Effective pore size and radius of capture for K+ ions in K-channels

Indexación: Web of Science; Scopus.Reconciling protein functional data with crystal structure is arduous because rare conformations or crystallization artifacts occur. Here we present a tool to validate the dimensions of open pore structures of potassium-selective ion channels. We used freely available algorithms to calculate the molecular contour of the pore to determine the effective internal pore radius (r(E)) in several K-channel crystal structurss. r(E) was operationally defined as the radius of the biggest sphere able to enter the pore from the cytosolic side. We obtained consistent r(E) estimates for MthK and Kv1.2/2.1 structures, with r(E) = 5.3-5.9 angstrom and r(E) = 4.5-5.2 angstrom, respectively. We compared these structural estimates with functional assessments of the internal mouth radii of capture (r(C)) for two electrophysiological counterparts, the large conductance calcium activated K-channel (r(C) = 2.2 angstrom) and the Shaker K-v-channel (r(C) = 0.8 angstrom), for MthK and Kv1.2/2.1 structures, respectively. Calculating the difference between r(E) and r(C), produced consistent size radii of 3.1-3.7 angstrom and 3.6-4.4 angstrom for hydrated K+ ions. These hydrated K+ estimates harmonize with others obtained with diverse experimental and theoretical methods. Thus, these findings validate MthK and the Kv1.2/2.1 structures as templates for open BK and Kv-channels, respectively.http://recursosbiblioteca.unab.cl:2226/articles/srep1989

Gating-induced large aqueous volumetric remodeling and aspartate tolerance in the voltage sensor domain of Shaker K+ channels

Indexación: Scopus.ACKNOWLEDGMENTS. We thank Chris Lingle and Yu Zhou (Washington University) for critical reading of the manuscript and Victoria Prado for Xenopus care and oocyte preparation. We also thank Millennium Scientific Initiative P029-022-F. This work was supported by Fondecyt Postdoctoral Grants 3170599 (to I.D.-F.) and 3160321 (to H.M.).Neurons encode electrical signals with critically tuned voltage-gated ion channels and enzymes. Dedicated voltage sensor domains (VSDs) in these membrane proteins activate coordinately with an unresolved structural change. Such change conveys the transmembrane translocation of four positively charged arginine side chains, the voltage-sensing residues (VSRs; R1–R4). Countercharges and lipid phosphohead groups likely stabilize these VSRs within the low-dielectric core of the protein. However, the role of hydration, a sign-independent charge stabilizer, remains unclear. We replaced all VSRs and their neighboring residues with negatively charged aspartates in a voltage-gated potassium channel. The ensuing mild functional effects indicate that hydration is also important in VSR stabilization. The voltage dependency of the VSR aspartate variants approached the expected arithmetic summation of charges at VSR positions, as if negative and positive side chains faced similar pathways. In contrast, aspartates introduced between R2 and R3 did not affect voltage dependence as if the side chains moved outside the electric field or together with it, undergoing a large displacement and volumetric remodeling. Accordingly, VSR performed osmotic work at both internal and external aqueous interfaces. Individual VSR contributions to volumetric works approached arithmetical additivity but were largely dissimilar. While R1 and R4 displaced small volumes, R2 and R3 volumetric works were massive and vectorially opposed, favoring large aqueous remodeling during VSD activation. These diverse volumetric works are, at least for R2 and R3, not compatible with VSR translocation across a unique stationary charge transfer center. Instead, VSRs may follow separated pathways across a fluctuating low-dielectric septum. © National Academy of Sciences. All rights reserved.https://www.pnas.org/content/115/32/820

Discrete breathers for understanding reconstructive mineral processes at low temperatures

Reconstructive transformations in layered silicates need a high tem- perature in order to be observed. However, very recently, some systems have been found where transformation can be studied at temperatures 600 C below the lowest experimental results previously reported, including sol-gel methods. We explore the possible relation with the existence of intrinsic localized modes, known as discrete breathers. We construct a model for nonlinear vibrations within the cation layer, obtain their parameters and calculate them numerically, obtaining their energies. Their statistics shows that although there are far less breathers than phonons, there are much more above the activation energy, being therefore a good candidate to explain the reconstructive transformations at low temperature.Comment: 27 pages, 11 figure

On acceptance conditions for membrane systems: characterisations of L and NL

In this paper we investigate the affect of various acceptance conditions on recogniser membrane systems without dissolution. We demonstrate that two particular acceptance conditions (one easier to program, the other easier to prove correctness) both characterise the same complexity class, NL. We also find that by restricting the acceptance conditions we obtain a characterisation of L. We obtain these results by investigating the connectivity properties of dependency graphs that model membrane system computations

