Computer simulation of the association of caffeine and actinocin derivatives in aqueous solutions

The association of caffeine and actinocin derivatives (ActII), analogs of the antitumor antibiotic actinomycin D, was studied by molecular dynamics simulation in explicit solvent (water and Na⁺ and Cl^? ions). Information was obtained describing in detail the association of caffeine and ActII in water and water-salt solution and the interaction of monomers and their associates with the ionic hydrate environment. The schemes of hydration of monomers of actinocin derivatives and caffeine and their self-and heteroassociates are determined. The calculated energies of monomer interaction in associates indicate that dimerization of these compounds in aqueous solutions is advantageous in energy. Both self-and heteroassociates are stabilized by van der Waals, electrostatic, and hydrophobic interactions, as well as intermolecular hydrogen bonds. The rearrangement of the hydration shells of monomers during their association in water is energy-unfavorable and destabilizes the associates. In water-salt solutions, it is energy-favorable for the systems containing associates of the singly charged ActII⁺ and caffeine-ActII⁺. The formation of caffeine-actinocin heterodimers is preferable in energy to the formation of self-associates. In this way caffeine can decrease the concentration of the actinocin derivatives in solution and thereby decrease their biological activity.     

超声-微波协同提取大青叶多糖及其分子特性和免疫活性研究

为研究大青叶多糖的分子特性和免疫活性,采用超声-微波协同提取大青叶多糖并测定其化学组成,衍生化后利用气质联用分析仪检测单糖组成和链接方式,用HPSEC-MALLS-RI联机系统测定分子质量及分布情况,最后利用RAW264. 7细胞分析大青叶多糖的免疫活性。结果表明,多糖最佳提取参数:料液比25∶1(V/m),温度90℃,蒸馏水浸提70 min,超声-微波提取50 min,微波功率500 W,超声功率50 W,多糖得率为10. 49%。大青叶多糖化学组成包括63. 8%总糖、13. 1%蛋白质、14. 2%硫酸根和12. 6%糖醛酸,单糖组成主要包括半乳糖、阿拉伯糖、鼠李糖和葡萄糖,分子质量为7. 85×105u,回转半径为183. 3 nm。同时分析了大青叶多糖的链接方式,体外生物活性实验表明大青叶多糖可以促进RAW264. 7细胞增殖并产生一氧化氮。     

Influence of high concentration monovalent cations on the protein partitioning in polyethyleneglycol 1500-phosphate aqueous two-phase systems

The influence of chloride salts of Na+, Rb+ and Cs+ at concentrations from 0.15 to 1.2M was studied with bovine albumin, trypsin, ovoalbumin and lysozyme partitioning in an aqueous two-phase system formed by polyethyleneglycol 1500 and potassium phosphate at pH 7.4. Monovalent cations favoured the protein transfer to the polyethyleneglycol rich phase in the following order: Rb+ > Na+ > Cs+. Structure making cations as Na+ induced a poor loss of structured water, producing little diminution of the molar partial specific volume of polyethyleneglycol, while Rb+ and Cs+, structure breaking cations, induced a significant decrease in the specific volume of the polyethylene glycol. The increase of available solution free volume in the top phase favours the protein transfer to the polyethyleneglycol rich phase. Na+ and Rb+ induced a slight decrease in the alpha helix content of the proteins, while Cs+ increased the secondary structure for all the proteins. All the cations induced a decrease in the hydrophobic surface of the proteins, this effect was more significant in the presence of Cs+.     

Influence of electromagnetic radiation on molecular solitons

The soliton model of charge and energy transport in biological macromolecules is used to suggest one of the possible mechanisms for electromagnetic radiation influence on biological systems. The influence of the electromagnetic field (EMF) on molecular solitons is studied both analytically and numerically. Numerical simulations prove the stability of solitons for fields of large amplitude, and allow the study of emission of phonons. It is shown that in the spectra of biological effects of radiation there are two characteristic frequencies of EMFs, one of which is connected with the most intensive energy absorption and emission of sound waves by the soliton, and the other of which is connected with the soliton photodissociation into a delocalized state.     

