Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling

1,2,3-Trichloropropane (TCP) is a highly toxic, recalcitrant byproduct of epichlorohydrin manufacture. Haloalkane dehalogenase (DhaA) from Rhodococcus sp. hydrolyses the carbon–halogen bond in various halogenated compounds including TCP, but with low efficiency (k _cat/K _m = 36 s^-1 M^-1). A Cys176Tyr-DhaA mutant with a threefold higher catalytic efficiency for TCP dehalogenation has been previously obtained by error-prone PCR. We have used molecular simulations and quantum mechanical calculations to elucidate the molecular mechanisms involved in the improved catalysis of the mutant, and enantioselectivity of DhaA toward TCP. The Cys176Tyr mutation modifies the protein access and export routes. Substitution of the Cys residue by the bulkier Tyr narrows the upper tunnel, making the second tunnel “slot” the preferred route. TCP can adopt two major orientations in the DhaA enzyme, in one of which the halide-stabilizing residue Asn41 forms a hydrogen bond with the terminal halogen atom of the TCP molecule, while in the other it bonds with the central halogen atom. The differences in these binding patterns explain the preferential formation of the (R)- over the (S)-enantiomer of 2,3-dichloropropane-1-ol in the reaction catalyzed by the enzyme.     

Synthesis of Zeolite L. Tuning Size and Morphology

Summary. A convenient synthesis of zeolite L is presented. The size of the crystals can be tuned between 30 and 6000nm, spanning a volume range of seven orders of magnitude. The zeolite L crystals, which typically feature a cylindrical morphology, are synthesized with various aspect ratios ranging from elongated to disc-shaped. The importance of obtaining zeolite crystals with well-defined size and morphology is discussed in view of potential applications of zeolite L containing organic dye molecules as guests.This revised version was published online in February 2005. In the previous version the issue was not marked as a special issue, and the issue title and the editor was missing     

Determination of protein phosphorylation by extracellular signal-regulated kinase using capillary electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry

Extracellular signal-regulated kinase (ERK) is a key regulatory enzyme mediating cell responses to mitogenic stimulation and is one of the key components in linking growth factor receptor activation to serine/threonine protein phosphorylation processes. Phosphorylation reaction by ERK plays an important role in many signal transduction pathways. ERK phosphorylates numerous substrates such as MBP, microtubule-associated protein 2 (MAP2) and nuclear protein. In particular, MBP is a substrate commonly employed for the detection of ERK activity and contains the consensus primary sequence PRT97P. In this paper, we compared the degree of the phosphorylation reaction of MBP substrate peptides by ERK with the three different MBP substrate peptides, MBP1(KNIVTPRTPPPSQGK), MBP2(VPRTPGGRR) and MBP3(APRTPGGRR) in order to select an efficient substrate peptide for phosphorylation reaction by ERK. The results showed that the MBP3 peptide is the most efficient substrate for phosphorylation reaction by ERK. Using MBP3 peptide, the phosphorylation reaction of MBP by ERK was monitored with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and capillary electrophoresis (CE). Our results demonstrate the feasibility of the CE method, the method being a simple and reliable technique in determining and characterizing various kinds of enzyme reaction especially including kinase enzymes.     

Studies on the Stereochemistry of 2-(Nitromethylidene)-Heterocycles

The ¹H-NMR spectra of 2-(nitromethylidene)pyrrolidine ( 7 ), 1-methyl-2-(nitromethylidene)imidazolidind ( 10 ) and 3-(nitromethylidene)tetrahydrothiazine ( 11 ) in CDCl₃ and (CD₃)₂SO indicate that these compounds have the intramolecularly H-bonded structures (Z)- 7 , (E)- 10 and (Z)- 11 while the N-methyl derivative 8 of 7 is (E)-configurated in both solvents. 1-Benzylamino-1-(methyltio)-2-nitroehtylene ( 13 ), an acylic model, has the H-bonded configuration (E)- 13 in CDCl₃ and in (CD₃)₂SO. 2-(Nitromethylidene)thiazolidine ( 3 ) has the (E)-configuration in CDCl₃ but exists in (CD₃)₂SO as a mixture of (Z)- and (E)-isomers with the former predominating. Both species are detected to varying proportions in a mixture of the two solvents. ¹⁵N-NMR spectroscopy of 3 ruled out unambiguously the nitronic acid structure 6 and the nitromethyleimine structure 5 . The N-methyl derivative 4 of 3 is (Z)-configurated in (CD₃)₂SO. Comparison of the olefinic proton shifts of (Z)- 3 and (Z)- 4 with those of analogues and also of 1,1-bis(methylti)-2-nitroethylene ( 12 ) shows decreased conjugation of the lone pair of electrons of the ring N-atom in (Z)- 3 and (Z)- 4 . This is also supported by ¹³C-NMR studies. Plausible explanations for the phenomenon are offered by postulating that the ring N-atoms are pyramidal in (Z)- 3 and (Z)- 4 and planar in other cases or, alternatively, that the conjugated nitroenamine system gets twisted due to steric interaction between the NO₂-group and the ring S-atom. Single-crystal X-ray studies of 3 and 8 show that the former exists in the (Z)-configuration and the latter in (E)-configuration; the ring N-atom in the former has slightly more pyramidal character than in the latter.     

