Alamethicin channels in a membrane: molecular dynamics simulations

Alamethicin (Alm) is a 20 residue peptide which forms a kinked alpha-helix in membrane and membrane-mimetic environments. Ion channels formed by intramembraneous aggregates of Alm are thought to be formed by bundles of approximately parallel Alm helices surrounding a central bilayer pore. Different channel conductance levels correspond to different numbers of helices per bundle, ranging from N = 5 to N > 8. Calculation of the predicted pKA values of the ring of Glu18 sidechains at the C-terminal mouth of the pore suggests that at neutral pH most or all of these sidechains will remain protonated. Nanosecond molecular dynamics (MD) simulations of N = 5, 6, 7 and 8 bundles of Alm helices in a POPC bilayer have been run, corresponding to a total simulation time of 4 ns. These simulations explore the stability and conformational dynamics of these helix bundle channels when embedded in a full phospholipid bilayer in an aqueous environment. The structural and dynamic properties of water in these model channels are examined. As in earlier in vacuo simulations (J. Breed, R. Sankararamakrishnan, I. D. Kerr and M. S. P. Sansom, Biophys. J., 1996, 70, 1643) the dipole moments of water molecules within the pores are aligned antiparallel to the helix dipoles. This helps to contribute to the stability of the helix bundles.     

Correlation of the Rates of Solvolysis of the Benzhydryldimethylsulfonium Ion. Application of the Aromatic Ring Parameter(1)

Values for the specific rates of solvolysis of the benzhydryldimethylsulfonium ion in 34 solvents have been analyzed using various forms of the extended Grunwald-Winstein equation. The specific rates are insensitive toward changes in solvent nucleophilicity (N(T)) values, and they correlate best against a combination of Y(+) values (based on the solvolyses of the 1-adamantyldimethylsulfonium ion) and aromatic ring parameter (I) values. Common-molecule return is observed, being especially powerful in solvents rich in fluoro alcohol; the logarithm of the associated mass law constant correlates inversely with the solvent N(T) values. The product selectivities in ethanol-water mixtures are also consistent with an S(N)1 mechanism for the solvolyses.     

Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein

Atomistic QM/MM simulations have been carried out on the complete photocycle of Photoactive Yellow Protein, a bacterial photoreceptor, in which blue light triggers isomerization of a covalently bound chromophore. The "chemical role" of the protein cavity in the control of the photoisomerization step has been elucidated. Isomerization is facilitated due to preferential electrostatic stabilization of the chromophore's excited state by the guanidium group of Arg52, located just above the negatively charged chromophore ring. In vacuo isomerization does not occur. Isomerization of the double bond is enhanced relative to isomerization of a single bond due to the steric interactions between the phenyl ring of the chromophore and the side chains of Arg52 and Phe62. In the isomerized configuration (ground-state cis), a proton transfer from Glu46 to the chromophore is far more probable than in the initial configuration (ground-state trans). It is this proton transfer that initiates the conformational changes within the protein, which are believed to lead to signaling.     

Superhydrophobic surface structures in thermoplastic polymers by interference lithography and thermal imprinting

We present a method to produce superhydrophobic surfaces in thermoplastic polymer substrates. The method involves the creation of a nickel stamp using a customized laser interference lithography technique and electroplating processes. This stamp is used to emboss sub-micrometer periodic structures into the thermoplastic. The modified surface is coated with a hydrophobic plasma-polymerized hexafluoropropene layer. Surfaces with different periodicity and relief depth were created. On the surface with the highest aspect ratio, advancing water contact angles of 167° were measured with a water contact angle hysteresis of below 5°.     

The derivatisation of avermectins and milbemycins in milk: new insights and improvement of the procedure

Derivatisation of the avermectines ivermectin (IVM), doramectin (DOR), abamectin (ABA) and eprinomectin (EPR), and the milbemycin moxidectin (MOX) to fluorescent derivatives is commonly used for quantitative analysis at relevant levels using high performance liquid chromatography (HPLC) with fluorescence detection. Problems associated with the differences in reactivity towards derivatisation (EPM) and limited stability of the derived products (IVM, DOR, ABA) may seriously hamper the applicability of the method and the reliability of the obtained results. A study was performed to obtain more insight in this derivatisation process from an organic chemistry point of view. This study demonstrated the occurrence of two main fluorescent derivatives: the trifluoroacetyl esters (flu-TFA) and the derivatives with a free hydroxy group at the glycosidic ring (flu-OH). Optimisation of the derivatisation conditions resulted in a fast and reproducible formation of the fluorescent derivatives for all analytes including EPM. The improved procedure involves the addition of 1-methylimidazole (MI), trifluoroacetic anhydride (TFAA), triethylamine (TEA) and trifluoroacetic acid (TFA) with a subsequent incubation for 30 min at 70 °C. With this procedure for IVM, DOR and ABA flu-TFA derivatives are obtained instead of flu-OH derivatives as generally described in literature. The derivatisation is reproducible in different milk samples and the derivatives proved to be stable for at least 80 h at room temperature. Using the optimised procedure a limit of detection (LoD) of 0.1 μg kg⁻¹ in milk was readily obtained.     

Comprehensive analysis of ß-lactam antibiotics including penicillins, cephalosporins, and carbapenems in poultry muscle using liquid chromatography coupled to tandem mass spectrometry

A comprehensive method for the quantitative residue analysis of trace levels of 22 ß-lactam antibiotics, including penicillins, cephalosporins, and carbapenems, in poultry muscle by liquid chromatography in combination with tandem mass spectrometric detection is reported. The samples analyzed for ß-lactam residues are hydrolyzed using piperidine in order to improve compound stability and to include the total residue content of the cephalosporin ceftifour. The reaction procedure was optimized using a full experimental design. Following detailed isotope labeling, tandem mass spectrometry studies and exact mass measurements using high-resolution mass spectrometry reaction schemes could be proposed for all ß-lactams studied. The main reaction occurring is the hydrolysis of the ß-lactam ring under formation of the piperidine substituted amide. For some ß-lactams, multiple isobaric hydrolysis reaction products are obtained, in accordance with expectations, but this did not hamper quantitative analysis. The final method was fully validated as a quantitative confirmatory residue analysis method according to Commission Decision 2002/657/EC and showed satisfactory quantitative performance for all compounds with trueness between 80 and 110 % and within-laboratory reproducibility below 22 % at target level, except for biapenem. For biapenem, the method proved to be suitable for qualitative analysis only.