Simulated evolution of emergent chiral structures in polyalanine

The relationship between monomer chirality and polymer structure has been studied using both theoretical and experimental methods. Atomistic models, such as the ones employed in computational protein folding and design, can be used to study the relationship between monomer chirality and the properties of polypeptides. Using a simulated evolution approach that combines side-chain epimerization with backbone flexibility, we recapitulate the relationship between basic forces that drive secondary structure formation and sequence homochirality. Additionally, we find heterochiral motifs including a C-terminal helix capping interaction and stable helix-reversals that result in bent helix structures. Our studies show that simulated evolution of chirality with backbone flexibility can be a powerful tool in the design of novel heteropolymers with tuned stereochemical properties.     

Formation and spatio-temporal evolution of periodic structures in lipid bilayers

Miscibility phase separation in lipid bilayers is widely implicated as an organizing principle in living cell membranes. However, the chemical and physical aspects of how membrane phase separation modulates protein activity remain obscure. Herein, we describe formation of ordered superstructures of coexisting liquid phases in bilayer membranes. Metastable stripe and hexagonal domain lattices are observed, as well as transitions between them. The high degree of order achieved by these methods facilitates statistical analysis of domain spatial distributions and enables measurement of domain interactions. Such long-range ordering principles may exist in more complicated membrane systems.     

Size-dependent shape evolution of silica nanoparticles into hollow structures

Hollow silica nanoparticles can be spontaneously generated without a template on the basis of the porous nature of silica and the high surface energy on the nanometer scale. We show that solid silica particles synthesized by the Stober and microemulsion methods initially develop small pores inside the nanoparticles under slightly basic conditions as a result of base-catalyzed etching. With further reaction, those small seed pores merge into a single void to reduce the surface energy of small pores, generating well-defined hollow nanoparticles. This behavior is unique to nanometer-sized porous materials, and the shape evolution is size-dependent, reinforcing the importance of evaluating the reactivity and structural changes of nanomaterials as well as their physical properties in different size ranges. The mechanism described here provides a simple way to generate uniform hollow nanoparticles of porous materials.     

The evolution of nonequilibrium laser plasma of metals with the formation of structures

Processes in a plasma formed by the evaporation of material by middle power laser radiation on a metallic surface are analyzed. In the regime considered the laser radiation is not absorbed by a metallic plasma and the radiation energy is spent in the main for the atomic evaporation. As a result of the plasma relaxation, hard metallic particles of sizes of the order of 10 nm are formed. They are joined in fractal aggregates of micron sizes, and fractal aggregates may be joined in aerogel-like structures of centimeters sizes. Such a laserplasma is an example of a plasma whose evolution leads to fractal object formation. A fireball is considered as a fractal object formed as a result of the evolution of an evaporated plasma. The considered object with aerogel-like structure that is formed in a gas has both scientific and practical interest.     

Some remarks on the evolution of research into the structures of mesogens and mesophases

Research on mesogens and mesophases began with the surprising observation of a fluid and birefringent phase formed by a pure compound having a calamitic (rod-like) molecule. The structures of the smectic A, nematic and cholesteric phases which emerged after this discovery were elucidated essentially by observations with a polarizing microscope. Smectic polymorphism was also established by microscopic observations. The structures of the different smectic mesophases previously predicted theoretically, was then obtained further type of purposely designed mesophase was the pyramidic type, also exhibiting a rich polymorphism. Research on mesogens and mesophases is a field in continuous expansion. main historical results on the are listed here. The discotic mesophase, and its polymorphism observed. A     

Conformations of individual quadruplex units studied in the context of extended human telomeric DNA

G-quadruplex conformations within a sequence of three quadruplex units of human telomeric DNA were studied by two-frequency pulsed electron paramagnetic resonance (EPR) spectroscopy. In contrast to some individual G-quadruplexes, within the higher-order human telomeric sequence a (3+1) hybrid structure is formed.     

