A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling,docking, de novo drug design and molecular dynamics analysis

When X-ray structure of a ligand-bound receptor is not available, homology models of the protein of interest can be used to obtain the ligand-binding cavities. The steroelectronic properties of these cavities are directly related to the performed molecular model coordinates. Thus, the use of different template structures for homology may result in variation of ligand-binding modes. We have recently reported the MD simulations of a potent CB ligand at bovine rhodopsin-based CB1 and CB2 receptors (Durdagi et al., Bioorg Med Chem 16:7377–7387, 2008). In this present study, a homology modeling study based on the β2-adrenergic receptor for both CB1 and CB2 receptors was performed, and the results were compared with rhodopsin-based models. In addition, the role of membrane bilayers to the adopted conformations of potent AMG3 CB ligand has been analyzed for receptor-free and membrane-associated receptor systems. The performed MD trajectory analysis results have shown that gauche conformations at the terminal segment of the alkyl side chain of AMG3 are not favored in solution. Different adopting dihedral angles defined between aromatic and dithiolane rings at the active sites of the CB1 and CB2 receptors, which are adapted lead to different alkyl side chain orientations and thus, may give clues to the medicinal chemists to synthesize more selective CB ligands. The binding sites of receptors derived by rhodopsin-based models have been regenerated using the β2-adrenergic based template receptors. The re-obtained models confirmed the ligand-binding pockets that were derived based on rhodopsin.     

The Physical Tourist

We organized and led a European study course for American undergraduate university students to explore the early history of relativity and quantum theory. We were inspired by The Physical Tourist articles published in this journal on Munich, Bern, Berlin, Copenhagen, and Göttingen. We describe this adventure both for others wishing to teach such a course and for anyone wishing to walk in the footsteps of the physicists who revolutionized physics in the early decades of the twentieth century.     

Newly generated cells are increased in hippocampus of adult mice lacking a serine protease inhibitor

Background  

Neurogenesis in the hippocampal dentate gyrus and the subventricular zone occurs throughout the life of mammals and newly generated neurons can integrate functionally into established neuronal circuits. Neurogenesis levels in the dentate gyrus are modulated by changes in the environment (enrichment, exercise), hippocampal-dependent tasks, NMDA receptor (NMDAR) activity, sonic hedgehog (SHH) and/or other factors.     

Electrochemical Detection of Droplets in Microfluidic Devices: Simultaneous Determination of Velocity,Size and Content

Microfluidic devices were designed to electrochemically detect in a two‐phase flow the velocity, size and content of aqueous droplets containing redox species. The principle of these determinations is based on the analysis of a unique chronoamperometric response recorded during the passage of a droplet over channel microelectrodes. Two configurations of electrochemical cell with different geometries were investigated both theoretically and experimentally. Velocity and size of droplets, as well as internal recirculating convection within droplets, were evaluated from chronoamperometric curves by specific transition times depending on the cell configuration. In addition, the droplet content was probed from the Faradaic current controlled by mass transport and by internal hydrodynamic regime. For droplet velocity and size, experimental data were systematically compared to optical measurements. All the results demonstrated the high performance of the electrochemical detection reached under these conditions. They successfully validate the concept of self‐consistent electrochemical detections of aqueous droplets within microchannels for the simultaneous determination of their velocity, size and content.     

Synthesis and crystal structures of some bis(3‐methyl‐1H‐indol‐2‐yl)(salicyl)methanes

Four 2,2′‐bisindolylmethanes (BIMs), a useful class of polyindolyl species joined to a central carbon, were synthesized using salicylaldehyde derivatives and simple acid catalysis; these are 2‐[bis(3‐methyl‐1H‐indol‐2‐yl)methyl]‐6‐methylphenol, (IIa), 2‐[bis(3‐methyl‐1H‐indol‐2‐yl)methyl]‐4,6‐dichlorophenol, (IIb), 2‐[bis(3‐methyl‐1H‐indol‐2‐yl)methyl]‐4‐nitrophenol, (IIc), and 2‐[bis(3‐methyl‐1H‐indol‐2‐yl)methyl]‐4,6‐di‐tert‐butylphenol, (IId). BIMs (IIa) and (IIb) were characterized crystallographically as the dimethyl sulfoxide (DMSO) disolvates, i.e. C₂₆H₂₄N₂O·2C₂H₆OS and C₂₅H₂₀Cl₂N₂O·2C₂H₆OS, respectively. Both form strikingly similar one‐dimensional hydrogen‐bonding chain motifs with the DMSO solvent molecules. BIM (IIa) packs into double layers of chains whose orientations alternate every double layer, while (IIb) forms more simply packed chains along the a axis. BIM (IIa) has a remarkably long c axis.     

