Three-dimensional models of glutamate receptors

Structural models of glutamate receptors have been produced as part of a multidisciplinary study of neuronal function--both ligand/receptor interactions and ion transport--at the atomic level. The models have concentrated on the agonist binding and transmembrane domains of ionotropic (i.e. ligand-gated) glutamate receptors (iGluRs), and have aided our understanding of the molecular determinants of (1) ligand binding and (2) channel activity. The model building process involved a combination of homology modelling, distance geometry, molecular mechanics, protein-ligand and protein-protein docking, electrostatic calculations and manual adjustment, in conjunction with restraints from site-directed mutagenesis, ligand binding and electrophysiological studies. The initial models were used to produce hypotheses which were tested experimentally; these models have been subsequently refined as part of an extremely effective multidisciplinary study using an iterative molecular modelling/experimental verification cycle in which restraints derived from experimental studies are used at all stages, and the findings from one round of modelling are used as restraints in the next. By studying a variety of agonists and antagonists, details have been built up of (1) those residues involved in ligand binding and (2) the role of agonist binding (i.e. agonist-induced conformational change) in channel gating. The models also aid our understanding of the conductance properties of the channels.     

An interface clusters mixture model for the structure of amorphous silicon monoxide (SiO)

The present state of research on the structure of amorphous silicon monoxide (SiO) is reviewed. The black, coal-like modification of bulk SiO is studied by a combination of diffraction, microscopy, spectroscopy, and magnetometry methods. Partial radial distribution functions of SiO are obtained by X-ray, neutron and electron diffraction. Disproportionation of SiO into Si and SiO₂ is verified. High resolution TEM gives an upper limit of less than 2 nm for the typical Si cluster size. The Si K-edge electron energy-loss near-edge structure (ELNES) data of SiO are interpreted in terms of the oxidation states Si⁴⁺ and Si⁰. X-ray photoelectron spectroscopy gives first details about possible stoichiometric inhomogeneities related to internal interfaces. The wipe-out effect in the ²⁹Si MAS NMR signal of SiO is confirmed experimentally. The new estimation of the wipe-out radius is about 1.1 nm. First-time W-band, Q-band, and X-band ESR and SQUID measurements indicate an interfacial defect structure. Frequency distributions of atomic nearest-neighbours are derived. The interface clusters mixture model (ICM model) suggested here describes the SiO structure as a disproportionation in the initial state. The model implies clusters of silicon dioxide and clusters of silicon surrounded by a sub-oxide matrix that is comparable to the well-known thin Si/SiO₂ interface and significant in the volume because of small cluster sizes.     

Square root 3 -Subdivision Schemes: Maximal Sum Rule Orders

   Abstract. Subdivision with finitely supported masks is an efficient method to create discrete multiscale representations of smooth surfaces for CAGD applications. Recently a new subdivision scheme for triangular meshes, called

Optimized and far-red-emitting variants of fluorescent protein eqFP611

Fluorescent proteins (FPs) emitting in the far-red region of the spectrum are highly advantageous for whole-body imaging applications because scattering and absorption of long-wavelength light is markedly reduced in tissue. We characterized variants of the red fluorescent protein eqFP611 with bright fluorescence emission shifted up to 639 nm. The additional red shift is caused by a trans-cis isomerization of the chromophore. The equilibrium between the trans and cis conformations is strongly influenced by amino acid residues 143 and 158. Pseudo monomeric tags were obtained by further genetic engineering. For the red chromophores of eqFP611 variants, molar extinction coefficients of up to approximately 150,000 were determined by an approach that is not affected by the presence of molecules with nonfunctional red chromophores. The bright fluorescence makes the red-shifted eqFP611 variants promising lead structures for the development of near-infrared fluorescent markers. The red fluorescent proteins performed well in cell biological applications, including two-photon imaging.     

Carbon chains of type C2n+1N(-) (n=2-6): A theoretical study of potential interstellar anions

Linear anions of type C(2n+1)N(-) (n=2-6), which are expected to be good candidates for experimental investigation by microwave spectroscopy and radio astronomy, were studied by means of the coupled cluster variant CCSD(T). Making use of corrections taken over from HC(3)NC(3)N(-) and HC(5)N, accurate equilibrium structures ( approximately 0.0005 A accuracy in bond lengths) have been established for all five anions. The electric dipole moments increase strongly with increasing chain length. For C(13)N(-), a very large equilibrium dipole moment of 16.53 D (with respect to center-of-mass coordinate system, negative end of dipole at terminal carbon site) is predicted. The lowest vertical detachment energies, leading to (2)Sigma states of the radicals for C(3)N(-) and C(5)N(-) and to (2)Pi states in the case of the larger anions, are calculated to lie in the range of 4.40-4.63 eV. The ground-state rotational and quartic centrifugal distortion constants of C(5)N(-) are predicted to be 1389.4 MHz and 33.8 Hz, respectively. All anions studied appear to be fairly normal semirigid linear molecules. Throughout, good agreement with available matrix isolation IR spectroscopic data is obtained and many predictions of spectroscopic properties are made.     

