Efficient quantification of the importance of contacts for the dynamical stability of proteins

Understanding the stability of the native state and the dynamics of a protein is of great importance for all areas of biomolecular design. The efficient estimation of the influence of individual contacts between amino acids in a protein structure is a first step in the reengineering of a particular protein for technological or pharmacological purposes. At the same time, the functional annotation of molecular evolution can be facilitated by such insight. Here, we use a recently suggested, information theoretical measure in biomolecular design - the Kullback-Leibler-divergence - to quantify and therefore rank residue-residue contacts within proteins according to their overall contribution to the molecular mechanics. We implement this protocol on the basis of a reduced molecular model, which allows us to use a well-known lemma of linear algebra to speed up the computation. The increase in computational performance is around 10(1)- to 10(4)-fold. We applied the method to two proteins to illustrate the protocol and its results. We found that our method can reliably identify key residues in the molecular mechanics and the protein fold in comparison to well-known properties in the serine protease inhibitor. We found significant correlations to experimental results, e.g., dissociation constants and Φ values.     

Bioinformatic analysis of molecular network of glucosinolate biosynthesis

Glucosinolates constitute a major group of secondary metabolites in Arabidopsis, which play an important role in plant interaction with pathogens and insects. Advances in glucosinolate research have defined the biosynthetic pathways. However, cross-talk and interaction between glucosinolate pathway and other molecular pathways are largely unknown. Here three bioinformatics tools were used to explore novel components and pathway connections in glucosinolate network. Although none of the software tools were prefect to predict glucosinolate genes, combination of results generated by all the tools led to successful prediction of all known glucosinolate genes. This approach was used to predict new genes in glucosinolate network. A total of 330 genes were found with high potential to relate to glucosinolate biosynthesis. Among them 64 genes were selected to construct glucosinolate network because their individual connection to at least one known glucosinolate gene was predicted by all the software tools. Microarray data of candidate gene mutants were used for validation of the results. The mutants of nine genes predicted by glucosinolate seed genes all exhibited changes in the expression of glucosinolate genes. Four of the genes have been well-known to functionally interact with glucosinolate biosynthesis. These results indicate that the approach we took provides a powerful way to reveal new players in glucosinolate networks. Creation of an in silico network of glucosinolate biosynthesis will allow the generation of many testable hypotheses and ultimately enable predictive biology.     

Review of Mesoscopic Modeling of Liquids in Materials Science

Mesoscopic theories can be used in the field of materials science to derive local average properties of relevance to the engineer such as flux, pressure, average density or composition. In the following density functional theory will be described and applied to different systems of interest and in particular, to materials formed from complex liquids as characterized by atomic structure and the type of interaction between the individual particles. The calculation of the solid to liquid transition will be explained in detail as a prototype for other order disorder transitions. The theory of polymers in solution will be revisited and used to calculate phase separation in mixtures. An extension of the theory to include the orientation of rodlike, long molecules will be applied to liquid crystals. In the presence of an interface, the system properties depend strongly on position in space and can be predicted from parameters obtained in the bulk in a square gradient approximation for sufficiently smooth and small deviations from the uniform distribution. A phase transition is often used to prepare heterogeneous materials by nucleation and growth. It will be shown how the equilibrium theory can be extended to study the dynamics of nonequilibrium phenomena.     

Characterization of the barrier properties of composites of HDPE and purified cellulose fibers

The present work presents and discusses the interrelation between composition, morphology, thermal history, mechanical and barrier properties to oxygen and limonene of composites of HDPE/MA-PE/cellulose fibers of significant interest in, among others, food packaging applications. From the overall results, it was observed that increasing the loading of purified alpha-cellulose fibers in the polyethylene matrix beyond 10 wt.% led to a decrease in the permeability coefficient of d-limonene, effect which was found to be primarily related to a decrease in the overall solubility of this strongly plasticizing aroma component. On the other hand, the oxygen permeability was found to decrease to a significant extend with increasing fiber content beyond 5 wt.%, but this effect was more strongly ascribed to a significant decrease in the diffusion coefficient. Therefore, the fibers are thought to generate a more tortuous path for the non-interacting gas molecules to travel across the composites thickness, even when tested at high relative humidity conditions. Optimum fiber loading levels in terms of overall property balance were found to be around 20 wt.%.     