Stability of molecular and rheological properties of the exopolysaccharide produced byCyanospira capsulata cultivated under different growth conditions

In order to assess the stability of molecular and rheological properties of the exopolysaccharide (EPS) produced byCyanospira capsulata the strain was cultivated under both continuous light and light-dark cycles in two culture devices, an open pond and a completely stirred reactor (CSR), having quite different surface-to-volume ratios and stirring systems. All EPS samples obtained from the cultures showed the same monosaccharidic composition and relative proportions among sugar units. However, Gel Permeation Chromatography demonstrated that EPS samples produced by cultures run in open ponds were more homogeneous in size than those obtained from cultures grown in CSR. In spite of this difference, no significant change in the flow properties was observed among the aqueous solutions of the different EPS samples.     

Influence of diet on the structure and function of the bacterial hindgut community of crickets

The effect of diets varying in carbohydrate and protein content on the structure and function of the hindgut microbiota of crickets was evaluated by determining bacterial densities, fermentation activity, and guanine plus cytosine (G + C) profiles of the DNA extracted from the microbial hindgut community. DNA isolated from the gut community was fractionated and quantified according to G + C content as a comprehensive, coarse-level measure of the composition and structure of the community. The bacterial densities measured by direct counts were not significantly different among the four diets. The crickets were initially reared in the laboratory on cricket chow, which resulted in a hindgut community dominated by bacteria with a G + C content between 32% and 57%. Crickets shifted to an alfalfa diet showed a similar hindgut community G + C profile, although microbial populations with DNA between 35% and 45% G + C were more abundant in alfalfa- than chow-fed crickets. The apparent complexity of the gut community was reduced in crickets fed beet-pulp and protein-based diets compared to those fed chow and alfalfa, and was dominated by populations with a low percentage G + C content. Hindgut communities in crickets fed pulp and protein diets also showed a decrease in hydrogen and carbon dioxide production, suggesting that these diets affected the biochemical activity of the hindgut community. The protein-based diet resulted in a decrease in the rate of evolution of volatile fatty acids, while the ratio of butyrate production to acetate and propionate production was significantly higher in these crickets. Our results show the emergence of a new microbial community structure concomitant with changes in microbial biochemical activity due to shifts in the cricket's dietary regime.     

Effects of molecular association on structure and dynamics of a collagenous peptide

Peptide GVKGDKGNPGWPGAPY from the triple-helix domain of type IV collagen aggregates in solution at a critical aggregation concentration of 18 mM. This molecular self association process is investigated by ¹H- and ¹³C-nmr spectroscopy. As a function of increasing peptide concentration, selective ¹H resonances are cooperatively chemically shifted by up to 0.04 ppm to apparently saturable values at high concentration. Pulsed field gradient nmr was used to derive translation diffusion constants that, as the peptide concentration is increased, also cooperatively and monotonically decrease to an apparent limiting value. An average number of 6 monomer units per aggregate have been estimated from diffusion constant and ¹³C relaxation data. Comparative ¹H nuclear Overhauser effect spectroscopy (NOESY) spectra accumulated at high and low peptide concentrations suggest that average internuclear distances are decreased as a result of peptide association. ¹³C-nmr multiplet spin-lattice relaxation and ¹³C- {¹H} NOE effects on ¹³C-enriched glycine methylene positions in the peptide demonstrate that overall molecular tumbling and backbone internal motions are attenuated in the aggregate state. Lowering the solution pD from pD 6 to pD 2 disrupts the aggregate state, suggesting a role for electrostatic interactions in the association process. Based on thermodynamic considerations, hydrophobic interactions also probably act to stabilize the aggregate state. These data are discussed in terms of an nmr/NOE constrained computer-modeled structure of the peptide. © 1993 John Wiley & Sons, Inc.     

influence of concentration and mannuronate/guluronate [correction of gluronate] ratio on steady flow properties of alginate aqueous systems.

Steady flow properties were measured at various concentrations for aqueous systems of alignates with different mannuronate/gluronate (M/G) ratios using a cone-plate type rheometer. The flow curve (a plot of shear stress vs. shear rate) shows a plateau region, which is ascribed to a heterogeneous structure, at low shear rate. This plateau region is more noticeable in the G-rich systems than in the M-rich systems. On the other hand, the flow curves for the systems with the same molecular weight but different M/G ratios are congruent in the high shear rate region. The zero shear viscosity can be reduced by the segment contact parameter, cMw, for the alginates with the same M/G ratio but different molecular weights. The zero shear viscosity is proportional to cMw in a low concentration region and is proportional to (cMw)3.4 at relatively high concentrations. The critical value of cMw for which the zero shear viscosity changes from proportionality with cMw to proportionality with (cMw)3.4 is ca. 900.     