Decaying lava extrusion rate at El Reventador Volcano, Ecuador measured using high-resolution satellite radar

Lava extrusion at erupting volcanoes causes rapid changes in topography and morphology on the order of tens or even hundreds of metres. Satellite radar provides a method for measuring changes in topographic height over a given time period to an accuracy of metres, either by measuring the width of radar shadow cast by steep sided features, or by measuring the difference in radar phase between two sensors separated in space. We measure height changes, and hence estimate extruded lava volume flux, at El Reventador, Ecuador between 2011 and 2016, using data from the Radarsat-2 and TanDEM-X satellite missions. We find 39 new lava flows were extruded between 9 February 2012 and 24 August 2016, with a cumulative volume of 44.8M m3 dense rock equivalent and a gradually decreasing eruption rate. The average dense rock rate of lava extrusion during this time is 0.31 ± 0.02 m3s−1, which is similar to the long term average from 1972 to 2016. Apart from a volumetrically small dyke opening event between 9 March and 10 June 2012, lava extrusion at El Reventador is not accompanied by any significant magmatic ground deformation. We use a simple physics-based model to estimate that the volume of the magma reservoir under El Reventador is greater than 3 km3. Our lava extrusion data can be equally well fit by models representing a closed reservoir depressurising during the eruption with no magma recharge, or an open reservoir with a time-constant magma recharge rate of up to 0.35 ± 0.01 m3s−

Solving the Bin-Packing Problem by Means of Tissue P System with 2-Division

The ability of tissue P systems with 2-division for solving NP problems in polynomial time is well-known and many solutions can be found in the literature to several of such problems. Nonetheless, there are very few papers devoted to the Bin-packing problem. The reason may be the difficulties for dealing with different number of bins, capacity and number of objects by using exclusively division rules that produce two offsprings in each application. In this paper we present the design of a family of tissue P systems with 2 division which solves the Bin-packing problem in polynomial time by combining design techniques which can be useful for further research

The motion of the 2D hydrodynamic Chaplygin sleigh in the presence of circulation

We consider the motion of a planar rigid body in a potential flow with circulation and subject to a certain nonholonomic constraint. This model is related to the design of underwater vehicles. The equations of motion admit a reduction to a 2-dimensional nonlinear system, which is integrated explicitly. We show that the reduced system comprises both asymptotic and periodic dynamics separated by a critical value of the energy, and give a complete classification of types of the motion. Then we describe the whole variety of the trajectories of the body on the plane.Comment: 25 pages, 7 figures. This article uses some introductory material from arXiv:1109.321

Immediate effects of diamond burr debridement in patients with spontaneous chronic corneal epithelial defects, light and electron microscopic evaluation

Purpose: To evaluate immediate effects of diamond burr debridement (DBD) on the cornea of canine patients diagnosed with spontaneous chronic corneal epithelial defects (SCCEDs).Animals studied: Eight client owned dogs with SCCEDs.Methods: Nine eyes from eight dogs with SCCEDs underwent superficial keratectomy (SK). The ulcerated area was divided into quadrants with a 300-micron restricted depth knife. Two of four quadrants underwent DBD for 40-60 s. A SK followed immediately. One burred section and one nonburred section were fixed with formaldehyde 10% and underwent light microscopy (LM). The remaining quadrants from five eyes were fixed with glutaraldehyde 2.5% and underwent transmission electron microscopy (TEM). Masked pathologists evaluated the samples. A student's paired t-test was used to analyze the data.Results: With LM all nonburred samples had a superficial stromal hyaline acellular zone (HAZ), seven of the burred samples had an intermittent HAZ and in two burred samples this zone was absent. The HAZ thickness of burred samples (1.062 ± 0.664 μm) was significantly thinner than that of the nonburred samples (4.309 ± 1.348 μm) (P < 0.0001). Transmission electron microscopy showed an absence of basement membrane and the presence of an amorphous, fine fibrillar material in the superficial stroma in nonburred samples. This material was intermittent or absent in burred samples.Conclusion: DBD significantly reduces the superficial stromal HAZ in SCCEDs. A reduction of its thickness may be responsible for the healing rates reported with DBD.Keywords: canine; cornea; diamond burr; spontaneous chronic corneal epithelial defects; superficial keratectomy; ulcer