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991.
Hervé Hogues Traian Sulea Enrico O. Purisima 《Journal of computer-aided molecular design》2014,28(4):417-427
We continued prospective assessments of the Wilma–solvated interaction energy (SIE) platform for pose prediction, binding affinity prediction, and virtual screening on the challenging SAMPL4 data sets including the HIV-integrase inhibitor and two host–guest systems. New features of the docking algorithm and scoring function are tested here prospectively for the first time. Wilma–SIE provides good correlations with actual binding affinities over a wide range of binding affinities that includes strong binders as in the case of SAMPL4 host–guest systems. Absolute binding affinities are also reproduced with appropriate training of the scoring function on available data sets or from comparative estimation of the change in target’s vibrational entropy. Even when binding modes are known, SIE predictions lack correlation with experimental affinities within dynamic ranges below 2 kcal/mol as in the case of HIV-integrase ligands, but they correctly signaled the narrowness of the dynamic range. Using a common protein structure for all ligands can reduce the noise, while incorporating a more sophisticated solvation treatment improves absolute predictions. The HIV-integrase virtual screening data set consists of promiscuous weak binders with relatively high flexibility and thus it falls outside of the applicability domain of the Wilma–SIE docking platform. Despite these difficulties, unbiased docking around three known binding sites of the enzyme resulted in over a third of ligands being docked within 2 Å from their actual poses and over half of the ligands docked in the correct site, leading to better-than-random virtual screening results. 相似文献
992.
Dr. Enrico Mugnaioli Dr. José Reyes‐Gasga Prof. Ute Kolb Dr. Joseph Hemmerlé Prof. Étienne F. Brès 《Chemistry (Weinheim an der Bergstrasse, Germany)》2014,20(23):6849-6852
Herein, we investigate human single hydroxyapatite crystals (enamel and dentine) by convergent‐beam electron diffraction (CBED) and automated electron‐diffraction tomography (ADT). The CBED pattern shows the absence of the mirror plane perpendicular to the c axis leading to the P63 space group instead of the P63/m space group considered for larger‐scale crystals, this is confirmed by ADT. This experimental evidence is of prime importance for understanding the morphogenesis and the architectural organization of calcified tissues. 相似文献
993.
Stefano Banfi Enrico Caruso Marzia Gariboldi Stefano Alemani Gianluca Nasini Ezio Bombardelli 《合成通讯》2013,43(7):1096-1109
A series of 5,10,15,20‐tetraarylporphyrins covalently linked to anthraquinones belonging to the class of emodin were synthesized following two different pathways. The first method exploits the functionalization of the methyl group in position 6 of O‐protected emodins, which can be converted either into a carboxylic acid or into a bromo‐methyl derivative. The modified emodins were then bound through amido or ether bonds to one of the tetraarylporphyrins meso phenyl rings bearing an amino or hydroxyl group, respectively. An alternative synthesis exploits the mixed condensation of triacetoxy‐emodinaldehyde (or trimethoxy‐emodinaldehyde) with pyrrole in the presence of variable amounts of benzaldehyde, thus affording two similar 5‐emodin‐10,15,20‐triphenylporphyrins differing from one another in the emodin hydroxyl group protection. These compounds are characterized by direct conjugation of the emodin moiety to the tetrapyrrolic ring. Preliminary experiments were performed in vitro on the human colon adenocarcinoma cell line HCT116 to evaluate the photocytotoxicity of the new compounds. 相似文献
994.
Excess molar volumes V E for 40 mixtures of heptane with a liquid alkane and apparent molar volumes in heptane for eight solid alkanes have been obtained at 298.15 K. They include five linear, 30 branched-chain, and 13 cyclic alkanes. Almost all systems exhibit negative V E values. For mixtures with open chain alkanes, V E increases from C5 to C7 and then decreases. A similar trend is shown by mixtures with cycloalkanes. V E values are compared with known H E data for mixtures with heptane and tetrachloromethane. Signs and trends of V E and H E are correlated with the free volume and interactional terms of the Flory theory. The partial molar volumes at infinite dilution in heptane, V°, have also been obtained and discussed together with literature data on other hydrocarbons and polar compounds. The calculated contributions to V° by CH3, CH2, CH and C groups are compared with previously determined contributions of polar groups. The lower contributions of the latter groups are explained with the volume contraction caused by dipole-induced dipole interaction. The volume effects associated with branching and cyclization have been evaluated and compared with the corresponding effects on solvation enthalpy. The branching effect, in the order of magnitude of few cm3·mol?1, and the larger negative values of cyclization volumes, down to ?24 cm3·mol?1, are discussed in terms of packing and solute–solvent interactions, in analogy to polar organic solutes either in heptane and tetrachloromethane. A negative cyclization effect is also exhibited by the solvation enthalpies. 相似文献
995.
Although the extraction of intact proteins from polyacrylamide gels followed by mass spectrometric molecular mass determination has been shown to be efficient, there is room for alternative approaches. Our study evaluates ethylene glycol diacrylate, a cleavable cross‐linking agent used for a new type of dissolvable gels. It attains an ester linkage that can be hydrolyzed in alkali conditions. The separation performance of the new gel system was tested by 1D and 2D SDS‐PAGE using the outer chloroplast envelope of Pisum sativum as well as a soluble protein fraction of human lymphocytes, respectively. Gel spot staining (CBB), dissolving, and extracting were conducted using a custom‐developed workflow. It includes protein extraction with an ammonia–SDS buffer followed by methanol treatment to remove acrylamide filaments. Necessary purification for MALDI‐TOF analysis was implemented using methanol–chloroform precipitation and perfusion HPLC. Both cleaning procedures were applied to several standard proteins of different molecular weight as well as ‘real’ biological samples (8–75 kDa). The protein amounts, which had to be loaded on the gel to detect a peak in MALDI‐TOF MS, were in the range of 0.1 to 5 μg, and the required amount increased with increasing mass. 相似文献
996.
Dr. Kripasindhu Sardar Enrico Petrucco Craig I. Hiley Dr. Jonathan D. B. Sharman Dr. Peter P. Wells Prof. Andrea E. Russell Dr. Reza J. Kashtiban Dr. Jeremy Sloan Prof. Richard I. Walton 《Angewandte Chemie (International ed. in English)》2014,53(41):10960-10964
The pyrochlore solid solution (Na0.33Ce0.67)2(Ir1?xRux)2O7 (0≤x≤1), containing B‐site RuIV and IrIV is prepared by hydrothermal synthesis and used as a catalyst layer for electrochemical oxygen evolution from water at pH<7. The materials have atomically mixed Ru and Ir and their nanocrystalline form allows effective fabrication of electrode coatings with improved charge densities over a typical (Ru,Ir)O2 catalyst. An in situ study of the catalyst layers using XANES spectroscopy at the Ir LIII and Ru K edges shows that both Ru and Ir participate in redox chemistry at oxygen evolution conditions and that Ru is more active than Ir, being oxidized by almost one oxidation state at maximum applied potential, with no evidence for ruthenate or iridate in +6 or higher oxidation states. 相似文献
997.
998.
Characterization of lipopeptides produced by Bacillus licheniformis using liquid chromatography with accurate tandem mass spectrometry
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999.