荧光关联光谱在高分子单链研究中的应用

荧光关联光谱(fluorescence correlation spectroscopy,FCS)是一项用于研究体系动力学性质的统计光谱技术,随着它被引入材料与化学研究领域,近年来取得了大量全新的研究成果.该技术在高分子科学研究中也逐渐发挥出越来越大的作用,特别是在聚合物结构和动力学方面,这表明它在高分子领域的巨大潜力.本文将从FCS的基本原理、实验技巧以及在一些具有挑战性体系中的应用等方面展开,着重介绍它在高分子溶液,如聚电解质溶液、高分子混致不溶现象,以及不同的表界面体系中取得的新成果,展示FCS区别于其他传统技术的特点和优势.     

Synthesis of a Pair of Derivatives of N-Methylpyrrole Polyamide

A pair of derivatives of tetrameric N-methylpyrrole polyamide were synthesized in order to develop a new method for the study of interaction of the polyamide derivatives with DNA. Indole acetic acid and nicotinic acid were introduced to the polyamide in the synthesized compound, which showed an expected red shift in the UV spectrum. These compounds may function as a potential tool in the detection of the polyamide binding to DNA.     

聚丙烯酰胺胶状杂质的形成因为

在聚丙烯酰胺(PAM)配制现场发现过滤器滤袋内存在大量黑色和黄色且有刺鼻腐臭气味的胶状条形物;这类杂质造成过滤装置严重堵塞和设备腐蚀.鉴于此,从细菌和无机离子含量两方面着手分析了聚丙烯酰胺胶状条形杂质的形成因为.结果表明:由于细菌和金属离子Fe3+含量的增加,PAM的侧酰胺基降解成羧基;而含大量金属离子的PAM溶液经缠...     

Kinetics of Thermal Decomposition of Plumbo-jarosite

An investigation was carried out on the kinetics of thermal decomposition of plumbo-jarosite. The kinetic models of dissociation of the compounds in the ore were identified. The results of the kinetic studies and the mechanism of the process are discussed. The thermal decomposition of plumbo-jarosite occurs in three stages: the first up to 763, the second up to 1023 and the third up to 1223 K, the corresponding activation energy values being 62.2, 60.3 and 98.0 kJ mol^–1 , respectively. This revised version was published online in July 2006 with corrections to the Cover Date.     

Dependence of the Rate of Electrodeposition of Metals at Mono- and Multielectrodes on Voltage in the Case of an Exaltation Mechanism of Mass Transport

Dependences of the rate of copper deposition on mono- and multielectrodes out of dilute solutions of acetic acid at voltages of 20–250 V are compared. It is established that the same rate of deposition in the case of a multielectrode (25 electrodes with a diameter of 0.1 mm) takes place at a voltage that is lower by 2.7 times than that in the case of a monoelectrode with a diameter of 0.5 mm and the same area. The same results are obtained during electrodeposition of cadmium and thallium. In order to explain this effect, a two-layered model of potential distribution is suggested. In accordance with this model, the resistance of electrolyte in the vicinity of a multielectrode is equal to the sum of the resistance of the layer nearest to the electrode (where it is determined by the sum of conductances to each microelectrode) and the external layer, where the potential distribution is close to hemispherical. It is shown that calculations in accordance with this model allow one to give an estimate of the effect's scale that agrees with experiment and to predict its possible limits following an increase in the number of electrodes that make up a multielectrode.     

Chemical Investigations of the Molecular Origin of Biological Radiation Damage

The radiation damage observed when UV and ionizing radiations react on biological objects is caused in many cases by changes in the nucleic acids. Exposure of these compounds to UV radiation in vitro and in vivo leads, inter alia, to dimerization of the pyrimidine bases with formation of cyclobutane derivatives, and to addition of water to the 5,6-double bond of the pyrimidine bases to form derivatives of the 6-hydroxyhydropyrimidine system. The structure of the irradiation products has been established. The dimerization prevents the reduplication of the DNA, and the addition of water appears to be the cause of UV mutations. Ionizing radiation in aqueous solution results e.g. in addition of H and/or HO radicals to the 5,6-double bond of the pyrimidine bases and cleavage of the imidazole ring of the purine bases. The mutations caused by ionizing radiation are probably also due, in part, to the formation of 6-hydroxydihydropyrimidine derivatives.     

