Barium blockade of the KcsA channel in open and closed conformation datasets
Abstract not provided
Rohaim, Ahmed↗
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Structure of the Human BK Ion Channel in Lipid Environment
Voltage-gated and ligand-modulated ion channels play critical roles in excitable cells. To understand the interplay among voltage sensing, ligand binding, and channel opening, the structures of ion channels in various functional states and in lipid membrane environments need to be determined. Here, the random spherically constrained (RSC) single-particle cryo-EM method was employed to study human large conductance voltage- and calcium-activated potassium (hBK or hSlo1) channels reconstituted into liposomes. The hBK structure was determined at 3.5 Å resolution in the absence of Ca 2+ . Instead of the common fourfold symmetry observed in ligand-modulated ion channels, a twofold symmetry was observed in hBK in liposomes. Compared with the structure of isolated hSlo1 Ca 2+ sensing gating rings, two opposing subunits in hBK unfurled, resulting in a wider opening towards the transmembrane region of hBK. In the pore gate domain, two opposing subunits also moved downwards relative to the two other subunits.
59 BASIC BIOLOGICAL SCIENCES↗
Statistical Hauser-Feshbach model calculation for (α, n) reaction cross section and discrete level population
We calculate the α-particle induced reactions on 17,18 O, 19 F, and 23 Na, in the energy range 0 ≤ E α ≤ 10 MeV, with a particular attention to the branching ratios of populated discrete levels in the (α,n) channels. Since there are too many open channels to employ the R-matrix theory, we apply the statistical Hauser-Feshbach model to calculate these reaction cross sections and branching ratios. The branching ratio is defined as b n = $\frac{σ_n}{Σ_iσ_i + σ_c}$ , where σ n is the n-th level production cross section after the neutron emission, and σ c is the production of the continuum state. In the cases of our target nuclei and the energy range of interest, the residual nuclei of the neutron emission channel are always in their discrete states, so that σ c can be negligible.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate
Channelrhodopsins (ChR) are light-sensitive cation channels used in optogenetics, a technique that applies light to control cells (e.g., neurons) that have been modified genetically to express those channels. Although mutations are known to affect pore kinetics, little is known about how mutations induce changes at the molecular scale. To address this issue, we first measured channel opening and closing rates of a ChR chimera (C1C2) and selected variants (N297D, N297V, and V125L). Then, we used atomistic simulations to correlate those rates with changes in pore structure, hydration, and chemical interactions among key gating residues of C1C2 in both closed and open states. Overall, the experimental results show that C1C2 and its mutants do not behave like ChR2 or its analogous variants, except V125L, making C1C2 a unique channel. Furthermore, our atomistic simulations confirmed that opening of the channel and initial hydration of the gating regions between helices I, II, III, and VII of the channel occurs with 1) the presence of 13-cis retinal; 2) deprotonation of a glutamic acid gating residue, E129; and 3) subsequent weakening of the central gate hydrogen bond between the same glutamic acid E129 and asparagine N297 in the central region of the pore. Also, an aspartate (D292) is the unambiguous primary proton acceptor for the retinal Schiff base in the hydrated channel.
