Protein partitioning in thermoseparating systems of a charged hydrophobically modified ethylene oxide polymer

The phase behavior of a thermoseparating cationic hydrophobically modified ethylene oxide polymer (HM-EO) containing tertiary amines has been investigated at different pH, salt and sodium dodecyl sulfate (SDS) concentrations, in order to find a water/HM-EO two-phase system suitable for protein partitioning. The used polymer forms micellar aggregates that can be charged. By changing pH and SDS concentrations the netcharge of the SDS/HM-EO aggregate can be shifted from positive to negative. Bovine serum albumin (BSA) and lysozyme were partitioned in the thermoseparated two-phase systems of the cationic polymer at different pH, salt and SDS concentrations. The dominant attractive interactions between the polymer aggregates and the studied proteins were shown to be of electrostatic (Coulomb) nature rather than hydrophobic interaction. At low ionic strength the positively charged polymeric aggregates attracted negatively charged BSA and repelled positively charged lysozyme. Upon addition of SDS the negatively charged aggregates attracted lysozyme and repelled BSA. Thus, it was possible to direct proteins with different charges to the polymeric phase and redirect them to a polymer-depleted phase by changing the netcharge of the polymeric aggregates. The effect of different salts on the partitioning of BSA in a system of slightly positively charged HM-EO was studied. NaCl and KBr have a significant effect on driving the BSA to the polymer-depleted phase, whereas KF and K2SO4 have a smaller effect on the partitioning. The cloud point temperature of the charged polymer decreased upon addition of SDS near the isoelectric molar ratio of SDS to polymer and also upon salt addition. In the latter case the decrease was smaller than expected from model calculations based on Flory-Huggins theory, which were performed for a charged thermoseparating polymer at different charges and salt concentrations.     

MS2Assign,automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides

In a previous report (Young et al., Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5802-5806), we provided a proof-of-principle for fold recognition of proteins using a homobifunctional amine-specific chemical crosslinking reagent in combination with mass spectrometry analysis and homology modeling. In this current work, we propose a systematic nomenclature to describe the types of peptides that are generated after proteolysis of crosslinked proteins, their fragmentation by tandem mass spectrometry, and an automated algorithm for MS/MS spectral assignment called "MS2Assign." Several examples are provided from crosslinked peptides and proteins including HIV-integrase, cytochrome c, ribonuclease A, myoglobin, cytidine 5-monophosphate N-acetylneuraminic acid synthetase, and the peptide thymopentin. Tandem mass spectra were obtained from various crosslinked peptides using post source decay MALDI-TOF and collision induced dissociation on a quadrupole-TOF instrument, along with their automated interpretation using MS2Assign. A variety of possible outcomes are described and categorized according to the number of modified lysines and/or peptide chains involved, as well as the presence of singly modified (dead-end) lysine residues. In addition, the proteolysis and chromatographic conditions necessary for optimized crosslinked peptide recovery are presented.     

On the semi-quantification of polycyclic aromatic hydrocarbons in contaminated soil by an enzyme-linked immunosorbent assay kit

Polycyclic aromatic hydrocarbons (PAHs) are of environmental concern, for instance when found in contaminated soils at sites where industrial activities have occurred. For efficient screening of such soils, the commercially available enzyme-linked immunosorbent assay (ELISA) kit, the PAH RIS^c® soil test, can be used. However, the site-specific performance may vary due to differences in soil properties and contamination profiles. Hence, in this study we have examined various contributing factors to the total ELISA measurements uncertainties. These factors include contributions from co-extracted (non-target) compounds, the extraction efficiency and differences in cross-reactivity among the target analytes. Reference values were obtained through pressurized liquid extraction (PLE) and gas chromatography coupled to mass spectrometry (GC-MS) analysis. The results showed that the ELISA does not seem to respond to non-target compounds in the soil extracts to any large extent. Furthermore, high molecular weight PAHs were found to be more efficiently extracted with PLE than with methanol agitation, which is used for ELISA. If this, and the cross-reactivity of the individual PAHs, were taken into consideration, the ELISA and GC-MS results were in good agreement.     

Photodissociation of diiodomethane in acetonitrile solution and fragment recombination into iso-diiodomethane studied with ab initio molecular dynamics simulations

Series of hydrates of the most stable glycine-H+/2H2+ in the gas phase are presented at the B3LYP level. The results show that only the amino hydrogens and hydroxyl hydrogens can be monohydrated for the glycine-H+, and the amino hydrogens are preferred. The H6(O4) of glycine-2H2+ is the best site for a water molecule to attach, i.e., the corresponding hydrate is the most stable one among its isomers. Calculations reveal that the binding energies of hydrated hydrogens decrease relative to their counterparts in the isolated glycine-H+/2H2+ complexes and they are positive values and without proton transfer except those of monohydrated glycine-2H2+ complexes with the combination modes of H3O+...(glycine-H+). The complex H3O+...(glycine-H+) is formed by the combination of a H2O molecule and one hydroxyl-site proton of glycine-2H2+, and with the proton transfer to H2O. Here the interaction between the proton of H3O+ and the glycine-H+ mainly depends on an electronic one instead of an initial covalent one of the isolated glycine-2H2+. The generation of the bond between the H3O+ and the glycine-H+ makes the energy of the complex higher than the energy sum of its two separated species (or two reactants of the complex), just like the case of M+...(glycine-H+) bond (M = Li,Na). The observation can explain satisfactorily why the combinations of both a proton and an alkali ion or two alkali ions to a glycine molecule can make the corresponding complex hold reservation energy bond(s), while the combination of two protons and a glycine in our previous work cannot [H. Ai et al., J. Chem. Phys. 117, 7593 (2002)]. For the glycine-2H2+, monohydration at the any site of its amino hydrogens can make the binding strength of any other neighboring proton (hydrogens) stronger relative to its counterpart in the isolated glycine-2H2+. Further hydration, especially at the site of either of hydroxyl hydrogens, would disfavor the reservation energy of the system.     