Synthesis and textural evolution of alumina particles with mesoporous structures

Alumina particles with mesostructures were synthesized through a chemical precipitation method by using different inorganic aluminum salts followed by a heterogeneous azeotropic distillation and calcination process. The obtained mesoporous γ-alumina particles were systematically characterized by the X-ray diffraction, transmission electron microscopy and nitrogen adsorption-desorption measurement. Effects of the aluminum salt counter anion, pH value and the azeotropic distillation process on the structural or textural evolution of alumina particles were investigated. It is found that Cl⁻ in the reaction solution can restrain the textural evolution of the resultant precipitates into two-dimensional crystallized pseudoboehmite lamellae during the heterogeneous azeotropic distillation, and then transformed into γ-Al₂O₃ particles with mesostructures after further calcination at 1173 K, whereas coexisting SO₄²⁻ can promote above morphology evolution and then transformed into γ-Al₂O₃ nanofibers after calcination at 1173 K. Moreover nearly all materials retain relatively high specific surface areas larger than 100 m² g⁻¹ even after calcinations at 1173 K.     

Comparison of the structures of human fibronectin and plasma cold-insoluble globulin

Human amniotic fluid fibronectin and plasma fibronectin (cold-insoluble globulin) are indistinguishable both immunologically and by amino acid composition. Cyanogen bromide and tryptic peptides also suggest substantial structural homology. However, carbohydrate analysis has demonstrated additional saccharides in fibronectin and an overall increase in carbohydrate content relative to cold-insoluble globulin. Furthermore, limited proteolytic cleavage of the two proteins indicates differences in primary structure or in conformation. Using affinity-purified antibodies to cold-insoluble globulin, a glucosamine-labeled pronase-resistant component, probably proteoglycan, was found to coprecipitate with fibronectin, suggesting an association between these two macromolecules in the connective tissue matrix.     

Raman spectroscopic investigation of cocaine hydrochloride on human nail in a forensic context

This study describes the application of Raman spectroscopy to the detection of drugs of abuse and noncontrolled substances used in the adulteration of drugs of abuse on human nail. Contamination of the nail may result from handling or abusing these substances. Raman spectra of pure cocaine hydrochloride, a seized street sample of cocaine hydrochloride (77%), and paracetamol could be acquired from drug crystals on the surface of the nail. An added difficulty in the analytical procedure is afforded by the presence of a nail varnish coating the nail fragment. By using confocal Raman spectroscopy, spectra of the drugs under nail varnish could be acquired. Spectra of the drugs could be readily obtained nondestructively within three minutes with little or no sample preparation. Raman spectra could be acquired from drug particles with an average size of 5–20 μm. Acquisition of Raman point maps of crystals from both pure and street samples of cocaine hydrochloride under nail varnish is also reported. Figure Raman spectrum and point Raman map of cocaine HCI     

In situ conversion builds MIL-101@NiFe-LDH heterojunction structures to enhance the oxygen evolution reaction

The construction of rich phase interfaces to increase active reaction area in hybrid materials is an excellent strategy to improve electrochemical performance. Under this guideline, MIL-101@OX-metal organic framework (MOF) is constructed by the "MOF on MOF" method, then converts to MIL-101@NiFe-layered double hydroxides (LDH) by in situ transformation in alkaline solution. MIL-101@NiFe-LDH shows excellent electrochemical water oxidation performance. It needs only an overpotential of 215 mV to drive 10 mA/cm² of oxygen evolution reaction (OER), which is less than that of NiFe-LDH, MIL-101. In addition, MIL-101@NiFe-LDH has the smallest Tafel slope (55.1 mV/dec) compared with NiFe-LDH (61.1 mV/dec), MIL-101 (150.8 mV/dec). The excellent water oxidation activity is due to the high phase interfaces derived from high specific surface area of MOF. This work offers an alternative method for making MOF/LDH heterostructures with an optimized phase interfaces and provides new insights for OER.     

Plasma-surface interaction in the context of ITER

The decreasing availability of energy and concern about climate change necessitate the development of novel sustainable energy sources. Fusion energy is such a source. Although it will take several decades to develop it into routinely operated power sources, the ultimate potential of fusion energy is very high and badly needed. A major step forward in the development of fusion energy is the decision to construct the experimental test reactor ITER. ITER will stimulate research in many areas of science. This article serves as an introduction to some of those areas. In particular, we discuss research opportunities in the context of plasma-surface interactions. The fusion plasma, with a typical temperature of 10 keV, has to be brought into contact with a physical wall in order to remove the helium produced and drain the excess energy in the fusion plasma. The fusion plasma is far too hot to be brought into direct contact with a physical wall. It would degrade the wall and the debris from the wall would extinguish the plasma. Therefore, schemes are developed to cool down the plasma locally before it impacts on a physical surface. The resulting plasma-surface interaction in ITER is facing several challenges including surface erosion, material redeposition and tritium retention. In this article we introduce how the plasma-surface interaction relevant for ITER can be studied in small scale experiments. The various requirements for such experiments are introduced and examples of present and future experiments will be given. The emphasis in this article will be on the experimental studies of plasma-surface interactions.     