First measurement of J/ ψ azimuthal anisotropy in PHENIX at forward rapidity in Au + Au collisions at $\sqrt{s_{\mathit{NN}}}=200$ GeV

In this paper, we calculate the decay rates of the D ⁺→D ⁰ e ⁺ ν, D _S ⁺→D ⁰ e ⁺ ν, , D _S ⁺→D ⁺ e ⁻ e ⁺ and B _S ⁰→B ⁰ e ⁻ e ⁺ semileptonic decay processes, in which only the light quarks decay, while the heavy flavors remain unchanged. The branching ratios of these decay processes are calculated with the flavor SU(3) symmetry. The uncertainties are estimated by considering the SU(3) breaking effect. We find that the decay rates are very tiny in the framework of the standard model. We also estimate the sensitivities of the measurements of these rare decays at future experiments, such as BES-III, super-B and LHC-b.     

Stability and band offsets between Si and LaAlO<Subscript>3</Subscript>

The replacement of traditional SiO₂ with high-k oxides allows the physical thickness of the gate dielectric to be thinner without the tunneling problem in Si-based metal-oxide-semiconductor field-effect transistors. LaAlO₃ appears to be a promising high-k material for use in future ultra large scale integrated devices. In the present paper, the electronic properties of Si/LaAlO₃ (001) heterojunctions are investigated by first-principles calculations. We studied the initial adsorption of Si atoms on the LaAlO₃ (001) surface, and found that Si atoms preferentially adsorb on top of oxygen atoms at higher coverage. The surface phase diagrams indicate that Si atoms may substitute oxygen atoms at the LaO-terminated surface. The band offsets, electronic density of states, and atomic charges are analyzed for the various Si/LaAlO₃ heterojunctions. Our results suggest that the Si/AlO₂ interface is suitable for the design of metal oxide semiconductor devices because the valence and conduction band offsets are both larger than 1 eV.     

Synthetic signal injection using inductive coupling

The limited bandwidths of volume selective RF pulses in localized in vivo MRS experiments introduce spatial artifacts that complicate spectral quantification of J-coupled metabolites. These effects are commonly referred to as a spatial interference or "four compartment" artifacts and are more pronounced at higher field strengths. The main focus of this study is to develop a generalized approach to numerical simulations that combines full density matrix calculations with 3D localization to investigate the spatial artifacts and to provide accurate prior knowledge for spectral fitting. Full density matrix calculations with 3D localization using experimental pulses were carried out for PRESS (TE=20, 70 ms), STEAM (TE=20, 70 ms) and LASER (TE=70 ms) pulse sequences and compared to non-localized simulations and to phantom solution data at 4 T. Additional simulations at 1.5 and 7 T were carried out for STEAM and PRESS (TE=20 ms). Four brain metabolites that represented a range from weak to strong J-coupling networks were included in the simulations (lactate, N-acetylaspartate, glutamate and myo-inositol). For longer TE, full 3D localization was necessary to achieve agreement between the simulations and phantom solution spectra for the majority of cases in all pulse sequence simulations. For short echo time (TE=20 ms), ideal pulses without localizing gradients gave results that were in agreement with phantom results at 4 T for STEAM, but not for PRESS (TE=20). Numerical simulations that incorporate volume localization using experimental RF pulses are shown to be a powerful tool for generation of accurate metabolic basis sets for spectral fitting and for optimization of experimental parameters.     

Magnetization depth profile of (Fe/Dy) multilayers

An experimental and numerical study of the magnetization in (Fe 3 nm/Dy 2 nm) multilayers is presented. The samples were thermally evaporated under ultra-high vacuum at two different substrate temperatures, 320 and 570 K. In order to get the magnetization depth profile of these transition metal/rare earth (TM/RE) multilayers, a fine investigation of the structural, chemical, and magnetic properties was carried out. The samples were studied by X-ray reflectivity (XRR), high resolution transmission electron microscopy (HRTEM), conversion electron Mössbauer spectrometry (CEMS), SQUID magnetometry and polarized neutron reflectivity (PNR). Magnetization profiles were obtained by Monte Carlo simulations to support the PNR fits. The key role of the crystalline structure is emphasized by magnetic depth profile measurements performed using polarized neutron reflectometry. The antiparallel configuration of Fe and Dy layers’ magnetizations was evidenced, as well as the perpendicular magnetic anisotropy (PMA), especially in the case of the sample prepared at 570 K.