Thermal Decomposition of 3'-Azidothymidine

The kinetics of thermal decomposition of 3'-azidothymidine (AZT) in melt at 140-201°C were studied by the thermogravimetric and manometric methods. The process follows the first-order kinetics and is decribed by the Arrhenius equation: k = 1014.7±0.5 exp[-(38100±900)/RT] (1/s). The kinetic and activation parameters are typical of thermal decomposition of aliphatic azides; they suggest that decomposition of the azido group is the rate-determining stage. The formation of nitrogen (1 mol per mole of AZT), furan, methyl alcohol, water, and carbon dioxide was confirmed by mass spectrometry. Thymine was found to be one of the condensed products of thermal decomposition of 3'-azidothymidine.     

A truncated Kv1.1 protein in the brain of the <Emphasis Type="Italic">megencephaly</Emphasis>mouse: expression and interaction

Background  

The megencephaly mouse, mceph/mceph, is epileptic and displays a dramatically increased brain volume and neuronal count. The responsible mutation was recently revealed to be an eleven base pair deletion, leading to a frame shift, in the gene encoding the potassium channel Kv1.1. The predicted MCEPH protein is truncated at amino acid 230 out of 495. Truncated proteins are usually not expressed since nonsense mRNAs are most often degraded. However, high Kv1.1 mRNA levels in mceph/mceph brain indicated that it escaped this control mechanism. Therefore, we hypothesized that the truncated Kv1.1 would be expressed and dysregulate other Kv1 subunits in the mceph/mceph mice.     

The NMDA antagonist memantine affects training induced motor cortex plasticity – a study using transcranial magnetic stimulation [ISRCTN65784760]

Background  

Training of a repetitive synchronised movement of two limb muscles leads to short-term plastic changes in the primary motor cortex, which can be assessed by transcranial magnetic stimulation (TMS) mapping. We used this paradigm to study the effect of memantine, a NDMA antagonist, on short-term motor cortex plasticity in 20 healthy human subjects, and we were especially interested in possible differential effects of different treatment regimens. In a randomised double-blinded cross over study design we therefore administered placebo or memantine either as a single dosage or as an ascending dosage over 8 days. Before and after one hour of motor training, which consisted of a repetitive co-contraction of the abductor pollicis brevis (APB) and the deltoid muscle, we assessed the motor output map of the APB muscle by TMS under the different conditions.     

On-line electrochemically controlled solid-phase extraction interfaced to electrospray and inductively coupled plasma mass spectrometry

Electrochemically controlled solid-phase extractions of anions were interfaced on-line to electrospray mass spectrometry (ESI-MS) and inductively coupled plasma mass spectrometry (ICP-MS), using polypyrrole coated electrodes and a thin-layer electrochemical (EC) flow cell. The results indicate that electrochemically controlled solid-phase extraction (EC-SPE) can be used as a versatile potential controlled sample preparation technique for a range of anions and that the properties of the polypyrrole coatings can be modified by altering the electrodeposition conditions. In the present study, the influence of interfering anions (i.e., fluoride and sulfate), and the anion used during the electropolymerisation, on the bromide extraction recovery was investigated for EC-SPE interfaced to ICP-MS. The results of these experiments show that the interference due to the presence of similar concentrations of sulfate can be reduced when using a polypyrrole coating electropolymerised in the presence of bromide ions. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) measurements were also used to study the morphology of the coatings, as well as the variations in the film thickness within the coatings. The effect of different desorption techniques on the bromide preconcentration factor in the ICP-MS on-line flow system was also examined. Stopped-flow desorption was found to give rise to significantly increased preconcentration factors in comparison with desorptions in flowing solutions. While the desorption efficiency depends on the type of desorption electrolyte (the electrolyte in which the desorption takes place), due to the competing influx of cations, the influence of the pH on the switching charge of the polypyrrole coating was found to be small, at constant ionic strength. To study the applicability of the EC-SPE technique with respect to real samples, investigations were also made with tap water samples spiked with different bromide concentrations. The results of these experiments, which were carried out using a modified thin-layer EC flow cell allowing in situ polymerisation of polypyrrole yielding a polymer plug covering the cross section of the channel, demonstrate that 3 microM concentrations of bromide could be detected in the tap water sample. This demonstrates that the extraction technique allows extractions of low concentrations of ions in the presence of significantly higher concentrations of other similar ions. The fact that the extraction and desorption steps are electrochemically controlled makes EC-SPE particularly well suited for inclusion in miniaturised lab-on-a-chip systems.     

Generalized ellipsometric method for the determination of all the optical constants of the system: Optically absorbing film on an absorbing substrate

A numerical method has been developed to evaluate all the optical parameters of the system of an optically absorbing film on an absorbing substrate using ellipsometric measurements. The generality and validity of the algorithm has been investigated for different ideal cases. In addition the effects of the actual limited precision of ellipsometric measurements as well as the problem of multiple solutions have been studied.