Mechanisms of coupling between DNA recognition specificity and catalysis in EcoRI endonuclease

Proteins that bind to specific sites on DNA often do so in order to carry out catalysis or specific protein-protein interaction while bound to the recognition site. Functional specificity is enhanced if this second function is coupled to correct DNA site recognition. To analyze the structural and energetic basis of coupling between recognition and catalysis in EcoRI endonuclease, we have studied stereospecific phosphorothioate (PS) or methylphosphonate (PMe) substitutions at the scissile phosphate GpAATTC or at the adjacent phosphate GApATTC in combination with molecular-dynamics simulations of the catalytic center with bound Mg2+. The results show the roles in catalysis of individual phosphoryl oxygens and of DNA distortion and suggest that a "crosstalk ring" in the complex couples recognition to catalysis and couples the two catalytic sites to each other.     

Lithostratigraphy and carbonate microfacies across the Permian–Triassic boundary near Julfa (NW Iran) and in the Baghuk Mountains (Central Iran)

Permian–Triassic boundary sections in the Julfa (NW Iran) and Abadeh (Central Iran) regions display a succession of three characteristic rock units, (1) the Paratirolites Limestone with the mass extinction horizon at its top, (2) the ‘Boundary Clay’, and (3) the earliest Triassic Elikah Formation with the conodont P–Tr boundary at its base. The carbonate microfacies reveals a facies change, in the sections near Julfa, within the Paratirolites Limestone with an increasing number of intraclasts, Fe–Mn crusts, and biogenic encrustation. A decline in carbonate accumulation occurs towards the top of the unit with a sponge packstone in the sections, and finally resulting in a complete demise of the carbonate factory. The succession of the ‘Boundary Clay’ differs in the two regions; thin horizons of sponge packstone are present in the Julfa region and ‘calcite fans’ of probably inorganic origin in the Abadeh Region. The skeletal carbonate factory of the Late Permian was restored with the deposition of microbial carbonates at the base of the Elikah Formation, where densely laminated bindstone, floatstone with sparry calcite spheres, and oncoid wackestone/floatstone predominate.     

Nutritional changes induce xylogenesis in callus ofHaplopappus gracilis (NUTT.) A. Gray

Xylogenesis was induced in cultures of calli ofHaplopappus gracilis (NUTT.) A. Gray by metabolic shocks brought about by changes in nutrition. Xylogenesis was observed to occur in response to three changes in callus nutrition, caused by the following modifications of Eriksson’s nutrient medium and culture conditions: i) omission of sucrose in the medium for 3 to 6 days and then transfer of the calli onto complete Eriksson’s medium; ii) replacement of sucrose by 0.36*mol l_-1 xylose for the whole culture period; iii) omission of nitrogen sources(i.e. glycine and NH₄NO₃ omission and replacement of KNO₃ with equimolar KCI) for the whole culture period. The induction of xylogenesis in response to nutritional stress inH. gracilis can be used as a suitable model system for research concerning plant cell differentiation.     

Platelet‐activating factor interaction with the human erythrocyte membrane

Platelet‐activating factor (PAF) is a soluble signal messenger present in blood at nanomolar concentration. PAF has a wide spectrum of biological activities and is produced by and effective in different cell types. Owing to its important physiological role, we wanted to characterize membrane intercalation and interaction of PAF‐16 (1‐O‐hexadecyl‐2‐acetyl‐sn‐glycero‐3‐phosphocholine) by studying its capacity to induce during short‐term incubations at high concentrations cell shape alterations, phosphatidylserine exposure, and hemolysis in human erythrocytes. Our results showed that PAF‐16 at micromolar concentrations rapidly (≤1 min) induces stable but wash‐sensitive echinocytosis and hemolysis, but no substantial phosphatidylserine exposure. In conclusion, our study characterizes PAF‐16 as a highly membrane partitioning non‐permeable molecule accumulating in the outer membrane leaflet. These membrane interacting properties of PAF should, also at physiological concentrations, be important part of its nature as a membrane affector molecule. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:345–348, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20297     

