Calculations of pH-dependent binding of proteins to biological membranes

Binding of proteins to membranes is often accompanied by titration of ionizable residues and is, therefore, dependent on pH. We present a theoretical treatment and computational approach for predicting absolute, pH-dependent membrane binding free energies. The standard free energy of binding, DeltaG, is defined as -RTln(P(b)/P(f)), where P(b) and P(f) are the amounts of bound and free protein. The apparent pK(a) of binding is the pH value at which P(b) and P(f) are equal. Proteins bind to the membrane in the pH range where DeltaG is negative. The components of the binding free energy are (a) the free energy cost of ionization state changes (DeltaG(ion)), (b) the effective energy of transfer from solvent to the membrane surface, (c) the translational/rotational entropy cost of binding, and (d) an ideal entropy term that depends on the relative volume of the bound and free state and therefore depends on lipid concentration. Calculation of the first term requires determination of pK(a) values in solvent and on the membrane surface. All energies required by the method are obtained from molecular dynamics trajectories on an implicit membrane (IMM1-GC). The method is tested on pentalysine and the helical peptide VEEKS, derived from the membrane-binding domain of phosphocholine cytidylyltransferase. The agreement between the measured and the calculated free energies of binding of pentalysine is good. The extent of membrane binding of VEEKS is, however, underestimated compared to experiment. Calculations of the interaction energy between two VEEKS helices on the membrane suggest that the discrepancy is mainly due to the neglect of protein-protein interactions on the membrane surface.     

Quantitative validation of different protein precipitation methods in proteome analysis of blood platelets

For the preparation of proteins for proteome analysis, precipitation is frequently used to concentrate proteins and to remove interfering compounds. Various methods for protein precipitation are applied, which rely on different chemical principles. This study compares the changes in the protein composition of human blood platelet extracts after precipitation with ethanol (EtOH) or trichloroacetic acid (TCA). Both methods yielded the same amount of proteins from the platelet preparations. However, the EtOH-precipitated samples had to be dialyzed because of the considerable salt content. To characterize single platelet proteins, samples were analyzed by two-dimensional fluorescence differential gel electrophoresis. More than 90% of all the spots were equally present in the EtOH- and TCA-precipitated samples. However, both precipitation methods showed a smaller correlation with nonprecipitated samples (EtOH 74.9%, TCA 79.2%). Several proteins were either reduced or relatively enriched in the precipitated samples. The proteins varied randomly in molecular weight and isoelectric point. This study shows that protein precipitation leads to specific changes in the protein composition of proteomics samples. This depends more on the specific structure of the protein than on the precipitating agent used in the experiment.     

Redox activity and diffusion of hydrophilic, hydrophobic, and amphiphilic redox active molecules in a bicontinuous cubic phase

The objective was to examine how a bicontinuous cubic phase influences the diffusion and electrochemical activity of dissolved molecules. The cubic phase is a structure with three-dimensional continuous channels of water separated by an apolar membrane. A redox active molecule can dissolve in three different environments. A hydrophobic molecule will prefer the interior of the membrane, a hydrophilic molecule will prefer the water channels, and an amphiphilic molecule will be situated with its headgroup at the surface of the membrane and its tail in the interior. The electrochemical activity was measured with cyclic voltammetry and the transport behavior with chronocoulometry. All the molecules were redox active in the cubic phase; that is, all the molecules could reach the surface of the electrode and react. The cubic phase made the kinetics of the charge transfer slower, showing a quasi-reversible behavior. The reason may be that a layer of the membrane adheres to the hydrophobic electrode surface. The diffusion experiment showed that the diffusion was slower than in solution. The molecules that were restricted to diffuse within the membrane gave particularly low mass transport rates.     

Real-time polymerase chain reaction detection of cauliflower mosaic virus to complement the 35S screening assay for genetically modified organisms

Labeling of genetically modified organisms (GMOs) is now in place in many countries, including the European Union, in order to guarantee the consumer's choice between GM and non-GM products. Screening of samples is performed by polymerase chain reaction (PCR) amplification of regulatory sequences frequently introduced into genetically modified plants. Primers for the 35S promoter from Cauliflower mosaic virus (CaMV) are those most frequently used. In virus-infected plants or in samples contaminated with plant material carrying the virus, false-positive results can consequently occur. A system for real-time PCR using a TaqMan minor groove binder probe was designed that allows recognition of virus coat protein in the sample, thus allowing differentiation between transgenic and virus-infected samples. We measured the efficiency of PCR amplification, limits of detection and quantification, range of linearity, and repeatability of the assay in order to assess the applicability of the assay for routine analysis. The specificity of the detection system was tested on various virus isolates and plant species. All 8 CaMV isolates were successfully amplified using the designed system. No cross-reactivity was detected with DNA from 3 isolates of the closely related Carnation etched ring virus. Primers do not amplify plant DNA from available genetically modified maize and soybean lines or from different species of Brassicaceae or Solanaceae that are natural hosts for CaMV. We evaluated the assay for different food matrixes by spiking CaMV DNA into DNA from food samples and have successfully amplified CaMV from all samples. The assay was tested on rapeseed samples from routine GMO testing that were positive in the 35S screening assay, and the presence of the virus was confirmed.     

