Toward Electrochemically Controllable Tristable Three‐Station [2]Catenanes

Encouraged by the prospect of producing an electrochemical, color‐switchable red–green–blue (RGB) dye compound, we have designed, synthesized, and characterized two three‐station [2]catenanes. Both are composed of macrocyclic polyethers containing three π‐electron‐rich stations, which act as recognition sites for a π‐electron‐deficient tetracationic cyclophane. The molecular structures of the two three‐station [2]catenanes were characterized fully by mass spectrometry and ¹H NMR spectroscopy. To anticipate the relative occupancies of the three stations in each [2]catenane by the cyclophane, model compounds with the same constitutions in the vicinity of the stations were synthesized. The relative ground‐state populations of the three stations occupied in both [2]catenanes were estimated from the thermodynamic parameters for 1:1 complexes between all these model compounds and the cyclophane, obtained from isothermal titration calorimetry (ITC). The electrochemical and electromechanical properties of the three‐station [2]catenanes were analyzed by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and spectroelectrochemistry (SEC). The first three‐station [2]catenane was found to behave like a bistable system, whereas the second can be described as a quasi‐tristable system.     

Transition metal complexes with thiosemicarbazide-based ligands. Part LIV. Nickel(II) complexes with pyridoxal semi- (PLSC) and thiosemicarbazone (PLTSC). Crystal and molecular structure of [Ni(PLSC)(H2O)3](NO3)2 and [Ni(PLTSC-H)py]NO3

This paper describes the synthesis of the first Ni(II) complexes with pyridoxal semicarbazone (PLSC), viz. Ni(PLSC)Cl₂ · 3.5H₂O (1), [Ni(PLSC)(H₂O)₃](NO₃)₂ (2), Ni(PLSC)(NCS)₂ · 4H₂O (3), [Ni(PLSC-2H)NH₃] · 1.5H₂O (4), as well as two new complexes with pyridoxal thiosemicarbazone (PLTSC), [Ni(PLTSC-H)py]NO₃ (5) and [Ni(PLTSC-H)NCS] (6). Complexes 1–3 are paramagnetic and have most probably an octahedral structure, for complex 2 this was proved by X-ray diffraction analysis. In contrast, complexes 4–6 are diamagnetic and have a square-planar structure, and in the case of complex 5 this was also confirmed by X-ray structural analysis. In all cases the Schiff bases are coordinated as tridentate ligands with an ONX (X = O, PLSC; X = S, PLTSC) set of donor atoms. With the complexes involving the neutral form of PLSC and the monoanionic form of PLTSC, the PL moiety is in the form of a zwitterion. In addition to the above-mentioned techniques, all the complexes were characterized by measuring their molar conductivities, UV–Vis and partial IR spectra.     

A Genetically Encoded β‐Lactamase Reporter for Ultrasensitive 129Xe NMR in Mammalian Cells

Molecular imaging holds considerable promise for elucidating biological processes in normal physiology as well as disease states, but requires noninvasive methods for identifying analytes at sub‐micromolar concentrations. Particularly useful are genetically encoded, single‐protein reporters that harness the power of molecular biology to visualize specific molecular processes, but such reporters have been conspicuously lacking for in vivo magnetic resonance imaging (MRI). Herein, we report TEM‐1 β‐lactamase (bla) as a single‐protein reporter for hyperpolarized (HP) ¹²⁹Xe NMR, with significant saturation contrast at 0.1 μm . Xenon chemical exchange saturation transfer (CEST) interactions with the primary allosteric site in bla give rise to a unique saturation peak at 255 ppm, well removed (≈60 ppm downfield) from the ¹²⁹Xe‐H₂O peak. Useful saturation contrast was also observed for bla expressed in bacterial cells and mammalian cells.     

Programming A Molecular Relay for Ultrasensitive Biodetection through 129Xe NMR

A supramolecular strategy for detecting specific proteins in complex media by using hyperpolarized ¹²⁹Xe NMR is reported. A cucurbit[6]uril (CB[6])‐based molecular relay was programmed for three sequential equilibrium conditions by designing a two‐faced guest (TFG) that initially binds CB[6] and blocks the CB[6]–Xe interaction. The protein analyte recruits the TFG and frees CB[6] for Xe binding. TFGs containing CB[6]‐ and carbonic anhydrase II (CAII)‐binding domains were synthesized in one or two steps. X‐ray crystallography confirmed TFG binding to Zn²⁺ in the deep CAII active‐site cleft, which precludes simultaneous CB[6] binding. The molecular relay was reprogrammed to detect avidin by using a different TFG. Finally, Xe binding by CB[6] was detected in buffer and in E. coli cultures expressing CAII through ultrasensitive ¹²⁹Xe NMR spectroscopy.     