Recent advances in molecular techniques for the detection of phylogenetic markers and functional genes in microbial communities

The detection and analysis of nucleic acids extracted from microbial communities are the ultimate ways to determine the diversity and functional capability of microbial communities in the environments. However, it remains a challenge to use molecular techniques for unequivocal determination and quantification of microbial species composition and functional activities. Considerable efforts have been made to enhance the capability of molecular techniques. Here an update of the recent developments in molecular techniques for environmental microbiology is provided.     

Effect of molecular structure on thermodynamic properties of carbohydrates. A calorimetric study of aqueous di- and oligosaccharides at subzero temperatures

For aqueous solutions of di- and oligosaccharides thermodynamic properties have been investigated at subzero temperatures using differential scanning calorimetry. The amount of unfrozen water observed is found to increase linearly with the glass transition temperatures of anhydrous carbohydrates. Furthermore, the amount of unfrozen water shows a linear relationship with known solution properties of aqueous carbohydrates, such as partial molar compressibility and heat of solution. The different effectiveness among various di- and oligosaccharides to avoid ice formation is associated with the combination of constitutive monosaccharides and attendant molecular structure features including the position and type of the glycosidic linkage between the constituent units. More unfrozen water is induced in the presence of a carbohydrate having a poorer compatibility with the three-dimensional hydrogen-bond network of water. A series of these results obtained imply that there is a common key of carbohydrate stereochemistry governing several different thermodynamic amounts of a given system involving carbohydrates. In this context, a modified stereospecific-hydration model can be used to interpret the present results in terms of stereochemical effects of carbohydrates.     

Spectral and molecular properties of peanut peroxidase isozymes

Properties of four peroxidase isozymes derived from peanut cells were examined. Electrophoresis on various concentrations of polyacrylamide gel indicated that they had the same molecular size. Filtration on Sephadex G-200 gels indicated the same Stoke's radius for all 4 isozymes. They had the same spectral properties in the oxidized, reduced and CO-reduced the pyridine hemochromogen forms, but they differed with regard to heat stability at 50° and 70° and their substrate specificity.     

Thermodynamics of conformational transition and chain association of ι-carrageenan in aqueous solution: Calorimetric and chirooptical data

Isothermal microcalorimetry, differential scanning calorimetry (DSC), and chirooptical data obtained for ι-carrageenan in NaCl, LiCl, and NaI aqueous solutions are presented. The experiments have been performed as a function of concentration both for the polymer and for the simple salt as a cosolute. The experimental findings consistently show the occurrence of a salt-induced disorder-to-order transition. From microcalorimetric experiments the exothermic enthalpy of transition ΔH_tr is obtained as the difference between the theoretical, purely electrostatic ΔH_el enthalpy change and the actual mixing enthalpy ΔH_mix, measured when a ι-carrageenan salt-free solution at constant polymer concentration is mixed with a 1:1 electrolyte solution of variable concentration. In the case of added NaCl, the absolute values of enthalpy changes |ΔH_tr| are in good agreement with those obtained for the opposite process, at comparable polymer and salt concentrations, from DSC melting curves. The microcalorimetric results show that the negative maximum value of ΔH_tr corresponding to the interaction of Li⁺ counterion with ι-carrageenan polyion results to be significantly lower than the corresponding values obtained for Na⁺ counterion. At variance with the microcalorimetric data, chirooptical results show that the salt-induced disorder-to-order transition, occurring in the 0.02–0.2M salt concentration range, appears to be complete at a concentration of about 0.08–0.1M of the simple ion, irrespective of the polymer concentration and of the nature of added electrolyte. © 1998 John Wiley & Sons, Inc. Biopoly 45: 105–117, 1998     

Electronic structure and molecular design of simplified polyimide systems

The electronic structures of newly designed polyimide systems (ethenetetracarboxylic 1,2:1,2-dianhydride-diaminoethyne (PI-A) and ethenetetracarboxylic 1,1:2,2-dianhydride-diaminoethyne(PI-B)) are studied in detail with respect to their optimized geometries on the basis of the one-dimensional tight-binding self-consistent field crystal-orbital method. The computational results have revealed that PI-B shows intriguing properties such as a very small band gap and a wide bandwidth near the frontier level, compared with PI-A and other polyimides. Since PI-B would be a promising candidate for a new electric conducting material, a reaction diagram for this polymer is also proposed.Also affiliated to Central Research Laboratories, Matsushita Electric Industrial Co., Moriguchi 570, Japan.     