An unprecedented tetranuclear niobium aqua ion with a capping mu4-sulfido ligand

The aqueous solution chemistry of niobium is rather unexplored, and well characterized aqua complexes are scarce. In this work, a new niobium aqua ion is obtained upon treatment of Zn-reduced ethanolic solutions of NbCl5 with HCl in the presence of a sulfide source. The red aqua ion, obtained upon cation-exchange chromatography, forms readily the thiocyanate complex which has been crystallized as Cs(4.26)Na(1.74)[Nb4SO5(NCS)10] . 0.33H2O. X-ray crystallography revealed an unprecedented metal-metal bonded tetranuclear Nb4(mu4-S)(mu2-O)5(4+) core with a capping mu4-S ligand.     

Simultaneous LC Analysis of Food Dyes in Soft Drinks

Liquid chromatography with diode-array detection has been used for simultaneous analysis of eight water-soluble synthetic colorants (E102, E104, E110, E122, E124, E129, E131, and E133) in non-alcoholic beverages. The colors were separated in 15 min on a C₁₈ reversed-phase column with a linear mobile phase gradient prepared from tetrabutylammonium hydrogen sulfate, methanol, and deionized water. The analytical characteristics of the separation were evaluated. Good linearity (r ² = 0.9988–0.9999), adequate limits of quantification, and high recovery (from 96.3 to 98.5%) were achieved. The method was used for analysis of 57 samples of soft drinks. The experimental results showed the colorants were present in 34 of the samples, and confirmed the method is sensitive, rapid, precise, and suitable for routine analysis of synthetic organic dyes.

     

Macromolecular nature of nanosheets of quasi‐TiO2 from (tetra‐isopropyl)orthotitanate modified by methacrylic acid

In this paper we concentrate on the general behavior of oxotitanium hydrosol, which was earlier developed by us as a precursor of the TiO₂ nanoparticles and nanocomposite. The oxotitanium hydrosol was synthesized by the chemical decomposition of a molecular complex of the methacrylic acid/(tetra‐isopropyl)orthotitanate (MAA/TIPT) by means of the hydrogen peroxide. The raw product chemical decomposition of MAA/TIPT is the colloidal suspension of the oxotitanium compound in the water. The oxotitanium compound was separated from hydrosol and identified on the basis of X‐ray and Raman spectroscopy investigations. The status of water in the hydrosol was also investigated by the Raman spectroscopy. The photophysical behaviors of the oxotitanium hydrosol on the basis of the light absorption and photoluminescence (PL) investigations are presented. The light absorption (260 nm) and PL emission (313 nm) allow us to identify the inorganic phase of hydrosol as nanosheets' crystallites of quasi‐TiO₂. Macromolecular nature of nanosheets of quasi‐TiO₂ was revealed only for a higher concentration solution of nanosheets' crystallites of quasi‐TiO₂ at the hydrosol. A macromolecular nature of nanosheets of quasi‐TiO₂ by the red shift of absorption edge and PL wavelength with increase in the concentration of the oxotitanium hydrosol as well as the formation of hydrogels and birefringence developed under an influence of mechanical shearing is evidenced. Copyright © 2009 John Wiley & Sons, Ltd.     

Weak intermolecular interactions in 11‐chloro‐2,3,4,5‐tetrahydro‐1H‐cyclohepta[b]quinoline

The title compound, C₁₄H₁₄ClN, is a chloro analogue of tacrine, an acetylcholinesterase inhibitor. The compound comprises a seven‐membered alicyclic ring whose CH donor groups are engaged in extensive intermolecular interactions. The important feature of this crystal structure is that, regardless of the presence of two typical hydrogen‐bonding acceptors, viz. chlorine and nitrogen, the corresponding C—H...Cl and C—H...N interactions take no significant role in crystal stabilization. The molecules form dimers through π–π interactions with an interplanar distance between interacting pyridine rings of 3.576 (1) Å. Within the dimers, the molecules are additionally interconnected by four C—H...π interactions. The dimers arrange into regular columns via further intermolecular C—H...π interactions.     

Oxidation stability of various Ti-alloys

Since titanium metal first became a commercial reality in 1950, corrosion resistance has been an important consideration in its selection as an engineering structural material. Titanium has gained acceptance in many media where its corrosion resistance and engineering properties have provided the corrosion and design engineer with a reliable and economic material. Titanium, like any other metal, is subject to corrosion in environments of air, oxygen, moisture, and so on. In this work, high-temperature stability of Ti and various Ti-alloys (by ASTM standard) was investigated. The best results showed that for Ti-Gr.5 alloy, the oxidation at 800 °C was 3.39% and at 900 °C 8.35%. For the comparison, commercial pure Ti-alloys Ti-Gr.2 and Ti-Gr.37 containing Al were used, whereas the oxidation resistance was much worse.