Inhibition of translation by small RNA-stabilized mRNA structures in human cells

RNA-mediated gene regulation and expression are critically dependent on both nucleic acid architecture and recognition. We present a novel mechanism for the regulation of gene expression through direct RNA-RNA interactions between small RNA and mRNA in human cells. Using mRNA reporters containing G-rich sequences in the 5'-untranslated region (5'-UTR), in the coding region, or both, we showed that G-rich small RNAs bind to the reporter mRNAs and form an intermolecular RNA G-quadruplex that can inhibit gene translation in living cells. Using a combination of circular dichroism (CD) and RNase footprinting in vitro, we found that the intermolecular G-quadruplexes show a parallel G-quadruplex structure. We next investigated whether the intermolecular G-quadruplex is present in living cells. Employing the fluorophore-labeled probes, we found that two G-rich RNA molecules form an intermolecular G-quadruplex structure in living cells. These results extend the concept of small RNA-mediated expression and suggest an important role for such RNA structures in the inhibition of mRNA translation.     

dbHDPLS: A database of human disease-related protein-ligand structures

Protein-ligand complexes perform specific functions, most of which are related to human diseases. The database, called as human disease-related protein-ligand structures (dbHDPLS), collected 8833 structures which were extracted from protein data bank (PDB) and other related databases. The database is annotated with comprehensive information involving ligands and drugs, related human diseases and protein-ligand interaction information, with the information of protein structures. The database may be a reliable resource for structure-based drug target discoveries and druggability predictions of protein-ligand binding sites, drug-disease relationships based on protein-ligand complex structures. It can be publicly accessed at the website: http://DeepLearner.ahu.edu.cn/web/dbDPLS/.     

Effects of monomer structures on the evolution of liquid–crystal texture and crystallization during thin-film polymerization

We investigated in situ the effects of monomer structures on the formation and evolution of liquid–crystal texture and crystallization during thin-film polymerization of a series of liquid–crystalline and crystalline polymers. The monomers used in this study consisted of 2,6-acetoxynaphthoic acid (ANA), p-acetoxybenzoic acid (ABA), acetoxy acetanilide (AAA), and isophthalic acid (IA). The polycondensation reactions were conducted on the heating stage of a polarizing microscope. The formation of liquid crystallinity was found to be strongly dependent on the straight-monomer structures of ANA and ABA and their percentages as well as the reaction temperature. For the ANA/AAA/IA and ABA/AAA/IA reaction systems, the critical straight-monomer content (ANA or ABA) existed to form the liquid–crystalline (LC) state. Interestingly, the critical content to form liquid crystallinity decreased with an increase in the reaction temperature. Above the critical content, the appearance of a defective LC phase and the annihilation of disclinations were observed during the polycondensation reactions. The number of defects decreased with increasing reaction time through annihilation. The annihilation rate increased whereas the defect density decreased with increasing straight-monomer content. For the same molar ratio, the reaction system containing ANA had a faster annihilation rate than that containing ABA. Below the critical content, crystalline polymers were formed. Nucleation and crystal growth were observed during the reactions, and the rate of crystal growth decreased with increasing ANA or ABA content. For the systems having the same molar ratio of ANA or ABA, the ANA/AAA/IA system had a higher tendency to yield the LC phase than the ABA/AAA/IA system because ANA has a longer mesogenic unit. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 3084–3096, 1999     

Simulation of human vision by image evolution in light-excitable nonlinear optical mediums

The nonlinear optical membrane used for image processing was prepared using tetraethyl silicate by sol-gel method under mild conditions. Ru(bpy)3Cl2 (bpy, bipyridine) was immobilized in the sol-gel matrix. This light-excitable membrane containing Ru(bpy)3Cl2 as photocatalyst could catalyze the Belousov-Zhabotinsky reaction by illumination. Our results indicated that a fine-definition image processing could be autoperformed when projecting a picture on this medium. The imaging process was an image evolution process, which was similar to that of the human vision process.     