Detection of hydrogen atom adduct of spin-trap DEPMPO. The relevance for studies of biological systems

We proposed EPR spectroscopy using spin-trap DEPMPO as a novel method for the detection of a hydrogen atom (*H) produced by chemical and biological systems. In complex EPR spectra of DEPMPO adducts in biological systems, spectral lines of unknown origin have been observed. We have assumed (Baci?, G.; Mojovi?, M. Ann. N. Y. Acad. Sci. 2005, 1048, 230-243) that those lines represent the spectrum of a hydrogen atom (*H) adduct i.e., DEPMPO/H. An electrochemical system known to produce only *H radicals was used here in order to obtain a separate spectrum of the DEPMPO/H adduct. An acquired spectrum as well as a computer spectral simulation of the DEPMPO/H adduct showed considerable resemblance with additional lines in the EPR spectra of DEPMPO adducts in biological systems-plant plasma membranes and cell walls. This shows that such a radical is produced by plants as well as that DEPMPO is suitable for detection in both electrochemical and biological systems.     

Liquid-liquid phase transitions in supercooled water studied by computer simulations of various water models

Liquid-liquid and liquid-vapor coexistence regions of various water models were determined by Monte Carlo (MC) simulations of isotherms of density fluctuation-restricted systems and by Gibbs ensemble MC simulations. All studied water models show multiple liquid-liquid phase transitions in the supercooled region: we observe two transitions of the TIP4P, TIP5P, and SPCE models and three transitions of the ST2 model. The location of these phase transitions with respect to the liquid-vapor coexistence curve and the glass temperature is highly sensitive to the water model and its implementation. We suggest that the apparent thermodynamic singularity of real liquid water in the supercooled region at about 228 K is caused by an approach to the spinodal of the first (lowest density) liquid-liquid phase transition. The well-known density maximum of liquid water at 277 K is related to the second liquid-liquid phase transition, which is located at positive pressures with a critical point close to the maximum. A possible order parameter and the universality class of liquid-liquid phase transitions in one-component fluids are discussed.     

Structural basis of swinholide A binding to actin

Marine toxins targeting the actin cytoskeleton represent a new and promising class of anti-cancer compounds. Here we present a 2.0 A resolution structure of swinholide A, a marine macrolide, bound to two actin molecules. The structure demonstrates that the actin dimer in the complex does not represent a physiologically relevant entity, for the two actin molecules do not interact with each other. The swinholide A actin binding site is the same as that targeted by toxins of the trisoxazole family and numerous actin binding proteins, highlighting the importance of this site in actin polymerization. The observed structure reveals the mechanism of action of swinholide A and provides a structural framework about which to design new agents directed at the cytoskeleton.     

Is it possible to predict the average surface hydrophobicity of a protein using only its amino acid composition?

Hydrophobicity is one of the most important physicochemical properties of proteins. Moreover, it plays a fundamental role in hydrophobic interaction chromatography, a separation technique that, at present time, is used in most industrial processes for protein purification as well as in laboratory scale applications. Although there are many ways of assessing the hydrophobicity value of a protein, recently, it has been shown that the average surface hydrophobicity (ASH) is an important tool in the area of protein separation and purification particularly in protein chromatography. The ASH is calculated based on the hydrophobic characteristics of each class of amino acid present on the protein surface. The hydrophobic characteristics of the amino acids are determined by a scale of aminoacidic hydrophobicity. In this work, the scales of Cowan-Whittaker and Berggren were studied. However, to calculate the ASH, it is necessary to have the three-dimensional protein structure. Frequently this data does not exist, and the only information available is the amino acid sequence. In these cases it would be desirable to estimate the ASH based only on properties extracted from the protein sequence. It was found that it is possible to predict the ASH from a protein to an acceptable level for many practical applications (correlation coefficient > 0.8) using only the aminoacidic composition. Two predictive tools were built: one based on a simple linear model and the other on a neural network. Both tools were constructed starting from the analysis of a set of 1982 non-redundant proteins. The linear model was able to predict the ASH for an independent subset with a correlation coefficient of 0.769 for the case of Cowan-Whittaker and 0.803 for the case of Berggren. On the other hand, the neural model improved the results shown by the linear model obtaining correlation coefficients of 0.831 and 0.836, respectively. The neural model was somewhat more robust than the linear model particularly as it gave similar correlation coefficients for both hydrophobicity scales tested, moreover, the observed variabilities did not overcome 6.1% of the mean square error. Finally, we tested our models in a set of nine proteins with known retention time in hydrophobic interaction chromatography. We found that both models can predict this retention time with correlation coefficients only slightly inferior (11.5% and 5.5% for the linear and the neural network models, respectively) than models that use the information about the three-dimensional structure of proteins.     

New approach to chemical modification of PIM-1 for gas separation membranes

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