Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange

Functional Status of Neuronal Calcium Sensor-1 Is Modulated by Zinc Binding

International audienceNeuronal calcium sensor-1 (NCS-1) protein is abundantly expressed in the central nervous system and retinal neurons, where it regulates many vital processes such as synaptic transmission. It coordinates three calcium ions by EF-hands 2-4, thereby transducing Ca 2+ signals to a wide range of protein targets, including G protein-coupled receptors and their kinases. Here, we demonstrate that NCS-1 also has Zn 2+-binding sites, which affect its structural and functional properties upon filling. Fluorescence and circular dichroism experiments reveal the impact of Zn 2+ binding on NCS-1 secondary and tertiary structure. According to atomic absorption spectroscopy and isothermal titration calorimetry studies, apo-NCS-1 has two high-affinity (4 × 10 6 M −1) and one low-affinity (2 × 10 5 M −1) Zn 2+-binding sites, whereas Mg 2+-loaded and Ca 2+-loaded forms (which dominate under physiological conditions) bind two zinc ions with submicromolar affinity. Metal competition analysis and circular dichroism studies suggest that Zn 2+-binding sites of apo-and Mg 2+-loaded NCS-1 overlap with functional EF-hands of the protein. Consistently, high Zn 2+ concentrations displace Mg 2+ from the EF-hands and decrease the stoichiometry of Ca 2+ binding. Meanwhile, one of the EF-hands of Zn 2+-saturated NCS-1 exhibits a 14-fold higher calcium affinity, which increases the overall calcium sensitivity of the protein. Based on QM/MM molecular dynamics simulations, Zn 2+ binding to Ca 2+-loaded NCS-1 could occur at EF-hands 2 and 4. The high-affinity zinc binding increases the thermal stability of Ca 2+-free NCS-1 and favours the interaction of its Ca 2+-loaded form with target proteins, such as dopamine receptor D2R and GRK1. In contrast, low-affinity zinc binding Frontiers in Molecular Neuroscience | www.frontiersin.org

Substitutions into amino acids that are pathogenic in human mitochondrial proteins are more frequent in lineages closely related to human than in distant lineages

Propensities for different amino acids within a protein site change in the course of evolution, so that an amino acid deleterious in a particular species may be acceptable at the same site in a different species. Here, we study the amino acid-changing variants in human mitochondrial genes, and analyze their occurrence in non-human species. We show that substitutions giving rise to such variants tend to occur in lineages closely related to human more frequently than in more distantly related lineages, indicating that a human variant is more likely to be deleterious in more distant species. Unexpectedly, substitutions giving rise to amino acids that correspond to alleles pathogenic in humans also more frequently occur in more closely related lineages. Therefore, a pathogenic variant still tends to be more acceptable in human mitochondria than a variant that may only be fit after a substantial perturbation of the protein structure

A Plethora of Epigenetic Minerals Reveals a Multistage Metasomatic Overprint of a Mantle Orthopyroxenite from the Udachnaya Kimberlite

More than forty mineral species of epigenetic origin have been identified in an orthopyroxenite from the Udachnaya-East kimberlite pipe, Daldyn kimberlite field, Siberian platform. Epigenetic phases occur as: (1) Mineral inclusions in the rock-forming enstatite, (2) daughter minerals within large (up to 2 mm) crystallized melt inclusions (CMI) in the rock-forming enstatite, and (3) individual grains and intergrowths in the intergranular space of the xenolith. The studied minerals include silicates (olivine, clinopyroxene, phlogopite, tetraferriphlogopite, amphibole-supergroup minerals, serpentine-group minerals, talc), oxides (several generations of ilmenite and spinel, rutile, perovskite, rare titanates of the crichtonite, magnetoplumbite and hollandite groups), carbonates (calcite, dolomite), sulfides (pentlandite, djerfisherite, pyrrhotite), sulfate (barite), phosphates (apatite and phosphate with a suggested crystal-chemical formula Na2BaMg[PO4]2), oxyhydroxide (goethite), and hydroxyhalides (kuliginite, iowaite). The examined epigenetic minerals are interpreted to have crystallized at different time spans after the formation of the host rock. The genesis of minerals is ascribed to a series of processes metasomatically superimposed onto the orthopyroxenite, i.e., deep-seated mantle metasomatism, infiltration of a kimberlite-related melt and late post-emplacement hydrothermal alterations. The reaction of orthopyroxene with the kimberlite-related melt has led to orthopyroxene dissolution and formation of the CMI, the latter being surrounded by complex reaction zones and containing zoned olivine grains with extremely high-Mg# (up to 99) cores. This report highlights the utility of minerals present in minor volume proportions in deciphering the evolution and modification of mantle fragments sampled by kimberlitic and other deep-sourced magmas. The obtained results further imply that the whole-rock geochemical analyses of mantle-derived samples should be treated with care due to possible drastic contaminations from “hiding” minor phases of epigenetic origin

Application of phosphocreatine in the treatment of a patient with acute myocardial infarction on the background of auxiliary circulation

The clinical case of maintaining the patient witha sharp transmural myocardial infarction frontseptal areas and tops of the left ventricle, thecardiogenic shock of the II degree and alveolar hypostasisof lungs are described. In the treatment of the patientauxiliary blood circulation in the form of installation ofan intra aortal balloon counterpulsation in the descendingdepartment of an aorta was applied. Also, phosphocreatine(PCR) of 8 g once with the subsequent appointmenton 2 g twice a day which has the expressed cardioprotectiveand antiarrhythmic effect in addition to standardtherapy in the first days of disease was appointed

Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism

The ubiquitous P-loop fold nucleoside triphosphatases (NTPases) are typically activated by an arginine or lysine ‘finger’. Some of the apparently ancestral NTPases are, instead, activated by potassium ions. To clarify the activation mechanism, we combined comparative structure analysis with molecular dynamics (MD) simulations of Mg-ATP and Mg-GTP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures of diverse P-loop NTPases, the conserved P-loop motif keeps the triphosphate chain of bound NTPs (or their analogs) in an extended, catalytically prone conformation, similar to that imposed on NTPs in water by potassium or ammonium ions. MD simulations of potassium-dependent GTPase MnmE showed that linking of alpha- and gamma phosphates by the activating potassium ion led to the rotation of the gamma-phosphate group yielding an almost eclipsed, catalytically productive conformation of the triphosphate chain, which could represent the basic mechanism of hydrolysis by P-loop NTPases

Preparation of Zirconia Nanofibers by Electrospinning and Calcination with Zirconium Acetylacetonate as Precursor

For the first time, zirconia nanofibers with an average diameter of about 75 nm have been fabricated by calcination of electrospun zirconium acetylacetonate/polyacrylonitrile fibers in the range of 500–1100 °C. Composite and ceramic filaments have been characterized by scanning electron microscopy, thermogravimetric analysis, nitrogen adsorption analysis, energy-dispersive X-ray spectroscopy, and X-ray diffractometry. The stages of the transition of zirconium acetylacetonate to zirconia have been revealed. It has been found out that a rise in calcination temperature from 500 to 1100 °C induces transformation of mesoporous tetragonal zirconia nanofibers with a high specific surface area (102.3 m2/g) to non-porous monoclinic zirconia nanofibers of almost the same diameter with a low value of specific surface area (8.3 m2/g). The tetragonal zirconia nanofibers with high specific surface area prepared at 500 °C can be considered, for instance, as promising supports for heterogeneous catalysts, enhancing their activity