Substrate specificity of the acyl transferase domains of EpoC from the epothilone polyketide synthase

The production of epothilone mixtures is a direct consequence of the substrate tolerance of the module 3 acyltransferase (AT) domain of the epothilone polyketide synthase (PKS) which utilises both malonyl- and methylmalonyl-CoA extender units. Particular amino acid motifs in the active site of AT domains influence substrate selection for methylmalonyl-CoA (YASH) or malonyl-CoA (HAFH). This motif appears in hybrid form (HASH) in epoAT3 and may represent the molecular basis for the relaxed specificity of the domain. To investigate this possibility the AT domains from modules 2 and 3 of the epothilone PKS were examined in the heterologous DEBS1-TE model PKS. Substitution of AT1 of DEBS1-TE by epoAT2 and epoAT3 both resulted in functional PKSs, although lower yields of total products were observed when compared to DEBS1-TE (2% and 11.5% respectively). As expected, epoAT3 was significantly more promiscuous in keeping with its nature during epothilone biosynthesis. When the mixed motif (HASH) of epoAT3 within the hybrid PKS was mutated to HAFH (indicative of malonyl-CoA selection) it resulted in a non-productive PKS. When this mixed motif was converted to YASH (indicative of methylmalonyl-CoA selection) the selectivity of the hybrid PKS for methylmalonyl-CoA showed no statistically significant increase, and was associated with a loss of productivity.     

Patterned immobilization of antibodies in mechanically induced cracks

A new approach of chemically immobilizing antibody within a pattern based on thin-film cracking is presented. An adjustable pattern width is achieved with resolutions varied from nano- to microscale by using loading stress on thin-film coated elastomer substrate in both one and two dimensions. By introduction of solution or chemical vapor deposition approaches, antibodies were covalently immobilized in the channels. To demonstrate the bioactivity, specificity, and response rate of antibody patterned structure, scanning electron microscopy was used to enumerating bacteria. The chemically coupled antibody is found to retain its specificity when incubated with different bacteria solutions. Trichloro(1H,1H,2H,2H-perfluoroctyl)silane coating on nonsensing regions exhibits a distinguished bacteria-resistant function that is beneficial for providing a low intrinsic background signal in detection. This technique shows a great potential for applications in the fields of sensing and tissue engineering.     

Action spectrum conversion factors that change erythemally weighted to previtamin D3-weighted UV doses

Abstract Many solar UV measurements, either terrestrial or personal, weight the raw data by the erythemal action spectrum. However, a problem arises when one tries to estimate the benefit of vitamin D(3) production based on erythemally weighted outdoor doses, like those measured by calibrated R-B meters or polysulphone badges, because the differences between action spectra give dissimilar values. While both action spectra peak in the UVB region, the erythemal action spectrum continues throughout the UVA region while the previtamin D(3) action spectrum stops near that boundary. When one uses the previtamin D(3) action spectrum to weight the solar spectra (D(eff)), one gets a different contribution in W m(-2) than what the erythemally weighted data predicts (E(eff)). Thus, to do proper benefit assessments, one must incorporate action spectrum conversion factors (ASCF) into the calculations to change erythemally weighted to previtamin D(3)-weighted doses. To date, all benefit assessments for vitamin D(3) production in human skin from outdoor exposures are overestimates because they did not account for the different contributions of each action spectrum with changing solar zenith angle and ozone and they did not account for body geometry. Here we describe how to normalize the ratios of the effective irradiances (D(eff)/E(eff)) to get ASCF that change erythemally weighted to previtamin D(3)-weighted doses. We also give the ASCF for each season of the year in the northern hemisphere every 5 degrees from 30 degrees N to 60 degrees N, based on ozone values. These ASCF, along with geometry conversion factors and other information, can give better vitamin D(3) estimates from erythemally weighted outdoor doses.     

