycerophospholipids. These results suggest that SM at the biomembrane plays important roles in regulating the cPLA2α-dependent release of AA by inhibiting the binding of cPLA2α to glycerophospholipids.     

A study of the dynamic properties of membrane proteins using M?ssbauer spectroscopy

While studying the parameters of "narrow" and "broad" lines appearing in M?ssbauer spectra of undehydrated membrane proteins heated from 80 to 280 K it has been for the first time found for proteins that the behavior of the complete area of spectrum S does not differ from that of Debye-Waller factor. An abrupt decrease of quadrupole splitting value from delta = 0.7 mm/s to delta = 0 within the temperature range 220-270 K. Computation of the spectra with their division into 3 components responding respectively by heat, diffusion and conformational movement made possible explanation of all the evolutionary changes proceeding in them with the temperature rise. Preservation of the complete area of the spectrum S (T) is conditioned by the increase of the component responsive to conformational changes of Fe atom within 230-270 K. These movements "suppress" quadrupole splitting observed in the spectra at low temperatures. Dynamic mobility is considered in terms of the Fe atom movement in the biphase potential.     

Nanomechanical properties of MscL α helices: A steered molecular dynamics study

Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs. Using this method, we could overcome the issues encountered with the commonly used constant-velocity SMD simulations, such as low mechanical stability of the helix during stretching and high dependency of the elastic properties on the pulling rate. We estimated Young's moduli of the α-helices of MscL to vary between 0.2 and 12.5 GPa with TM2 helix being the stiffest. We also studied the effect of water on the properties of the pore-lining TM1 helix. In the absence of water, this helix exhibited a much stiffer response. By monitoring the number of hydrogen bonds, it appears that water acts like a ‘lubricant’ (softener) during TM1 helix elongation. These data shed light on another physical aspect underlying hydrophobic gating of MS channels, in particular MscL.     

Monte Carlo study of the formation and conformational properties of dimers of Aβ42 variants

Small soluble oligomers, and dimers in particular, of the amyloid β-peptide (Aβ) are believed to play an important pathological role in Alzheimer's disease. Here, we investigate the spontaneous dimerization of Aβ42, with 42 residues, by implicit solvent all-atom Monte Carlo simulations, for the wild-type peptide and the mutants F20E, E22G and E22G/I31E. The observed dimers of these variants share many overall conformational characteristics but differ in several aspects at a detailed level. In all four cases, the most common type of secondary structure is intramolecular antiparallel β-sheets. Parallel, in-register β-sheet structure, as in models for Aβ fibrils, is rare. The primary force driving the formation of dimers is hydrophobic attraction. The conformational differences that we do see involve turns centered in the 20-30 region. The probability of finding turns centered in the 25-30 region, where there is a loop in Aβ fibrils, is found to increase upon dimerization and to correlate with experimentally measured rates of fibril formation for the different Aβ42 variants. Our findings hint at reorganization of this part of the molecule as a potentially critical step in Aβ aggregation.     

Stabilization of trypsin by chemical modification with β-cyclodextrin monoaldehyde

The monoaldehyde derivative of -cyclodextrin was attached to trypsin via reductive alkylation with NaBH₄. The thermostability was enhanced from 49.5 °C to 60 °C for modified trypsin. The activation free energy of thermal inactivation at 50 °C was increased by 3.2 kJ mol^–1. The conjugated enzyme retained 100% of its initial activity after 3 h incubation at pH 9.     

Tryptophan interactions of gramicidin A′ channels in lipids: a time-resolved fluorescence study

The evolution of the incorporation of cation transport channels into lysolecithin micelles by gramicidin A was followed by measuring the ns time-resolved fluorescence of the tryptophan residues. In all samples, the tryptophan fluorescence could be resolved into three exponentially decaying components. The three decay times ranged from 6 to 8 ns, 1.8 to 3 ns, and 0.3 to 0.8 ns, depending on the emission wavelength. The fractional fluorescence of each component changed with incubation time. The long lifetime component had a reduced contribution to the total fluorescence while the short decay time component increased. The fluorescence spectra could be resolved into three distinct fluorescent components having maxima at 340 nm, 330 nm and 323 nm after 90 min of incubation, and 335 nm, 325 nm and 320 nm after 24 h of incubation. These maxima were, respectively, associated with the long, medium and short decay components. The fluorescence decay behaviour was interpreted as representing three families of tryptophans, the short lifetime component being due to a stacking interaction between tryptophan residues. The variation with incubation time suggests a two-step process in the channel-lipid organization. The first is associated with the conformational change of the polypeptide as it takes up a left-handed helical head-to-head dimer structure in the lipid. The second step is proposed to involve changes originating from membrane assembly and intermolecular interactions between channels as they form hexameric clusters.     

Locust solid cuticle—A time sequence of mechanical properties

Studies on locust femur solid cuticle indicate that there is a continuum of biomechanically important properties from one instar to the next, and that there is a constant ratio of stiffness to mass which is only interrupted at ecdysis. The biochemical nature of both larval and adult solid cuticle is interpreted in terms of both the tangent modulus and the breaking strength of the femur cuticle. The mechanical behaviour of the different layers in the cuticle is discussed.     

