Properties of the Liquid-Vapor Interface of Acetone-Water Mixtures. A Computer Simulation and ITIM Analysis Study

Molecular dynamics simulations of the liquid-vapor interface of acetone-water mixtures of different compositions, covering the entire composition range have been performed on the canonical (N, V, T) ensemble at 298 K, using a model combination that excellently describes the mixing properties of these compounds. The properties of the intrinsic liquid surfaces have been analyzed in terms of the Identification of the Truly Interfacial Molecules (ITIM) method. Thus, the composition, width, roughness, and separation of the subsurface molecular layers, as well as self-association, orientation, and dynamics of exchange with the bulk phase of the surface molecules have been analyzed in detail. Our results show that acetone molecules are strongly adsorbed at the liquid surface, and this adsorption extends to several molecular layers. Like molecules in the surface layer are found to form relatively large lateral self-associates. The effect of the vicinity of the vapor phase on a number of properties of the liquid phase vanishes beyond the first molecular layer, with the second subsurface layer already part of the bulk liquid phase in these respects. The orientational preferences of the surface molecules are governed primarily by the dipole-dipole interaction of the neighboring acetone molecules, and hydrogen bonding interaction of the neighboring acetone-water pairs. (Figure Presented). © 2015 American Chemical Society

A candidate ion-retaining state in the inward-facing conformation of sodium/galactose symporter: Clues from atomistic simulations

The recent Vibrio parahaemolyticus sodium/galactose (vSGLT) symporter crystal structure captures the protein in an inward-facing substrate-bound conformation, with the sodium ion placed, by structural alignment, in a site equivalent to the Na2 site of the leucine transporter (LeuT). A recent study, based on molecular dynamics simulations, showed that the sodium ion spontaneously leaves its initial position diffusing outside vSGLT, toward the intracellular space. This suggested that the crystal structure corresponds to an ion-releasing state of the transporter. Here, using metadynamics, we identified a more stable Na+ binding site corresponding to a putative ion-retaining state of the transporter. In addition, our simulations, consistently with mutagenesis studies, highlight the importance of D189 that, without being one of the NA(+)-coordinating residues, regulates its binding/release

Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations

The tripartite complex AcrAB-TolC is the major efflux system in Escherichia coli. It extrudes a wide spectrum of noxious compounds out of the bacterium, including many antibiotics. Its active part, the homotrimeric transporter AcrB, is responsible for the selective binding of substrates and energy transduction. Based on available crystal structures and biochemical data, the transport of substrates by AcrB has been proposed to take place via a functional rotation, in which each monomer assumes a particular conformation. However, there is no molecular-level description of the conformational changes associated with the rotation and their connection to drug extrusion. To obtain insights thereon, we have performed extensive targeted molecular dynamics simulations mimicking the functional rotation of AcrB containing doxorubicin, one of the two substrates that were co-crystallized so far. The simulations, including almost half a million atoms, have been used to test several hypotheses concerning the structure-dynamics-function relationship of this transporter. Our results indicate that, upon induction of conformational changes, the substrate detaches from the binding pocket and approaches the gate to the central funnel. Furthermore, we provide strong evidence for the proposed peristaltic transport involving a zipper-like closure of the binding pocket, responsible for the displacement of the drug. A concerted opening of the channel between the binding pocket and the gate further favors the displacement of the drug. This microscopically well-funded information allows one to identify the role of specific amino acids during the transitions and to shed light on the functioning of AcrB

Nanomolar oxytocin synergizes with weak electrical afferent stimulation to activate the locomotor CPG of the rat spinal cord in vitro.