Influence of the overall pressure on electrical conductivity of the amorphous semiconductor Ge15Te81S2As2

The experimental results obtained with the chalcogenide glass Ge₁₅Te₈₁S₂As₂ with imposed overall pressure up to 700 MPa are presented. The material exhibits the switching effect and the memory effect. It is shown that the overall pressure changes remarkably d.c. electrical conductivity of the amorphous semiconductor. It is assumed that the changes in conductivity are caused by changes in activation energy. The changes in activation energy within the range of considered pressures are, as follows from our measurements, E/p–10·95×10^–5 eV/MPa +p × 10·41 W 10^–7 eV/MPa². The assumption of the activation energy dependence on pressurep are confirmed also by measurements of dependence In vs. 1/T at various pressures.     

An Unconventional Polymerization Route to Hydrophilic Fluorescent Organic Nanoparticles for Multicolor Cellular Bioimaging

We demonstrated an unconventional polymerization route to synthesize hydrophilic fluorescent organic nanoparticles (FONs) for multicolor cellular bioimaging in this contribution. The route benefits from our unexpected discovery of a rapid polymerization reaction between 1,6‐hexanediol dipropiolate and 2,4,6‐triazide‐1,3,5‐triazine under the catalysis of N,N,N′,N′′,N′′‐pentamethyldiethylenetriamine (PMDETA). Interestingly, the 2,4,6‐triazide‐1,3,5‐triazine and PMDETA system can also induce rapid free radical polymerization at room temperature. The as‐prepared FONs exhibited promising water solubility and stability with an average diameter of 20 nm. The excitation wavelength‐dependent fluorescent properties endow the FONs with blue, yellow, and red fluorescent emission under UV, blue, and green excitation, respectively. The cytotoxicity of FONs was investigated by using a Cell Counting Kit (CCK‐8) assay, which indicated good biocompatiblity. More importantly, the cell uptake experiment verified the FONs were excellent fluorescent nanoprobes for multicolor cellular bioimaging. Therefore, this unconventional route provides a novel fabrication strategy of highly hydrophilic FONs for biomedical applications.     

Isobaric vapor liquid equilibria data for the binary system (glycidyl butyrate + acetone,glycidyl butyrate + carbon tetrachloride,glycidyl butyrate + chloroform) at atmospheric pressure 101 kPa

Isobaric vapor liquid equilibria (VLE) for the binary mixtures of glycidyl butyrate(1) + acetone(2), glycidyl butyrate(1) + carbon tetrachloride(2) and glycidyl butyrate(1) + chloroform(2) at 101 kPa were studied. The experimental data were satisfactorily correlated with the models of Wilson, NRTL and UNIQUAC activity coefficients. The activity coefficients for the equilibrium data were obtained by the nonlinear least square method. The average relative deviations between experimental temperatures and calculated temperatures by the Wilson, NRTL and UNIQUAC models were 0.16, 0.16, 0.23% for glycidyl butyrate(1) + chloroform( 2), 0.38, 0.12, 0.27% for glycidylbutyrate(1) + carbon tetrachloride(2), and 0.67, 0.13, 0.54% for glycidyl butyrate(1) + acetone(2). Azeotrope behavior was not found for these systems. The thermodynamic consistency of the correlations was checked by the Herrington’s area test.     

The synthesis of iron–nickel alloy nanoparticles using a reverse micelle technique

Nanosized Fe_0.2Ni_0.8 particles were prepared by reducing their salts with sodium borohydride (NaBH₄) in cationic water-in-oil (w/o) microemulsions of water/cetyl-trimethyl-amonium bromide (CTAB) and n-butanol/isooctane at 25 °C. According to the TEM and X-ray diffraction analyses, the synthesized particles were around 4–12 nm in size. Due to their nanodimensions, the particles had a primitive cubic (pc) structure rather than the body-centered cubic (BCC) structure of the bulk material. An examination of the synthesis from the reverse micelle reveals that the morphology of the iron–nickel alloy nanoparticles depends mainly on the microemulsion's composition. The magnetization of the nanoparticles was much lower than that of the bulk material, reflecting the influence of the nanodimensions on the particles’ magnetizations.     

The LPCTrap experiment: measurement of the β–ν angular correlation in 6He using a transparent Paul trap

We report on the status of the LPCTrap experiment, devoted to measure the β–ν angular correlation in the pure Gamow–Teller decay of ⁶He. This measurement is motivated by the search for the presence of tensor type contributions to the weak interaction. The ⁶He ions are confined in a novel transparent Paul trap. The β particles and the recoil ions are detected in coincidence to deduce the angular correlation parameter. The commissioning run performed in 2005 has given the proof of principle of this experiment. Up to 10⁵ coincidences were recorded during a second run in 2006.