Effects of oxidation on copper-binding properties of Aβ1-16 peptide: A pulse radiolysis study

Abstract

The reaction of hydroxyl radicals (^?OH) with Aβ1-16 peptide was carried out using pulse radiolysis to understand the effect of oxidation of peptide on its copper-binding properties. This reaction produced oxidized, dimeric and trimeric Aβ1-16 peptide species. The formation of these products was established with the help of fluorescence spectroscopy and mass spectrometry. The mass spectral data indicate that the major site of oxidation is at His6, while the site for dimerization is at Tyr10. Diethyl pyrocarbonate-treated Aβ1-16 peptide did not produce any trimeric species upon oxidation with ^?OH. The quantitative chemical modification studies indicated that one of the three histidine residues is covalently modified during pulse radiolysis. The copper-binding studies of the oxidized peptide revealed that it has similar copper-binding properties as the unoxidized peptide. Further, the cytotoxicity studies point out that both oxidized and unoxidized Aβ1-16 peptide are equally efficient in producing free radicals in presence of copper and ascorbate that resulted in comparable cell death.     

Zwitterionic conformers of pyrrolysine and their interactions with metal ions—a theoretical study

A total of 16 pyrrolysine conformers in their zwitterionic forms are studied in gas and simulated aqueous phase using a polarizable continuum model (PCM). These conformers are selected on the basis of our study on the intrinsic conformational properties of non-ionic pyrrolysine molecule in gas phase [Das and Mandal (2013) J Mol Model 19:1695?1704]. In aqueous phase, the stable zwitterionic pyrrolysine conformers are characterized by full geometry optimization and vibrational frequency calculations using B3LYP/6-311++G(d,p) level of theory. Single point calculations are also carried out at MP2/6-311++G(d,p) level. Characteristic intramolecular hydrogen bonds present in each conformer, their relative energies, theoretically predicted vibrational spectra, rotational constants and dipole moments are systematically reported. The calculated relative energy range of the conformers at B3LYP/6-311++G(d,p) level is 5.19 kcal mol^?1 whereas the same obtained by single point calculations at MP2/6-311++G(d,p) level is 4.58 kcal mol^?1. A thorough analysis reveals that four types of intramolecular H-bonds are present in the conformers; all of which play key roles in determining the energetics and in imparting the observed conformations to the conformers. The vibrational frequencies are found to shift invariably toward the lower side of frequency scale corresponding to the presence of the H-bonds. This study also points out that conformers with diverse structural motifs may differ in their thermodynamical stability by a narrow range of relative energy. The effects of metal coordination on the relative stability order and structural features of the conformers are examined by complexing five zwitterionic conformers of pyrrolysine with Cu⁺² through their carboxylate groups. The interaction enthalpies and Gibbs energies, rotational constants, vibrational frequencies and dipole moments of the metal complexes calculated at B3LYP level are also reported. The zwitterionic conformers of pyrrolysine are not stable in gas phase; after geometry optimization they are converted to the non-ionic forms.     

Stabilization of mammalian liver branched-chain α-ketoacid dehydrogenase by thiamin pyrophosphate

Thiamin pyrophosphate, CoASH, and NAD⁺ have been shown to reversibly bind to the purified bovine liver mitochondrial branched-chain α-ketoacid dehydrogenase complex. When saturated with thiamin pyrophosphate, the complex was more stable to heat and chymotrypsin inactivation. Under identical saturating conditions a conformational change in the complex was observed by circular dichroism spectroscopy. We postulate that thiamin pyrophosphate can increase the biological half-life of the in vivo, membrane-bound complex through conformational changes induced by the binding of this cofactor.     

Identification of distinct physiochemical properties of toxic prefibrillar species formed by Aβ peptide variants

The formation of amyloid-β peptide (Aβ) aggregates at an early stage during the self-assembly process is an important factor in the development of Alzheimer's disease. The toxic effect is believed to be exerted by prefibrillar species of Aβ. It is therefore important to identify which prefibrillar species are toxic and characterize their distinct properties. In the present study, we investigated the in vitro aggregation behavior of Aβ-derived peptides possessing different levels of neurotoxic activity, using fluorescence spectroscopy in combination with transmission electron microscopy. The toxicity of various Aβ aggregates was assessed by using cultures of human neuroblastoma cells. Through combined use of the fluorescence probe 8-anilino-1-napthalenesulfonate (ANS) and the novel luminescent probe pentamer formyl thiophene acetic acid (p-FTAA), we were able to identify those Aβ peptide-derived prefibrillar species which exhibited cellular toxicity. In particular, species, which formed early during the aggregation process and showed strong p-FTAA and ANS fluorescence, were the species that possessed toxic activities. Moreover, by manipulating the aggregation conditions, it was possible to change the capacity of the Aβ peptide to form nontoxic versus toxic species.