Evaluation of automated direct sample introduction with comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry for the screening analysis of dioxins in fish oil

An automated direct sample introduction technique coupled to comprehensive two-dimensional gas chromatography-time of flight mass spectrometry (DSI-GC x GC/TOF-MS) was applied for the development of a relatively fast and easy analytical screening method for 17 polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) and 4 non-ortho polychlorinated biphenyls (PCBs) in fish oil. Comparison of instrumental performance between DSI-GC x GC/TOF-MS and the traditional gas chromatographic high resolution mass spectrometric (GC-HRMS) method showed good agreement of results for standard solutions analyzed in blind fashion. Relatively high tolerance of the DSI technique for lipids in the final extracts enabled a streamlined sample preparation procedure that only required gel permeation chromatography (GPC) and solid-phase extraction (SPE) cleanup with graphitized carbon black. The sample size for the method was 2g of cod liver oil, which achieved limits of quantitation (LOQs) of 0.019-7.8 pg/g toxic equivalent quotients for the individual PCDD/Fs. Lower detection limits can be achieved by using larger sample size and scaling up the sample preparation procedure, but this adds to the labor, time, solvent consumption, and expense of the approach. However, the streamlined method yielded 0.94 pg/g and 2.3 pg/g LOQs for 2,3,7,8-tetrachloro dibenzofuran (TCDF) and 3,3',4,4',5-pentachloro biphenyl (CB126), which were sufficiently low for regulatory monitoring of 2g samples. Therefore, instead of congener specific analysis, this streamlined analytical screening method for TCDF and CB126 has the potential to monitor fish oil contaminated with dioxin and dioxin-like PCBs at or above current food safety limits. Acceptable recoveries for nearly all analytes at three different spiking levels in fish oil samples were achieved with good repeatability.     

Stereostructure assignment of flexible five-membered rings by GIAO 13C NMR calculations: prediction of the stereochemistry of elatenyne

The stereochemistry of conformationally mobile five-membered rings is often hard to assign from NMR data, and [2,2']bifuranyl systems are even more challenging. GIAO (13)C NMR chemical shifts have been calculated for a series of [2,2']bifuranyl and pyranopyran species, taking into account their conformational flexibility using weighted averages of the data for all low energy conformers. We show that calculation of (13)C NMR chemical shifts using the geometries obtained using molecular mechanics greatly reduces the computational expense without a significant loss of accuracy, even in this demanding system. The results were sufficiently accurate to distinguish not only the pyran and furanyl isomers but also between all the diastereoisomeric forms. As a result of this validation, we predict the stereochemistry for the recently proposed revised structure of the natural product elatenyne, which contains a [2,2']bifuranyl core.     

Solid-phase synthesis of asymmetrically substituted "AB3-type" phthalocyanines

Synthesis of phthalocyanines with asymmetrical substitution on the periphery is often difficult due the problems in purification of the phthalocyanine mixtures obtained. Using a poly(ethylene glycol) (PEG)-based support with a Wang-type linker, we have developed the synthesis of monohydroxylated, oligoethylene glycol substituted phthalocyanines utilizing an amidine-base-promoted phthalonitrile tetramerization reaction. The use of a hydrophilic support allows symmetrical phthalocyanine product formed in solution to be readily and completely removed by washing while leaving the "AB3" product on the support. Acid cleavage with 10% trifluoroacetic acid provides the pure unsymmetrically substituted Pc. This method was applied to several metallo Pcs. Additionally, methods to avoid premature reactions on-resin that give A2B2 products are provided.     

Density functional theory and CCSD(T) evaluation of ionization potentials,redox potentials,and bond energies related to zirconocene polymerization catalysts

Quantum-mechanical-based computational design of molecular catalysts requires accurate and fast electronic structure calculations to determine and predict properties of transition-metal complexes. For Zr-based molecular complexes related to polyethylene catalysis, previous evaluation of density functional theory (DFT) and wavefunction methods only examined oxides and halides or select reaction barrier heights. In this work, we evaluate the performance of DFT against experimental redox potentials and bond dissociation enthalpies (BDEs) for zirconocene complexes directly relevant to ethylene polymerization catalysis. We also examined the ability of DFT to compute the fourth atomic ionization potential of zirconium and the effect the basis set selection has on the ionization potential computed with CCSD(T). Generally, the atomic ionization potential and redox potentials are very well reproduced by DFT, but we discovered relatively large deviations of DFT-calculated BDEs compared to experiment. However, evaluation of BDEs with CCSD(T) suggests that experimental values should be revisited, and our CCSD(T) values should be taken as most accurate.     

