33 research outputs found
Behavior and Impact of Zirconium in the SoilâPlant System: Plant Uptake and Phytotoxicity
Because of the large number of sites they pollute, toxic metals that contaminate terrestrial ecosystems are increasingly of environmental and sanitary concern (Uzu et al. 2010, 2011; Shahid et al. 2011a, b, 2012a). Among such metals is zirconium (Zr), which has the atomic number 40 and is a transition metal that resembles titanium in physical and chemical properties (Zaccone et al. 2008). Zr is widely used in many chemical industry processes and in nuclear reactors (Sandoval et al. 2011; Kamal et al. 2011), owing to its useful properties like hardness, corrosion-resistance and permeable to neutrons (Mushtaq 2012). Hence, the recent increased use of Zr by industry, and the occurrence of the Chernobyl and Fukashima catastrophe have enhanced environmental levels in soil and waters (Yirchenko and Agapkina 1993; Mosulishvili et al. 1994 ; Kruglov et al. 1996)
Structural Insight into the Rotational Switching Mechanism of the Bacterial Flagellar Motor
Structural analysis of a clockwise-biased rotation mutant of the bacterial
flagellar rotor protein FliG provides a new model for the arrangement of FliG
subunits in the motor, and novel insights into rotation switching
Measurement of the angular coefficients in Z-boson events using electron and muon pairs from data taken at âs=8 TeV with the ATLAS detector
The angular distributions of Drell-Yan charged lepton pairs in the vicinity of the Z-boson mass peak probe the underlying QCD dynamics of Z-boson production. This paper presents a measurement of the complete set of angular coefficients A0â7 describing these distributions in the Z-boson Collins-Soper frame. The data analysed correspond to 20.3 fbâ1 of pp collisions at sâ=8s=8 TeV, collected by the ATLAS detector at the CERN LHC. The measurements are compared to the most precise fixed-order calculations currently available (O(α2s))(O(αs2)) and with theoretical predictions embedded in Monte Carlo generators. The measurements are precise enough to probe QCD corrections beyond the formal accuracy of these calculations and to provide discrimination between different parton-shower models. A significant deviation from the (O(α2s))(O(αs2)) predictions is observed for A0 â A2. Evidence is found for non-zero A5,6,7, consistent with expectations
On the selective ion binding hypothesis for potassium channels
The mechanism by which K+ channels select for K+ over Na+ ions has been debated for the better part of a century. The prevailing view is that K+ channels contain highly conserved sites that selectively bind K+ over Na+ ions through optimal coordination. We demonstrate that a series of alternating sites within the KcsA channel selectivity filter exists, which are thermodynamically selective for either K+ (cage made from two planes of oxygen atoms) or Na+ ions (a single plane of four oxygen atoms). By combining Bennett free energy perturbation calculations with umbrella sampling, we show that when K+ and Na+ are both permitted to move into their preferred positions, the thermodynamic preference for K+ over Na+ is significantly reduced throughout the entire selectivity filter. We offer a rationale for experimental measures of thermodynamic preference for K+ over Na+ from Ba2+ blocking data, by demonstrating that the presence of Ba2+ ions exaggerates K+ over Na+ thermodynamic stability due to the different binding locations of these ions. These studies reveal that K+ channel selectivity may not be associated with the thermodynamics of ions in crystallographic K+ binding sites, but requires consideration of the kinetic barriers associated with the different multi-ion permeation mechanisms
Fast gating in the Shaker K(+) channel and the energy landscape of activation
An early component of the gating current in Shaker K(+) channels with a time constant of â12 ÎŒsec has been recorded with a high-speed patchâclamp setup. This fast component was found to be part of the gating current associated with the opening and closing of the channel. With regard to an energy-landscape interpretation of protein kinetics, the voltage and temperature dependence of the fast component may be explained by a combination of drift diffusion and barrier jumping in the initial stages of channel activation. The data were modeled by a gating particle undergoing Brownian motion in a one-dimensional diffusion landscape that featured diminishing electrical resistance and entropy in the direction of channel activation. The final open state of the channel was reasoned to be narrow and deep to account for successful subtraction of linear-charge displacements at positive potentials. The overall picture of gating that emerges from these studies is that the channel experiences incremental organization from a relaxed state in the early steps of activation to a rigidly structured open state
Quantum Control of NaI Photodissociation Reaction Product States by Ultrafast Tailored Light Pulses
Pore opening and closing of a pentameric ligand-gated ion channel
Nerve signaling in humans and chemical sensing in bacteria both rely on the controlled opening and closing of the ion-conducting pore in pentameric ligand-gated ion channels. With the help of a multiscale simulation approach that combines mixed elastic network model calculations with molecular dynamics simulations, we study the opening and closing of the pore in Gloeobacter violaceus channel GLIC at atomic resolution. In our simulations of the GLIC transmembrane domain, we first verify that the two endpoints of the transition are open and closed to sodium ion conduction, respectively. We then show that a two-stage tilting of the pore-lining helices induces cooperative drying and iris-like closing of the channel pore. From the free energy profile of the gating transition and from unrestrained simulations, we conclude that the pore of the isolated GLIC transmembrane domain closes spontaneously. The mechanical work of opening the pore is performed primarily on the M2-M3 loop. Strong interactions of this short and conserved loop with the extracellular domain are therefore crucial to couple ligand binding to channel opening
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase
DNA methylation, various DNA repair mechanisms, and possibly early events in the opening of DNA as required for transcription and replication are initiated by flipping of a DNA base out of the DNA double helix. The energetics and structural mechanism of base flipping in the presence of the DNA-processing enzyme, cytosine 5-methyltransferase from HhaI (M.HhaI), were obtained through molecular dynamics based upon free-energy calculations. Free-energy profiles for base flipping show that, when in the closed conformation, M.HhaI lowers the free-energy barrier to flipping by 17 kcal/mol and stabilizes the fully flipped state. Flipping is shown to occur via the major groove of the DNA. Structural analysis indicates that flipping is facilitated by destabilization of the DNA double-helical structure and substitution of DNA base-pairing and base-stacking interactions with DNAâprotein interactions. The fully flipped state is stabilized by DNAâprotein interactions that are enhanced upon binding of coenzyme. This study represents an atomic detail description of the mechanism by which a protein facilitates specific structural distortion in DNA