Influence of Apoptin on Up-regulation of the Expression of Bad and Bax

The chicken anemia virus protein, apoptin, which manifests selectivity and specificity to tumor cells, induces a p53-independent and Bcl-2-insensitive type of apoptosis in various human tumor cells. In this study, the apoptin gene was cloned from the total DNA of chicken anemia virus, and the recombinant vector was constructed. We used oligonucleotide microarray to study the changes of four genes, including Bcl-2, Bcl-xL, Bad and Bax. The post-transfection with the recombinant was also studied. The pro-apoptotic genes(Bad and Bax) and anti-apoptosis genes(Bcl-2 and Bcl-xL) were up-regulated in contrast to the controls. According to the published data, either Bcl-2 or Bcl-xL can form non-functional heterodimers by Bad and Bax binding together, resulting in blocking partly the release of cytochrome c from mitochondria. However, apoptosis could be inhibited by neither the endogenous Bcl-xL nor Bcl-2 over-expression. The experiments show that the apoptin-induced apoptotic pathway is related to the up-regulation of Bad and Bax. Bad was up-regulated by apoptin; then this up-regulated product of Bad was in favor of displacing Bax from binding to Bcl-xL or Bcl-2. Consequently. Bax exerted a pro-apoptotic dysfunction to mitochondria, thereby inducing the release of cytochrome c. Finally, apoptin induced the apoptosis of HHCC cells. These results indicate that the oligonucleotide microarray can reveal the genes related to the apoptosis induced by apoptin in HHCC cells.     

The Applicability of Essential Oils in Different Stages of Production of Animal-Based Foods

Essential oils (EOs) have been used for centuries, and interest in these compounds has been revived in recent years. Due to their unique chemical composition as well as antimicrobial, immunostimulatory, anti-inflammatory and antioxidant properties, EOs are used in pharmacology, cosmetology and, increasingly, in animal breeding and rearing, and processing of animal raw materials. Essential oils have become a natural alternative to preservatives, taste enhancers and, most importantly, antibiotics, because the European Union banned the use of antibiotics in metaphylaxis in animal husbandry in 2006. In the animal production chain, EOs are used mainly as feed additives to improve feed palatability and increase feed intake, improve animal resistance and health status, and to prevent and treat diseases. Recent research indicates that EOs can also be applied to sanitize poultry houses, and they can be used as biopesticides in organic farming. Essential oils effectively preserve meat and milk and, consequently, improve the safety, hygiene and quality of animal-based foods. Novel technologies such as encapsulation may increase the bioavailability of EOs and their application in the production of food and feed additives.     

Industrial Application of the Semiconductor Properties of Dyes

Effects of industrial interest have been detected in investigations on the dark conductivity and photoconductivity of dyes. For example, it was found that organic dyes can be used in the same way as inorganic photoconductors in vidicon television pickup tubes for the reproduction of images. Among other things, pointers were obtained to the formation of rectifying and photoelectrically sensitive pn junctions, to relatively high thermoelectromotive forces of doped and polymeric dyes, to the possibility of use in reprography, and to a high catalytic activity connected with the conductivity, which is already being utilized in fuel cells.     

The application of the OTA of kerogen to the evaluation of the rockmass heating

Oxyreactive thermal analysis (OTA) carried out in the conditions of full access of oxygen to each reacting particle of the sample investigated is a suitable method for the determination of important properties of the organic matter dispersed in the rocks. Its results may be easily evaluated to the form of values to be used in a clear diversification and classification system of organic matter/kerogen, as well as to the evaluation of its transformation process in a rockmass. The OTA also enables the distinguishing of the transformation stages and the investigation of the results of the gaseous products liberation from organic matter and kerogen. The OTA method may be applied as a complementary one for the Rock Eval analysis and be used for the organic geochemical and bituminological studies for geological bitumen prospecting.This revised version was published online in November 2005 with corrections to the Cover Date.     

