Specificity in the Cu interactions with prion protein fragments and related His-rich peptides from mammals to fishes

The prion proteins may play a critical role in copper homeostasis and the antioxidant activity in the brain. This review presents the state of art in the studies on Cu²⁺ prion systems. The proteins discussed are from different species from mammals to fishes. All proteins are His-rich and the research discussed clearly indicates the basic role of imidazole side chains and the adjacent amide nitrogen atoms in metal ion binding. Prions represent the family of proteins with new mode of Cu²⁺ binding which includes the amide nitrogen coordination. The multi-imidazole coordination is also likely and it can play a critical role in the antioxidant activity of the copper–prion complexes. The combination of the imidazole and amide nitrogen atoms to Cu²⁺ ions could also be relevant in histidine-rich peptide antibiotics including demegen. The impact of peptide sequence and His positions on copper binding ability is also discussed.     

Multi-compound electrophoretic assays for tyramine oxidase with a UV area detector imaging multiple windows on a looped capillary

Active pixel sensor UV area imaging and capacitively coupled contactless conductivity detection have been applied in an electrophoretically mediated microanalysis (EMMA) assay for substrate specificity of tyramine oxidase (Arthrobacter sp.). Use of the UV area imaging detector to monitor four windows in a capillary with three loops provided intrinsic self-referencing for all species and identified tyramine and 2-phenethylamine as the only reactive components in a multi-compound mixture. Continuous engagement EMMA experiments showed significant benefits by comparison with plug-plug EMMA, improving sensitivity by extending enzyme-substrate interaction times and allowing measurement of time-dependent reaction in the substrate zones passing the four windows.     

Tyrosinase/laccase bienzyme biosensor for amperometric determination of phenolic compounds

Tyrosinase/laccase bienzyme biosensor for amperometric determination of phenolic compounds was constructed. Enzymes were immobilized in titania gel matrix. The obtained biosensor was successfully used for determination of 2,6-dimethoxyphenol, 4-tertbutylcatechol, 4-methylcatechol, 3-chlorophenol and catechol. The highest sensitivity and the widest linear range were noticed for catechol, 234 mA L mol^− 1 and 2.0 × 10^− 7–3.2 × 10^− 5 mol/L, respectively. Detection limit for catechol, at signal-to-noise ratio of 3 was 1.3 × 10^− 7 mol/L.     

The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff

Using tRNA molecule as an example, we evaluate the applicability of the Poisson-Boltzmann model to highly charged systems such as nucleic acids. Particularly, we describe the effect of explicit crystallographic divalent ions and water molecules, ionic strength of the solvent, and the linear approximation to the Poisson-Boltzmann equation on the electrostatic potential and electrostatic free energy. We calculate and compare typical similarity indices and measures, such as Hodgkin index and root mean square deviation. Finally, we introduce a modification to the nonlinear Poisson-Boltzmann equation, which accounts in a simple way for the finite size of mobile ions, by applying a cutoff in the concentration formula for ionic distribution at regions of high electrostatic potentials. We test the influence of this ionic concentration cutoff on the electrostatic properties of tRNA.     

Substituted 2-nitrobenzyltrichloroacetate esters for photodirected oligonucleotide detritylation in solid films

Oligonucleotide microarray fabrication by chemical synthesis using photoacid generators in solid films could have advantages over existing methods, but has not matched the accuracy of conventional synthesis where detritylation is performed with acid solutions. To address this problem, we explored the kinetics and equilibria of nucleoside detritylation in solid films, using trichloroacetic acid (TCA) generated by photolysis from its esters with substituted 2-nitrobenzyl alcohols. We synthesised 25 such esters, all alpha-phenyl substituted, and assessed their potential as solid film photoacid generators. They included sets with (i) mono- or dimethoxy-, (ii) 5-halo-, (iii) alkyl- or aryl-substituted 5-amino-, or (iv) 5-aryl-substituents in the 2-nitro- or 2,6-dinitrobenzyl ring. Absorption maxima of their UV spectra ranged from 230 to 410 nm, with quantum yields at 365 nm from < 0.01 to nearly 1.0. The esters formed optically clear solid films on glass slides without added polymer. Kinetics of intrafilm photoacid generation, proton activity changes and detritylation were measured in situ. The most effective esters for light sensitivity and detritylation were 5-chloro-, 5-bromo-, 4,5-dimethoxy-, and 4- or 5-aryl-substituted 2,6-dinitrobenzyl esters. Photoacid-induced increases in proton activity and detritylation were severely inhibited by polymers containing electronegative heteroatoms, but not by polymers lacking them. In solid films, intrafilm detritylation with photogenerated TCA was fast, but stopped at an equilibrium well short of completion. Both experiment and theory emphasise the inadequacy of attempting to force detritylation with high intrafilm acid activity.     

Interaction in the ternary complexes of HCl-methanol-X, X = H2O or NH3: Ab initio calculations and on-the-fly molecular dynamics

Dynamics, structures, energetics, and vibrational spectra of the ternary complexes of hydrogen chloride with either methanol and water or methanol and ammonia were investigated by on-the-fly molecular dynamics and ab initio and density functional theory (DFT) with aug-cc-pvDZ basis sets. Addition of CH3OH to the HCl-NH3 system catalyzes the proton transfer from HCl to NH3. However, the dynamics of the system show that the proton is not localized on NH3; rather, it is shared between N and Cl.     

Correlations and dissociations between BOLD signal and P300 amplitude in an auditory oddball task: a parametric approach to combining fMRI and ERP

A parametric method is proposed to examine the relationship between neuronal activity, measured with event related potentials (ERPs), and the hemodynamic response, observed with functional magnetic resonance imaging (fMRI), during an auditory oddball paradigm. After verifying that the amplitude of the evoked response P300 increases as the probability of oddball target presentation decreases, we explored the corresponding effect of target frequency on the fMRI signal. We predicted and confirmed that some regions that showed activation changes following each oddball are affected by the rate of presentation of the oddballs, or the probability of an oddball target. We postulated that those regions that increased activation with decreasing probability might be responsible for the corresponding changes in the P300 amplitude. fMRI regions that correlated with the amplitude of the P300 wave were supramarginal gyri, thalamus, insula and right medial frontal gyrus, and are presumably sources of the P300 wave. Other regions, such as anterior and posterior cingulate cortex, were activated during the oddball paradigm but their fMRI signal changes were not correlated with the P300 amplitudes. This study thus shows how combining fMRI and ERP in a parametric design identifies task-relevant sources of activity and allows separation of regions that have different response properties.     

Generation of the vorticity mode by sound in a vibrationally relaxing gas

The procedure of derivation of a new dynamical equation governing the vorticity mode that is generated by sound, is discussed in detail. It includes instantaneous quantities and does not require averaging over sound period. The resulting equation applies to both periodic and aperiodic sound as the origin of the vorticity mode. Under certain conditions, the direction of streamlines of the vorticity mode may be inverted as compared with that in a fluid with standard attenuation. This reflects an anomalous absorption of sound, when transfer of momentum of the vorticity mode into momentum of sound occurs. The theory is illustrated by a representative example of the generation of vorticity in a vibrationally relaxing gas in the field of periodic weakly diffracting acoustic beam.