Condensed phase photoelectron asymmetry

Large directional asymmetries were observed in photoelectron distributions from core and valence levels in metals and adsorbate atoms. Intensities varied by factors up to 25 as the angle between A and p was varied. The energy dependence of asymmetry showed atomic behavior similar to that expected for free atoms, modified for the tendency p∥A.     

Bio-orthogonal affinity purification of direct kinase substrates

Protein phosphorylation is a major mechanism of post-translational protein modification used to control cellular signaling. A challenge in phosphoproteomics is to identify the direct substrates of each protein kinase. Herein, we describe a chemical strategy for delivery of a bio-orthogonal affinity tag to the substrates of an individual protein kinase. The kinase of interest is engineered to transfer a phosphorothioate moiety to phosphoacceptor hydroxyl groups on direct substrates. In a second nonenzymatic step, the introduced phosphorothioate is alkylated with p-nitrobenzylmesylate (PNBM). Antibodies directed against the alkylated phosphorothioate epitope recognize these labeled substrates, but not alkylation products of other cellular nucleophiles. This strategy is demonstrated with Cdk1/cyclinB substrates using ELISA, western blotting, and immunoprecipitation in the context of whole cell lysates.     

Electron spin echo at S-band: Nuclear modulations and decay in C60 powder

At S-band (≈ 3 GHz) the modulation amplitude of the Electron Spin Echo patterns is increased with respect to the amplitude at X-band: as a consequence, it is possible to reveal the presence of nuclei not detectable at X-band. In this paper the results obtained by running ESE experiments at S-band on a C₆₀ powder sample containing radicals are shown and discussed. The two- and three-pulse Electron Spin Echo patterns exhibit both¹³C modulation and proton modulation not detected at X-band. The experimental data are quantitatively analyzed by simulating the time-domain patterns and their Fourier transforms. It results that a noticeable amount of proton nuclei surrounds the intrinsic paramagnetic centers. On the basis of the analysis, a possible explanation of their existence is given.     

Polarity effects on wavelength dependence of the fluorescence quantum yield for indole

The change in fluorescence quantum yield for indole as a function of excitation wavelength between 250 and 220 nm is found to vary with the static dielectric constant of various alcohol—water mixtures at 296 K. The supports the intermediacy of a CTTS state in the photoionization process.     

Electron spin echo envelope modulation from trapped electrons in a glassy medium

An amplitude modulation of the electron spin echo envelope has been observed for radiation-produced trapped electrons in 10 M NaOD/D₂O at 77°K but not in 10 M N₂OH/H₂O. The modulation has been simulated theoretically by generalizing the single crystal model of Rowan et al. to disordered systems. The modulation has been interpreted as due to dipolar interactions with deuterons in molecules of the second solvation shell around the trapped electrons.     

Forbidden matrix proton spin flip satellites in trapped electron EPR spectra

Observation of the 35 GHz EPR spectrum of γ-irradiated 10 M NaOH/H₂O and 10 M NaOD/D₂O glassy ices at 77°K has revealed proton spin flip satellites associated with the trapped elctron EPR line. This suggests that forbidden satellite transitions contribute to the lineshape of the trapped electron line in the 9 GHz spectrum which has commonly been studied.     

Modified AutoDock for accurate docking of protein kinase inhibitors

Protein kinases are an important class of enzymes controlling virtually all cellular signaling pathways. Consequently, selective inhibitors of protein kinases have attracted significant interest as potential new drugs for many diseases. Computational methods, including molecular docking, have increasingly been used in the inhibitor design process [1]. We have considered several docking packages in order to strengthen our kinase inhibitor work with computational capabilities. In our experience, AutoDock offered a reasonable combination of accuracy and speed, as opposed to methods that specialize either in fast database searches or detailed and computationally intensive calculations.However, AutoDock did not perform well in cases where extensive hydrophobic contacts were involved, such as docking of SB203580 to its target protein kinase p38. Another shortcoming was a hydrogen bonding energy function, which underestimated the attraction component and, thus, did not allow for sufficiently accurate modeling of the key hydrogen bonds in the kinase-inhibitor complexes.We have modified the parameter set used to model hydrogen bonds, which increased the accuracy of AutoDock and appeared to be generally applicable to many kinase-inhibitor pairs without customization. Binding to largely hydrophobic sites, such as the active site of p38, was significantly improved by introducing a correction factor selectively affecting only carbon and hydrogen energy grids, thus, providing an effective, although approximate, treatment of solvation.