Energetic basis of human telomeric DNA folding into G-quadruplex structures

Recent theoretical studies performed on the folding/unfolding mechanism of the model telomeric human DNA, 5'-AGGGTTAGGGTTAGGGTTAGGG-3' (Tel22), have indicated that in the presence of K(+) ions Tel22 folds into two hybrid G-quadruplex structures characterized by one double and two reversal TTA loops arranged in a different way. They predicted a new unfolding pathway from the initial mixture of hybrid G-quadruplexes via the corresponding intermediate triplex structures into the final, fully unfolded state. Significantly, no experimental evidence supporting the suggested pathway has been reported. In the current work, we performed a comprehensive global thermodynamic analysis of calorimetric (DSC, ITC) and spectroscopic (CD) data obtained on monitoring the folding/unfolding of Tel22 induced by changes of temperature and K(+) concentration. We show that unfolding of Tel22 may be described as a monomolecular equilibrium three-state process that involves thermodynamically distinguishable folded (F), intermediate (I), and unfolded (U) state. Considering that calorimetric methods cannot distinguish between energetically similar G-quadruplex or triplex conformations predicted by the theoretical model one can conclude that our results represent the first experimental support of the suggested unfolding/folding mechanism of Tel22. This conclusion is confirmed by the fact that the estimated number of K(+) ions released upon each unfolding step in our thermodynamic model agrees well with the corresponding values predicted by the theoretical model and that the observed changes in enthalpy, entropy, and heat capacity accompanying the F → I and I → U transitions can be reasonably explained only if the intermediate state I is considered to be a triplex structural conformation.     

Identification of phospholipid structures in human blood by direct-injection quadrupole-linear ion-trap mass spectrometry

Direct-injection electrospray ionization mass spectrometry in combination with information-dependent data acquisition (IDA), using a triple-quadrupole/linear ion trap combination, allows high-throughput qualitative analysis of complex phospholipid species from child whole blood. In the IDA experiments, scans to detect specific head groups (precursor ion or neutral loss scans) were used as survey scans to detect phospholipid classes. An enhanced resolution scan was then used to confirm the mass assignments, and the enhanced product ion scan was implemented as a dependent scan to determine the composition of each phospholipid class. These survey and dependent scans were performed sequentially and repeated for the entire duration of analysis, thus providing the maximum information from a single injection. In this way, 50 different phospholipids belonging to the phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, phosphatidylcholine and sphingomyelin classes were identified in child whole blood.     

Affinity of the anthracycline antitumor drugs Doxorubicin and Sabarubicin for human telomeric G-quadruplex structures

Combining various techniques in solution we proved that Doxorubicin, also called Adriamycin, and Sabarubicin, also known as MEN 10755, bind to the human telomeric sequence, 5'-d[GGG(TTAGGG)(3)]-3' (21-mer), assuming a G-quadruplex structure in the presence of K(+). Complexes of drugs with the 21-mer in 1?:?1 and 2?:?1 stoichiometry coexist in solution. Association constants were obtained from titration experiments and confirmed by isothermal titration calorimetry. The fluorescence of the drugs was quenched upon complexation. UV circular dichroism (CD) spectra of the complexes were characterized by the G-quadruplex signal and indicated that drug binding influences the equilibrium between quadruplex conformations. The visible CD spectra were exclusively due to the drug and show differences in the complexation modes of the two drugs. Spectroscopic and thermodynamic parameters of the 1?:?1 complexes point to drug stacking with the G-quadruplex top or bottom tetrad. Thermodynamic data suggests that the binding of the second drug molecule in the 2?:?1 complex may occur in a groove. Complexation caused a small increase in the thermal stability of the G-quadruplex main conformation, shifting T(m) from 62 to 67 °C.     

The structures of Bi3PbWO8Cl and Bi4NbO8Cl and the evolution of the bipox structure series

A new adaptive structure series is described which is a mixture of Aurivillius phases and Sillen's phases. The structures of two of the simplest members of this series are presented.