Modeling of multilayer drying of polymer films

A model was developed to predict the drying behavior of multilayer polymer films on inert substrates. The model considers simultaneous heat and mass transfer controlled by complex thermodynamic and transport properties of polymer solutions. Key components of the model are the incorporation of the free volume theory to predict diffusivities in each polymer layer, the use of heat and mass transfer coefficients to describe complex transport phenomena in the gas phase, the incorporation of exact equilibrium boundary conditions at polymer–polymer interface, and the use of the Flory–Huggins theory to describe both liquid–liquid and vapor–liquid equilibria. The model can be applied to guide processing, product formulation, scale‐up, and oven design. As an example, the model is applied to simulate the drying of a two‐layer coating of poly vinyl acetate (in toluene) over polystyrene (also in toluene) on a polyester substrate. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1665–1675, 1999     

The effect of structural characteristics of porous hydrophobized electrodes on selectivity of electrolysis of organic substances

A theoretical study of the effect of the electrode structure on the electrosynthesis in hydrophobized electrodes (HPE) for a case of further electrochemical conversion of the target product is performed by the example of nitromethane electroreduction to methyl hydroxylamine followed by its reduction to methylamine. The effect of the electrode structure on the selectivity of electrosynthesis in HPE was shown to be related to the effective diffusivity and conductivity.     

紫外拉曼光谱研究焙烧气氛对氧化锆相变的影响

 以紫外拉曼光谱技术研究了在不同焙烧气氛中氧化锆样品的表面晶相结构及其转变过程．结果表明，在有氧气氛中焙烧的氧化锆样品易转变为单斜相，而在惰性气氛中焙烧可以有效地稳定样品体相和表面的四方相结构．在缺氧气氛中焙烧的样品暴露于空气中后，表面极易转变为单斜相，而其体相仍为四方相结构，这表明四方相氧化锆在样品表面是极不稳定的．     

透射电子显微镜在聚合物不同层次结构研究中的应用

聚合物材料的性能与功能取决于各级结构,其中化学结构决定材料的基本功能与性能,而不同层次聚集态结构能够改变材料的性能和赋予材料特殊功能,如高取向超高分子量聚乙烯的模量比相应非取向样品提高3个数量级,聚偏氟乙烯的β和γ结晶结构则能赋予其压电、铁电等特殊功能.因此,明确聚合物不同层次聚集态结构的形成机制、实现各层次结构的精准...     

Comparison of the properties of chemical cellulose pulps

The literature related to differences between chemical cellulose pulps produced by different pulping processes has been reviewed. Kraft pulps tend to be stronger, particularly in tear strength, while sulfite pulps hydrate and beat more readily. Organosolv pulps tend to mirror the properties of sulfite more than those of kraft pulps. A number of theories have been offered to explain the different properties of the chemical pulps; however, none has been universally accepted. It may be that acidic processes develop weak points in the fibers which are magnified in tear strength losses since, at a constant tensile strength, a 10% loss in fiber strength can lead to a 25–30% loss in tear strength. The effects of acidic pulping may also be magnified in greater fiber breakage and damage in the subsequent refining stages. However, strength improvements for inferior pulps can be realized through post-chemical treatments. Caustic treatments appear to give the greatest improvements, presumably due to increases in acidic group content which results in enhanced swelling properties, and possible subtle reorientation of cell wall polymers. The strength of hornified, recycled fibers can also be enhanced with such treatments, although simple beating will restore considerable strength, but at the expense of drainage rates. It is clear that the processes are complex and involve both the chemistry and physics of the fibers and how these attributes combine to affect the subsequent beating of the fibers for bonding and strength development.     

The use of surfactants in the cleaning of works of art

Surfactants have been historically used for cleaning artifacts, but it was only in the last decades that serendipitous approaches were replaced by research in the field of soft matter and colloid science. Surfactants are components of nanostructured fluids, which were assessed for the removal of soil and aged coatings from paintings and are fundamental in processes that range from the inclusion of grime in micelles to the swelling and dewetting of polymer layers. Intriguing aspects involve the synthesis and use of biodegradable and self-cleavable surfactants, and the confinement of nanostructured fluids in gels, which boost the selectiveness of cleaning interventions. The performances of these advanced systems surpass those of traditional cleaning materials such as solvent blends and thickeners. The most important results are here reviewed and future perspectives given. Besides granting the transfer of cultural heritage to future generations, advanced cleaning materials are relevant to transversal fields, such as detergency, cosmetics, and drug delivery.