Synthesis and photoinduced intramolecular processes of fulleropyrrolidine-oligothienylenevinylene-ferrocene triads

Two new triads based on N-methylfulleropyrolidine, oligothienylenevinylenes (nTV) and ferrocene (Fc), namely C(60)-nTV-Fc (n=2, 4) have been synthesized. A HOMO-LUMO gap as low as 1.09-1.11 eV was experimentally determined by cyclic voltammetry. In both polar and nonpolar solvents, photoinduced charge-separation (CS) processes in C(60)-nTV-Fc predominantly take place from the singlet excited states of C(60) and nTV; this result was indicated by steady and time-resolved emission spectroscopy. In the case of C(60)-4TV-Fc, the CS state was indicated by the nanosecond transient absorption spectra. In C(60)-2TV-Fc, although the CS process was also confirmed by the fluorescence quenching in nonpolar and polar solvents, the lifetimes of the CS states were shorter than those of C(60)-4TV-Fc. It was revealed that the introduction of Fc donor moiety at the end of the longer nTV chain in the C(60)-nTV dyad systems effectively increases the CS efficiency and the lifetimes of CS states.     

Synthesis, structural characterization, catalytic properties, and theoretical study of compounds containing an Al-O-M (M = Ti, Hf) core

Two single oxygen-bridged heterobimetallic oxides of Al(III) with group 4 metals (Ti, Hf) have been prepared. The reaction of LAlMeOH (1) [L = CH(N(Ar)(CMe))2, Ar = 2,6-iPr2C6H3] with dimethylmetallocenes of Ti and Hf in toluene (80 degrees C) and ether (room temperature), respectively, resulted in the formation of LAl(Me)(mu-O)M(Me)Cp2 [M = Ti (2), Hf (3)] in moderate to good yield. Compounds 2 and 3 were characterized by elemental analysis, IR, NMR (1H and 13C), EI-MS, and single-crystal X-ray structural analysis. Furthermore, compound 2 showed good catalytic activity in ethylene and styrene homopolymerization, while compound 3 is less active in ethylene polymerization. The styrene polymerization yields atactic polystyrene.     

Dual triggering of DNA binding and fluorescence via photoactivation of a dinuclear ruthenium(II) arene complex

The dinuclear RuII arene complexes [{(eta6-arene)RuCl}2(mu-2,3-dpp)](PF6)2, arene=indan (1), benzene (2), p-cymene (3), or hexamethylbenzene (4) and 2,3-dpp=2,3-bis(2-pyridyl)pyrazine, have been synthesized and characterized. Upon irradiation with UVA light, complexes 1 and 2 readily underwent arene loss, while complexes 3 and 4 did not. The photochemistry of 1 was studied in detail. In the X-ray structure of [{(eta6-indan)RuCl}2(mu-2,3-dpp)](PF6)2 (1), 2,3-dpp bridges two RuII centers 6.8529(6) A apart. In water, aquation of 1 in the dark occurs with replacement of chloride with biexponential kinetics and decay constants of 100+/-1 min-1 and 580+/-11 min-1. This aquation was suppressed by 0.1 M NaCl. UV or visible irradiation of 1 in aqueous or methanolic solution led to arene loss. The fluorescence of the unbound arene is approximately 40 times greater than when it is complexed. Irradiation of 1 also had a significant effect on its interactions with DNA. The DNA binding of 1 is increased after irradiation. The non-irradiated form of 1 preferentially formed DNA adducts that only weakly blocked RNA polymerase, while irradiation of 1 transformed the adducts into stronger blocks for RNA polymerase. The efficiency of irradiated 1 to form DNA interstrand cross-links was slightly greater than that of cisplatin in both 10 mM NaClO4 and 0.1 M NaCl. In contrast, the interstrand cross-linking efficiency of non-irradiated 1 in 10 mM NaClO4 was relatively low. An intermediate amount of cross-linking was observed when the sample of DNA already modified by non-irradiated 1 was irradiated. DNA unwinding measurements supported the conclusion that both mono- and bifunctional adducts with DNA can form. These results show that photoactivation of dinuclear RuII arene complexes can simultaneously produce a highly reactive ruthenium species that can bind to DNA and a fluorescent marker (the free arene). Importantly, the mechanism of photoreactivity is also independent of oxygen. These complexes, therefore, have the potential to combine both photoinduced cell death and fluorescence imaging of the location and efficiency of the photoactivation process.     

Surface tension and capillary waves at the nematic-isotropic interface in ternary mixtures of liquid crystal, colloids, and impurities

In mixtures of thermotropic liquid crystals with spherical poly(methyl methacrylate) particles, self-supporting networklike structures are formed during slow cooling past the isotropic-to-nematic phase transition. Experimental results support the hypothesis that a third component, alkane remnants slowly liberated from the particles, plays a crucial role. A theoretical model, based on the phenomenological Landau-de Gennes, Carnahan-Starling, and hard-sphere crystal theories, is developed to describe the continuous phase separation in a ternary nematic-impurity-colloid mixture. The interfacial tension and the dispersion relation of the surface modes of the nematic-isotropic interface are determined. The colloids decrease the interfacial tension and the damping rate of surface waves, whereas impurities act in an opposite way. This should strongly influence the formation of abovementioned networklike structures and could help explain some of their rheological properties.