Changes in structure and hydrophobic surface properties of beta-lactoglobulin determined by partition in aqueous two-phase polymeric systems.

The non-polar surface properties of beta-lactoglobulin and especially its interaction with poly(ethylene glycol)-bound palmitate has been studied as a function of pH, temperature and protein concentration. The maximum interaction between beta-lactoglobulin and polymer-bound palmitate occurs at pH 4.3 and pH 7.8. The change in conformation of beta-lactoglobulin around pH 7.5 seems to involve exposure of apolar amino acids to the solvent which results in an increased affinity for hydrocarbons. This is contrary to the situation at pH 4.8--6.0 where the corresponding change in conformation does not affect the protein-hydrocarbon interaction. The results suggest that partition studies in an aqueous two-phase system is a very useful tool to detect changes in conformation and aggregation and to characterize the corresponding hydrophobic surface properties of a protein.     

Pectinmethylesterase isoforms fromVigna radiata hypocotyl cell walls: kinetic properties and molecular cloning of a cDNA encoding the most alkaline isoform

Peptide maps and partial amino acid sequences of the 3 main pectinmethylesterases (PMEs) solubilized from mung bean hypocotyl cell walls demonstrated that these proteins were different isozymes originating from a small multigene family. A cDNA clone encoding the most alkaline PME (PE) have been obtained by PCR using degenerate oligonucleotide primers. Combining the protein and nucleotide sequencing data, the complete amino acid sequence of PE was determined. The nature protein is composed of 318 amino acids with a calculatedM _r of 34 677 and an estimated pI of 9.84 consistent with the values previously obtained by SDS-PAGE and IEF. It shares most of the conserved regions of previously known PMEs. Enzymatic activities of the three isoforms were differently affected by the presence of cations in the incubation medium but, in all cases, infra-optimal cation concentrations induced two opposite effects: a decrease in theV _max and an increase in the affinity of the enzymes for their substrate. The presence of cations in the assay modulates both the number of enzyme molecules available to the demethylation reaction and the conformation of the pectin and, in turn, the affinity of the PMEs for their substrate.     

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.

We demonstrate in this work that the surface tension, water-organic solvent, transfer-free energies and the thermodynamics of melting of linear alkanes provide fundamental insights into the nonpolar driving forces for protein folding and protein binding reactions. We first develop a model for the curvature dependence of the hydrophobic effect and find that the macroscopic concept of interfacial free energy is applicable at the molecular level. Application of a well-known relationship involving surface tension and adhesion energies reveals that dispersion forces play little or no net role in hydrophobic interactions; rather, the standard model of disruption of water structure (entropically driven at 25 degrees C) is correct. The hydrophobic interaction is found, in agreement with the classical picture, to provide a major driving force for protein folding. Analysis of the melting behavior of hydrocarbons reveals that close packing of the protein interior makes only a small free energy contribution to folding because the enthalpic gain resulting from increased dispersion interactions (relative to the liquid) is countered by the freezing of side chain motion. The identical effect should occur in association reactions, which may provide an enormous simplification in the evaluation of binding energies. Protein binding reactions, even between nearly planar or concave/convex interfaces, are found to have effective hydrophobicities considerably smaller than the prediction based on macroscopic surface tension. This is due to the formation of a concave collar region that usually accompanies complex formation. This effect may preclude the formation of complexes between convex surfaces.     

Quantifying the impact of protein tertiary structure on molecular evolution

To investigate the evolutionary impact of protein structure, the experimentally determined tertiary structure and the protein-coding DNA sequence were collected for each of 1,195 genes. These genes were studied via a model of sequence change that explicitly incorporates effects on evolutionary rates due to protein tertiary structure. In the model, these effects act via the solvent accessibility environments and pairwise amino acid interactions that are induced by tertiary structure. To compare the hypotheses that structure does and does not have a strong influence on evolution, Bayes factors were estimated for each of the 1,195 sequences. Most of the Bayes factors strongly support the hypothesis that protein structure affects protein evolution. Furthermore, both solvent accessibility and pairwise interactions among amino acids are inferred to have important roles in protein evolution. Our results also indicate that the strength of the relationship between tertiary structure and evolution has a weak but real correlation to the annotation information in the Gene Ontology database. Although their influences on rates of evolution vary among protein families, we find that the mean impacts of solvent accessibility and pairwise interactions are about the same.