Photoinduced electron transfer dynamics in porphyrin donor dyads

Intramolecular photoinduced electron transfer (PET) processes occurring in dyads with a free base porphyrin-tetraazaanthracene donor (P) and either a tetracyanonaphthoquinidodimethane (TCQ) or benzoquinone (BQ) acceptor linked by a rigid six σ-bond polynorbornane bridge ([6]) have been investigated. For P[6]BQ, PET in the polar solvent benzonitrile (_s = 25.9) occurs with a rate constant (k_PET) of 1.6 × 10⁸ s⁻¹ but is not evident in solvents less polar than tetrahydrofuran (_s = 7.52). For P[6]TCQ, highly efficient forward PET occurs in both polar and non-polar solvents (k_PET > 2 × 10¹⁰ s⁻¹). For P[6]TCQ the lifetime of the resulting charge-separated state decreases markedly with increasing solvent polarity. The results are discussed in the context of the likely mechanisms for electronic coupling and current theories for PET processes in such linked molecular systems.     

Xanthene-Based Nitric Oxide-Responsive Nanosensor for Photoacoustic Imaging in the SWIR Window

Shortwave infrared (SWIR) dyes are characterized by their ability to absorb light from 900 to 1400 nm, which is ideal for deep tissue imaging owing to minimized light scattering and interference from endogenous pigments. An approach to access such molecules is to tune the photophysical properties of known near-infrared dyes. Herein, we report the development of a series of easily accessible (three steps) SWIR xanthene dyes based on a dibenzazepine donor conjugated to thiophene ( SCR-1 ), thienothiophene ( SCR-2 ), or bithiophene ( SCR-3 ). We leverage the fact that SCR-1 undergoes a bathochromic shift when aggregated for in vivo studies by developing a ratiometric nanoparticle for NO ( rNP-NO ), which we employed to successfully visualize pathological levels of nitric oxide in a drug-induced liver injury model via deep tissue SWIR photoacoustic (PA) imaging. Our work demonstrates how easily this dye series can be utilized as a component in nanosensor designs for imaging studies.     

Characterization of the cell surface and cell wall chemistry of drinking water bacteria by combining XPS, FTIR spectroscopy, modeling, and potentiometric titrations

Aquabacterium commune, a predominant member of European drinking water biofilms, was chosen as a model bacterium to study the role of functional groups on the cell surface that control the changes in the chemical cell surface properties in aqueous electrolyte solutions at different pH values. Cell surface properties of A. commune were examined by potentiometric titrations, modeling, X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared (FTIR) spectroscopy. By combining FTIR data at different pH values and potentiometric titration data with thermodynamic model optimization, the presence, concentration, and changes of organic functional groups on the cell surface (e.g., carboxyl, phosphoryl, and amine groups) were inferred. The pH of zero proton charge, pH(zpc) = 3.7, found from titrations of A. commune at different electrolyte concentrations and resulting from equilibrium speciation calculations suggests that the net surface charge is negative at drinking water pH in the absence of other charge determining ions. In situ FTIR was used to describe and monitor chemical interactions between bacteria and liquid solutions at different pH in real time. XPS analysis was performed to quantify the elemental surface composition, to assess the local chemical environment of carbon and oxygen at the cell wall, and to calculate the overall concentrations of polysaccharides, peptides, and hydrocarbon compounds of the cell surface. Thermodynamic parameters for proton adsorption are compared with parameters for other gram-negative bacteria. This work shows how the combination of potentiometric titrations, modeling, XPS, and FTIR spectroscopy allows a more comprehensive characterization of bacterial cell surfaces and cell wall reactivity as the initial step to understand the fundamental mechanisms involved in bacterial adhesion to solid surfaces and transport in aqueous systems.