59 BASIC BIOLOGICAL SCIENCES↗
Silicone-Rubber Microvalves Actuated by Paraffin
Microvalves containing silicone-rubber seals actuated by heating and cooling of paraffin have been proposed for development as integral components of microfluidic systems. In comparison with other microvalves actuated by various means (electrostatic, electromagnetic, piezoelectric, pneumatic, and others), the proposed valves (1) would contain simpler structures that could be fabricated at lower cost and (2) could be actuated by simpler (and thus less expensive) control systems. Each valve according to the proposal would include a flow channel bounded on one side by a flat surface and on the other side by a curved surface defined by an arched-cross-section, elastic seal made of silicone rubber [polydimethylsilane (PDMS)]. The seal would be sized and shaped so that the elasticity of the PDMS would hold the channel open except when the seal was pressed down onto the flat surface to close the channel. The principle of actuation would exploit the fact that upon melting or freezing, the volume of a typical paraffin increases or decreases, respectively, by about 15 percent. In a valve according to the proposal, the seal face opposite that of the channel would be in contact with a piston-like plug of paraffin. In the case of a valve designed to be normally open at ambient temperature, one would use a paraffin having a melting temperature above ambient. The seal would be pushed against the flat surface to close the channel by heating the paraffin above its melting temperature. In the case of a valve designed to be normally closed at ambient temperature, one would use a paraffin having a melting temperature below ambient. The seal would be allowed to spring away from the flat surface to open the channel by cooling the paraffin below its melting temperature. The availability of paraffins that have melting temperatures from 70 to +80 C should make it possible to develop a variety of normally closed and normally open valves. The figure depicts examples of prototype normally open and normally closed valves according to the proposal. In each valve, an arch cross section defining a channel having dimensions of the order of tens of micrometers would be formed in a silicone-rubber sheet about 40 m thick. The silicone rubber sheet would be hermetically sealed to a lower glass plate that would define the sealing surface and to an upper glass plate containing a well. The well would be filled with paraffin and capped with a rigid restraining layer of epoxy. In the normally open valve, the paraffin would have a melting temperature above ambient (e.g., 40 C) and the wall of the well would be coated with a layer of titanium that would serve as an electric heater. In the normally closed valve, the paraffin would have a melting temperature below ambient (e.g.-5 C). Instead of a heater in the well, the normally closed valve would include a thermoelectric cooler on top of the epoxy cap.
Svelha, Danielle↗
Coupled-channels method for rearrangement collisions
Classification and construction of open-channel projection operators for rearrangement collisions using subspaces of total Hilbert space of system
Volkin, H. C.↗
Solution of electromagnetic scattering problems using time domain techniques
New methods are developed to calculate the electromagnetic diffraction or scattering characteristics of objects of arbitrary material and shape. The methods extend the efforts of previous researchers in the use of finite-difference and pulse response techniques. Examples are given of the scattering from infinite conducting and nonconducting cylinders, open channel, sphere, cone, cone sphere, coated disk, open boxes, and open and closed finite cylinders with axially incident waves.
Britt, Charles L.↗
Chronic, intermittent loading alters mechanosensitive channel characteristics in osteoblast-like cells
The effects of chronic, intermittent strain on the mechanosensitive cation (SA-cat) channels in UMR-106.01 osteoblast-like osteosarcoma cells were studied using patch-clamp techniques. Chronically strained cells demonstrated significantly larger increases in whole cell conductance when subjected to additional mechanical strain than nonstrained controls (69.0 +/- 15.1 vs. 14.1 +/- 3.1%; P < 0.001). This increase could be blocked by the SA-cat channel inhibitor, gadolinium, and corresponded to a three- to fivefold increase in SA-cat channel activity. Chronic strain increased the number of open channels in response to stretch and induced spontaneous SA-cat channel activity in 33% of the patches of strained cells. Graded increases in negative patch pressure demonstrated that SA-cat channels in chronically strained cells were activated at significantly lower levels of mechanical perturbation than nonstrained controls. These data suggest that chronic, cyclic strain reduces the activation threshold of the SA-cat channel and further strengthen our hypothesis that this channel may act as a mechanotransducer for the activation of bone remodeling by physical strain.
NASA Discipline Musculoskeletal↗
Heat transfer model for moving packed-bed particle-to-sCO 2 heat exchangers integrated with metal foams
Particle-to-supercritical carbon dioxide (sCO 2 ) heat exchangers (HXs) play a vital role in coupling heat transfer fluid (HTF) from high-temperature thermal receivers to power cycle working fluids (WF). Heat transfer enhancement is essential for adopting particle-based moving packed-bed heat exchangers (MPBHXs) in next-generation thermal energy storage (TES) systems, as MPBHXs usually exhibit low particle bed-to-wall heat transfer coefficients. High-porosity metal foams have shown their effectiveness in heat transfer enhancement. Here, this work presents a continuum heat transfer model to demonstrate the heat transfer enhancement in MPBHXs when the particle bed channel is filled with high porosity metal foams compared to open channel MPBHXs. The presence of metal foams increases the effective thermal conductivity in the particle channel and enhances the interstitial heat transfer coefficient between the moving particle bed and the stationary metal foams. The present model considers coupled two-dimensional (2D) heat transfer in the particle channel with metal foams and 1D heat transfer in the sCO 2 channel and the dividing wall. The temperature profiles for the particle bed, metal foam, dividing wall, and sCO 2 stream, as well as the local heat flux profiles between those, are studied in detail for various foam porosities, from which the particle bed-to-wall heat transfer coefficient, overall heat transfer coefficient, and total heat transfer rate for the MPBHX are determined. The effects of major MPBHX design and operating parameters on the particle bed-to-wall heat transfer coefficient and overall heat exchange capacity are thoroughly examined; thus, the MPBHX performance improvement with metal foams is quantified for each case. The present heat transfer model can provide valuable insights into the metal-foam MPBHX design and optimization, scale-up, and operating parameters selection.