Synergizing the effect of afferent fibre stimulation with pharmacological interventions is a desirable goal to trigger spinal locomotor activity, especially after injury. Thus, to better understand the mechanisms to optimize this process, we studied the role of the neuropeptide oxytocin (previously shown to stimulate locomotor networks) on network and motoneuron properties using the isolated neonatal rat spinal cord. On motoneurons oxytocin (1 nM-1 \u3bcM) generated sporadic bursts with superimposed firing and dose-dependent depolarization. No desensitization was observed despite repeated applications. Tetrodotoxin completely blocked the effects of oxytocin, demonstrating the network origin of the responses. Recording motoneuron pool activity from lumbar ventral roots showed oxytocin mediated depolarization with synchronous bursts, and depression of reflex responses in a stimulus and peptide-concentration dependent fashion. Disinhibited bursting caused by strychnine and bicuculline was accelerated by oxytocin whose action was blocked by the oxytocin antagonist atosiban. Fictive locomotion appeared when subthreshold concentrations of NMDA plus 5HT were coapplied with oxytocin, an effect prevented after 24 h incubation with the inhibitor of 5HT synthesis, PCPA. When fictive locomotion was fully manifested, oxytocin did not change periodicity, although cycle amplitude became smaller. A novel protocol of electrical stimulation based on noisy waveforms and applied to one dorsal root evoked stereotypic fictive locomotion. Whenever the stimulus intensity was subthreshold, low doses of oxytocin triggered fictive locomotion although oxytocin per se did not affect primary afferent depolarization evoked by dorsal root pulses. Among the several functional targets for the action of oxytocin at lumbar spinal cord level, the present results highlight how small concentrations of this peptide could bring spinal networks to threshold for fictive locomotion in combination with other protocols, and delineate the use of oxytocin to strengthen the efficiency of electrical stimulation to activate locomotor circuits

Distribution of oxytocin-immunoreactive neuronal elements in the rat spinal cord

We investigated the distribution of oxytocin in rat spinal cord using immunocytochemistry and radioimmunoassay (RIA). Each segment of the spinal cord from cervical to coccygeal contained oxytocin-immunoreactive fibers. The Rexed laminae I and II of the dorsal horn showed moderate to intense immunoreactivity. A dense network was found around the central canal where some fibers apposed the ependyma. The autonomic centers of the spinal cord at the thoracolumbar and sacral segments were heavily innervated. Few fibers were found around the motoneurons. In the white matter, the immunoreactivity was localized mainly in the dorsal part of the lateral funiculus, in the pars funicularis of the nucleus intermediolateralis and in a longitudinal network of the lateral funiculus below the spinal cord surface. Some fibers from this network entered the pia mater. RIA measurements revealed that the cervical spinal cord had lower oxytocin content than that found in either the thoracic, lumbar, sacral or coccygeal region. Our results show that the distribution of oxytocin-immunoreactive fibers in the spinal cord correlates with anatomic locations related to nociceptive, autonomic and motor functions. We assume that oxytocin-containing axons play a role in secreting oxytocin directly into the liquor space of the spinal cord

Beyond chelation:EDTA tightly binds taq DNA polymerase, MutT and dUTPase and directly inhibits dNTPase activity

Abstract EDTA is commonly used as an efficient chelator of metal ion enzyme cofactors. It is highly soluble, optically inactive and does not interfere with most chemicals used in standard buffers making EDTA a common choice to generate metal-free conditions for biochemical and biophysical investigations. However, the controversy in the literature on metal-free enzyme activities achieved using EDTA or by other means called our attention to a putative effect of EDTA beyond chelation. Here, we show that EDTA competes for the nucleotide binding site of the nucleotide hydrolase dUTPase by developing an interaction network within the active site similar to that of the substrate. To achieve these findings, we applied kinetics and molecular docking techniques using two different dUTPases. Furthermore, we directly measured the binding of EDTA to dUTPases and to two other dNTPases, the Taq polymerase and MutT using isothermal titration calorimetry. EDTA binding proved to be exothermic and mainly enthalpy driven with a submicromolar dissociation constant considerably lower than that of the enzyme:substrate or the Mg:EDTA complexes. Control proteins, including an ATPase, did not interact with EDTA. Our findings indicate that EDTA may act as a selective inhibitor against dNTP hydrolyzing enzymes and urge the rethinking of the utilization of EDTA in enzymatic experiments