Preparation, single-crystal X-ray diffraction and high-resolution NMR spectroscopic analyses of N-[(1,4-anhydro-5-deoxy-2,3-O-isopropylidene-D,L-ribitol)-5-yl]trimethylammonium iodide

The synthesis and isolation of 1,4-anhydro-5-deoxy-5-iodo-2,3-O-isopropylidene-D,L-ribitol and N-[(1,4-anhydro-5-deoxy-2,3-O-isopropylidene-D,L-ribitol)-5-yl]trimethylammonium iodide are described. The products were examined by (1)H, (13)C NMR spectroscopy, and N-[(1,4-anhydro-5-deoxy-2,3-O-isopropylidene-D,L-ribitol)-5-yl]trimethylammonium iodide was additionally analyzed by X-ray crystallography.     

Echinophilic proteins stomatin, sorcin, and synexin locate outside gangliosideM1 (GM1) patches in the erythrocyte membrane

The detergent (Triton X-100, 4 °C)-resistant membrane (DRM)-associated membrane proteins stomatin, sorcin, and synexin (anexin VII) exposed on the cytoplasmic side of membrane were investigated for their lateral distribution in relation to induced ganglioside_M1 (GM1) raft patches in flat (discocytic) and curved (echinocytic) human erythrocyte membrane. In discocytes, no accumulation of stomatin, sorcin, and synexin in cholera toxin subunit B (CTB) plus anti-CTB-induced GM1 patches was detected by fluorescence microscopy. In echinocytes, stomatin, sorcin, and synexin showed a similar curvature-dependent lateral distribution as GM1 patches by accumulating to spiculae induced by ionophore A23187 plus calcium. Stomatin was partly and synexin and sorcin were fully recruited to the spiculae. However, the DRM-associated proteins only partially co-localized with GM1 and were frequently distributed into different spiculae than GM1. The study indicates that stomatin, sorcin, and synexin are echinophilic membrane components that mainly locate outside GM1 rafts in the human erythrocyte membrane. Echinophilicity is suggested to contribute to the DRM association of a membrane component in general.     

Sensitive quantification of chosen drugs by reversed-phase chromatography with electrochemical detection at a glassy carbon electrode

Reversed-phase-high-performance liquid chromatographic method with electrochemical detection has proven to be a highly sensitive and selective method for determination of trace components in complex biological samples, and the electrochemical detector becomes an important alternative tool to ultraviolet and fluorescence detectors. A rapid and sensitive method for the accurate determination of metoclopramide, hydrochlorothiazide, imipramine and diclofenac in serum or plasma samples is described. The method is based on liquid-liquid extraction. The compounds were separated on C-18 column as stationary phase with a different binary mixture as mobile phase. Proposed method was validated with respect to specificity, linearity range, limit of detection and quantitation, precision, accuracy and successfully applied in a pharmacokinetic studies.     

Endovesicle formation and membrane perturbation induced by polyoxyethyleneglycolalkylethers in human erythrocytes

Polyoxyethyleneglycolalkylether (CmEn, m=12, n=8) can induce a large torocyte-like endovesicle in human erythrocytes. The present study aimed to examine how variations in the molecular structure of CmEn (m=10,12,14,16,18; n=1-10,23) affect the occurrence of torocyte endovesicles. Our results show that torocytes occur most frequently when m=12,14 and n=8,9. At this molecular configuration the detergents induce inward membrane bending (stomatocytic S1-S2 shapes) resulting in the formation of a large membrane invagination. These detergents have a strong membrane perturbing, i.e., haemolytic, effect. Theoretical calculations indicate that a torocyte-shaped inside-out membrane vesicle can be created from a large membrane invagination due to the impact of laterally mobile anisotropic membrane inclusions. Such inclusions may be detergent-membrane component complexes or unanchored integral membrane proteins. It is shown that a nonhomogeneous lateral distribution of anisotropic membrane inclusions may stabilise the torocyte endovesicle shape, characterised by having opposite membranes in the thin central region of the vesicles separated by a certain distance. Tubular, conical or inverted conical isotropic inclusions cannot do so.