42 ENGINEERING↗
Combined Beam-column Stresses of Aluminum-alloy Channel Sections
The results of a research program to obtain design data on the strength of open-channel aluminum-alloy sections subjected to combined column and beam action. The results of the tests of about 70 specimens were graphed for stresses due to axial load and stresses due to bending loading as functions of length to radius of gyration of the specimens. From these graphs a design chart was derived that is suitable for ready use.
COLUMNS, ALUMINUM-ALLOY - ALCOA 24ST - STRENGTH↗
Quantum dynamics of positron-hydrogen scattering and three-body bound state formation with an assisting laser field: predictions of a reduced-dimensionality model
Abstract We investigate the quantum dynamics of target excitation and positronium formation in the positron-hydrogen atom scattering without and with an external assisting laser field within a reduced-dimensional quantum model. Strong interference fringes between the incident and reflected positron wave packets are observed in the reaction region. We further investigate the critical behavior of transition probabilities near the channel-opening thresholds for hydrogen excitation and positronium formation and find a strong competition between channels with similar threshold energies, but different parities. The transmission ratios of the incident positron in different reaction channels are calculated, and it is shown that only positronium formation in the ground state prefers forward scattering. Our simulation of the positron-hydrogen scattering with an assisting laser field indicates that the three-particle bound states can be formed during the collisions due to the photon emission induced by the external laser field.
Optics↗
Unified description of the coupled-channels and statistical Hauser-Feshbach nuclear reaction theories for low energy neutron incident reactions
We incorporate the coupled-channels optical model into the statistical Hauser-Feshbach nuclear reaction theory, where the scattering matrix is diagonalized by performing the Engelbrecht-Weidenmüller transformation. This technique has been implemented in the coupled-channels optical model code ECIS by J. Raynal, and we extend this method so that all the open channels in a nucleon-induced reaction on a deformed nucleus can be calculated consistently.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Hybrid MD-Nernst Planck Model of Alpha-hemolysin Conductance Properties
Motivated by experiments in which an applied electric field translocates polynucleotides through an alpha-hemolysin protein channel causing ionic current transient blockade, a hybrid simulation model is proposed to predict the conductance properties of the open channel. Time scales corresponding to ion permeation processes are reached using the Poisson-Nemst-Planck (PNP) electro-diffusion model in which both solvent and local ion concentrations are represented as a continuum. The diffusion coefficients of the ions (K(+) and Cl(-)) input in the PNP model are, however, calculated from all-atom molecular dynamics (MD). In the MD simulations, a reduced representation of the channel is used. The channel is solvated in a 1 M KCI solution, and an external electric field is applied. The pore specific diffusion coefficients for both ionic species are reduced 5-7 times in comparison to bulk values. Significant statistical variations (17-45%) of the pore-ions diffusivities are observed. Within the statistics, the ionic diffusivities remain invariable for a range of external applied voltages between 30 and 240mV. In the 2D-PNP calculations, the pore stem is approximated by a smooth cylinder of radius approx. 9A with two constriction blocks where the radius is reduced to approx. 6A. The electrostatic potential includes the contribution from the atomistic charges. The MD-PNP model shows that the atomic charges are responsible for the rectifying behaviour and for the slight anion selectivity of the a-hemolysin pore. Independent of the hierarchy between the anion and cation diffusivities, the anionic contribution to the total ionic current will dominate. The predictions of the MD-PNP model are in good agreement with experimental data and give confidence in the present approach of bridging time scales by combining a microscopic and macroscopic model.
