Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.     

Template evaporation method for controlling anatase nanocrystal size in ordered macroporous TiO2

The importance of pure-phase titanium oxide materials as catalysts, sensors, and photonic band-gap materials has been growing steadily. Recently, more attention has been focused on nanostructured titanium oxide showing controlled and periodic porosity on a nanometric scale. The nanocrystal size control of porous nanostructured titanium oxide in an anatase form is a crucial step for the organic template method. Simple template removal by evaporation in an inert atmosphere is reported in this article and compared with the calcination technique usually reported in the literature. The proposed method allows the formation of a double-porous (macro and meso) anatase phase. We demonstrate that it highly preserves the macropore order into a titanium oxide material and induces narrowly dispersed mesopores by controlling the nano-crystal size that is kept around 6 nm. For the proposed method, polystyrene beads are particularly suitable as templates, being evaporated in the temperature range of anatase existence. The final high surface area makes the materials appealing for applications as photocatalysts or sensors.     

The SO(3,3) group as a common basis for Dirac's and Proca's equations

Dirac's and Proca's equations are unified in the sense that the algebras of Dirac -matrices and Duffin-Kemmer-matrices are shown to furnish two distinct matrix representations of the Lie algebra of the SO(3,3)-group. This fact is then interpreted as evidence for the classical picture of particles described by the above-mentioned equations to be a relativistic top. It is also argued that the shape of the top is rod-like.     

Generation of Ethyl Metathiophosphate by Thermal Fragmentation of O-Ethyl N-Substituted Phosphoramidothioates

O-Ethyl N-1-adamantylphosphoramidothioate was synthesized and found to fragment on heating in inert solvents to form the pyrophosphate AdNHP(S)(OEt)OP(S)(OEt)OH. The proposed mechanism involves an elimination of the amine portion with release of ethyl metathiophosphate (EtOP(S)O), as was confirmed in previous work for the comparable structure with oxygen. This transient compound then phosphorylates the starting phosphoramidothioate. O-Ethyl N,N-diethylphosphoramidothioate was also synthesized, and while it gave a similar pyro compound on heating, the reaction mixture was more complex. Both phosphoramidothioates, however, served effectively as thiophosphorylating agents toward alcohols, a silanol, and the silanol groups on the surface of silica gel. Exploratory experiments showed that these phosphoramidothioates also could thiophosphorylate the OH group of a monoester of phosphoric acid, as well as that of phosphinic acids, forming anhydrides with the partial structure     

Intermolecular contact interactions and their temperature dependence

A model, based on inverse gas chromatography experiments, has been developed for intermolecular interaction and its temperature dependence. The model ascribes to each substance a four-component solubility parameter; the four components reflect the van der Waals, polar, electron donor, and electron acceptor interactive properties. Their values depend on temperature in the same manner as does the cohesive energy. The latter was found to depend only on the critical temperature, the acentric factor, and the reduced temperature. The model was used for evaluation of the solubility parameters from polymer-solvent interaction coefficients and their temperature dependence with high accuracy. For binary solventsolvent mixtures, the free energy of mixing and its temperature dependence, as well as enthalpy of mixing can be derived from this model with a good accuracy.     

Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family

Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions.     

Structure and reactivity of xanthocorrinoids. Part V. Formation of trans-diol derivatives of 5,6-dihydrocobyrinic acid from xanthocorrinoids under acidic conditions

On treatment with H₂SO₄/MeOH, epimerization of hexamethyl cis-5,6-dihydroxycobyrinate c,8-lactam ( 3 ) takes place quantitatively at C(6), yielding the corresponding trans-diol 4 . The corresponding lactone 7 , whose structure has been established by X-ray analysis, is obtained from xanthocorrinoids 5 and 6 under similar conditions.     

Zur Existenz von zwei Kristallmodifikationen der Mellitsäure

Zusammenfassung Es wurde röntgenorgraphisch und mit Hilfe derDTA, festgestellt, daß die Mellitsäure nur in einer Modifikation, der orthorhombischen¹, vorliegt. Die Darstellung der Mellitsäure^2,3 wurde in Einzelheiten modifiziert. Die Reinheit der Präparate wurde spektroskopisch, im IR- bzw. UV-Gebiet, und mit Hilfe der Papierchromatographie geprüft.

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by means of X-ray analysis and DTA it was found that mellitic acid exists only in the orthorhombic modification. The preparation of mellitic acid was modified in part. The purity ot the samples obtained was checked by IR-and UV-spectroscopy and by paper chromatography.

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Zur Kenntnis von Salzen einiger aromatischer Polycarbonsäuren, 3. Mitt.; 2. Mitt.:B. Hájek, E. Kálalová undF. Petr, Z. Chem.5, 230 (1965).

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Gewidmet dem Andenken an Professor Dr.Hans Meyer meinen Lehrer an der ehemaligen Deutschen Universität in Prag. Prof.Meyer geboren am 31. März 1871 in Wien, gestorben am 28. November 1942 in Theresienstadt, beschäftigte sich eingehend (mitH. Raudnitz u. a.) mit der Darstellung und Untersuchung der Mellitsäure und ihrer Derivate.     

Extraction of americium,lanthanides and some fission product elements by bidentate phosphonates

The extraction of Am, Eu, Ce(III), Zr(IV), and Sr from aqueous nitric acid— nitrate media by dibutyl N,N-diethylcarbamylphosphonate and dibutyl N,N-diethylcar-bamylmethylenephosphonate dissolved in carbon tetrachloride was studied. The trivalent actinide and lanthanide elements may be separated in certain aqueous phase acidity regions from Fe(III), Zr(IV), and Sr, whereas the separation of actinide elements from the lanthanide elements is poor. The extractant to metal ratio in the extracted complexes of Am, Eu, and Ce(III) is 3. The interferences in the extraction due to acidic impurities in the extracting agent are discussed.     

Parametrized convolutionless Generalized-Master-Equation approach to the exciton and electron propagation in the Agranovich and Galanin model

Expressing the influence of reservoirs (lattice modes, solvent etc.) on the exciton or electron propagation in homogeneous systems via two relaxation times in the Agranovich and Galanin model, the convolutionless Generalized Master Equations for the site occupation probabilities are derived. Two different projection operator techniques are used. Identity of the two approaches is verified for a dimer and physical contents of the result are discussed.