Cozmuta, Ioana↗
On steady alternate bars forced by a localized asymmetric drag distribution in erodible channels
Studying the effect of different in-stream fluvial turbines siting on river morphodynamics allowed us to witness the onset of a time-averaged, large-scale, alternate distortion of bed elevations, which could not be exclusively related to the turbine rotor blockage. The longitudinal profiles of this two-dimensional bathymetric perturbation resemble those of steady fluvial bars. In this contribution we generalize the problem addressing a spatially impulsive, asymmetric distribution of drag force in the channel cross-section. Furthermore, this is experimentally investigated through the deployment of differently sized grids perpendicular to the flow, and analytically explored as a finite perturbation of an open channel flow over an erodible sediment layer, as described by a coupled flow–sediment shallow water equation. The steady solutions of this fluvial morphodynamic problem, physically represented by alternate bars scaling with the channel width, highlight the importance of the resonant conditions in defining the spatial extent of the bed deformation. The equations further suggest that in very shallow flows any asymmetric obstruction may lead to an upstream propagation of the steady bars, consistent with previous studies on the effects of channel curvature. In broad terms, this study provides the preliminary framework to control the onset of river meandering through imposed finite perturbations of the cross-section. In a more applied sense, it provides a tool to predict non-local scour–deposition patterns associated with the deployment of energy converters or other flow obstructions.
42 ENGINEERING↗
Conformational motions and ligand-binding underlying gating and regulation in IP 3 R channel
Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP 3 and Ca 2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP 3 R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP 3 , Ca 2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP 3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP 3 R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.
59 BASIC BIOLOGICAL SCIENCES↗
An intercomparison technique for measuring thermal attachment cross sections and rate constants in distinct final channels
A new technique is introduced for comparing negative-ion signal rates in which a common ion is produced by dissociative attachment in a series of molecules. Measurements are carried out at electron energies less than 100 MeV and at resolutions of 6-8 MeV (FWHM). The technique is demonstrated by detection of the Cl(-) signal in CFCl3, CCl4, CF2Cl2, 1,1,2-C2Cl3F3, 1,1,1-C2Cl3F3 and C2Cl4. Measurements for 1,1,1-C2Cl3F3 show that there is a significant open channel, other than Cl(-) formation, which accounts for about 60 percent of negative-ion formation in thermal-multiple-collision (swarm) experiments. Channel cross sections and rate constants are given for the process Cl(-)/1,1,1-Cl2Cl3F3, as well as in C2Cl4, for the separate channels Cl(-)/C2Cl4 and C2Cl4(-)/C2Cl4.
Alajajian, S. H.↗
Zr‐Porphyrin Metal–Organic Framework as nanoreactor for boosting the formation of hydrogen clathrates
Abstract We report the first experimental evidence for rapid formation of hydrogen clathrates under mild pressure and temperature conditions within the cavities of a zirconium‐metalloporphyrin framework, specifically PCN‐222. PCN‐222 has been selected for its 1D mesoporous channels, high water‐stability, and proper hydrophilic behavior. Firstly, we optimize a microwave (MW)‐assisted method for the synthesis of nanosized PCN‐222 particles with precise structure control (exceptional homogeneity in morphology and crystalline phase purity), taking advantage of MW in terms of rapid/homogeneous heating, time and energy savings, as well as potential scalability of the synthetic method. Second, we explore the relevance of the large mesoporous 1D open channels within the PCN‐222 to promote the nucleation and growth of confined hydrogen clathrates. Experimental results show that PCN‐222 drives the nucleation process at a lower pressure than the bulk system (1.35 kbar vs 2 kbar), with fast kinetics (minutes), using pure water, and with a nearly complete water‐to‐hydrate conversion. Unfortunately, PCN‐222 cannot withstand these high pressures, which lead to a significant alteration of the mesoporous structure while the microporous network remains mainly unchanged.
Carrillo‐Carrión, Carolina↗