Permeation of water through the KcsA K+ channel

Previous studies have reported that the KcsA potassium channel has an osmotic permeability coefficient of 4.8 x 10(-12) cm3/s, giving it a significantly higher osmotic permeability coefficient than that of some membrane channels specialized in water transport. This high osmotic permeability is proposed to occur when the channel is depleted of potassium ions, the presence of which slow down the water permeation process. The atomic structure of the potassium-depleted KcsA channel and the mechanisms of water permeation have not been well characterized so far. Here, all-atom molecular dynamics simulations, in conjunction with an umbrella sampling strategy and a nonequilibrium approach to simulate pressure gradients are employed to illustrate the permeation of water in the absence of ions through the KcsA K+ channel. Equilibrium molecular dynamics simulations (95 ns combined total length) identified a possible structure of the potassium-depleted KcsA channel, and umbrella sampling calculations (160 ns combined total length) revealed that this structure is not permeable by water molecules moving along the channel axis. The simulation of a pressure gradient across the channel (30 ns combined total length) identified an alternative permeation pathway with a computed osmotic permeability of approximately (2.7 +/- 0.9) x 10(-13) cm3/s. Water fluxes along this pathway did not proceed through collective water motions or transitions to vapor state. All of the major results of this study were robust against variations in a wide set of simulation parameters (force field, water model, membrane model, and channel conformation).     

Sitting above the maze: recent model discoveries in molecular science

The 2013 Nobel Prize in Chemistry has convinced the world that how important the role that computational sciences play in chemical and materials sciences. In this review, computational methods and rational molecule design, including quantum mechanics and molecular mechanics methods, have been applied to study electronic structures and the interactions in a number of important applications at molecular level. The applications which include bioactive compounds, drug candidates and photoactive molecules at Swinburne University in the past several years are discussed. The research is in close collaboration with world class experimental groups from spectroscopy, organic and medicinal synthesis laboratories and most recently to γ-ray spectroscopy as well as other theory groups in the world. Ionisation spectra of biomolecules and bioactive compounds including amino acids, DNA bases, cyclic dipeptides, drug candidates, complexes and photoactive molecules are discussed. Most recent projects such as infrared spectral studies of ferrocene, rational design of organic dyes in solar cell applications, and recent development in γ-ray spectra of positron annihilation in molecules are highlighted.     

Self-diffusivity,hydrogen bonding and density of different water models in carbon nanotubes

In this paper, the density, hydrogen bonding and self-diffusivity of water confined in carbon nanotubes are investigated. Molecular dynamics is used to simulate a large variety of nanotubes with various water models. Our results produce, for the first time, the complete trend of these properties from narrow nanotubes, where water shows particularly anomalous behaviour, to large ones where its characteristics are similar to those of bulk.     

Hydrogen bond analysis of confined water in mesoporous silica using the reactive force field

ABSTRACT

The structural and dynamical properties of water confined in nanoporous silica with a pore diameter of 2.7?nm were investigated by performing large-scale molecular dynamics simulations using the reactive force field. The radial distribution function and diffusion coefficient of water were calculated, and the values at the centre of the pore agreed well with experimental values for real water. In addition, the pore was divided into thin coaxial layers, and the average number of hydrogen bonds, hydrogen bond lifetime and hydrogen bond strength were calculated as a function of the radial distance from the pore central axis. The analysis showed that hydrogen bonds involving silanol (Si–OH) have a longer lifetime, although the average number of hydrogen bonds per atom does not change from that at the pore centre. The longer lifetime, as well as smaller diffusion coefficient, of these hydrogen bonds is attributed to their greater strength.     

Coarse-grained reduction and analysis of a network model of cortical response: I. Drifting grating stimuli

We present a reduction of a large-scale network model of visual cortex developed by McLaughlin, Shapley, Shelley, and Wielaard. The reduction is from many integrate-and-fire neurons to a spatially coarse-grained system for firing rates of neuronal subpopulations. It accounts explicitly for spatially varying architecture, ordered cortical maps (such as orientation preference) that vary regularly across the cortical layer, and disordered cortical maps (such as spatial phase preference or stochastic input conductances) that may vary widely from cortical neuron to cortical neuron. The result of the reduction is a set of nonlinear spatiotemporal integral equations for phase-averaged firing rates of neuronal subpopulations across the model cortex, derived asymptotically from the full model without the addition of any extra phenomological constants. This reduced system is used to study the response of the model to drifting grating stimuli—where it is shown to be useful for numerical investigations that reproduce, at far less computational cost, the salient features of the point-neuron network and for analytical investigations that unveil cortical mechanisms behind the responses observed in the simulations of the large-scale computational model. For example, the reduced equations clearly show (1) phase averaging as the source of the time-invariance of cortico-cortical conductances, (2) the mechanisms in the model for higher firing rates and better orientation selectivity of simple cells which are near pinwheel centers, (3) the effects of the length-scales of cortico-cortical coupling, and (4) the role of noise in improving the contrast invariance of orientation selectivity.     

Temperature dependence of two parameters in a photosynthesis model

The temperature dependence of the photosynthetic parameters V_cmax, the maximum catalytic rate of the enzyme Rubisco, and J_max, the maximum electron transport rate, were examined using published datasets. An Arrehenius equation, modified to account for decreases in each parameter at high temperatures, satisfactorily described the temperature response for both parameters. There was remarkable conformity in V_cmax and J_max between all plants at T_leaf < 25 °C, when each parameter was normalized by their respective values at 25 °C (V_cmax0 and J_max0), but showed a high degree of variability between and within species at T_leaf > 30 °C. For both normalized V_cmax and J_max, the maximum fractional error introduced by assuming a common temperature response function is < ± 0·1 for most plants and < ± 0·22 for all plants when T_leaf < 25 °C. Fractional errors are typically < ± 0·45 in the temperature range 25–30 °C, but very large errors occur when a common function is used to estimate the photosynthetic parameters at temperatures > 30 °C. The ratio J_max/V_cmax varies with temperature, but analysis of the ratio at T_leaf = 25 °C using the fitted mean temperature response functions results in J_max0/V_cmax0 = 2·00 ± 0·60 (SD, n = 43).     

Structural coupling between FKBP12 and buried water

Globular proteins often contain structurally well-resolved internal water molecules. Previously, we reported results from a molecular dynamics study that suggested that buried water (Wat3) may play a role in modulating the structure of the FK506 binding protein-12 (FKBP12) (Park and Saven, Proteins 2005; 60:450-463). In particular, simulations suggested that disrupting a hydrogen bond to Wat3 by mutating E60 to either A or Q would cause a structural perturbation involving the distant W59 side chain, which rotates to a new conformation in response to the mutation. This effectively remodels the ligand-binding pocket, as the side chain in the new conformation is likely to clash with bound FK506. To test whether the protein structure is in effect modulated by the binding of a buried water in the distance, we determined high-resolution (0.92-1.29 A) structures of wild-type FKBP12 and its two mutants (E60A, E60Q) by X-ray crystallography. The structures of mutant FKBP12 show that the ligand-binding pocket is indeed remodeled as predicted by the substitution at position 60, even though the water molecule does not directly interact with any of the amino acids of the binding pocket. Thus, these structures support the view that buried water molecules constitute an integral, noncovalent component of the protein structure. Additionally, this study provides an example in which predictions from molecular dynamics simulations are experimentally validated with atomic precision, thus showing that the structural features of protein-water interactions can be reliably modeled at a molecular level.     

Inspecting fluctuation and coordination around chromophore inside green fluorescent protein from water to nonpolar solvent

Green fluorescent protein (GFP) is a widely used biomarker that demands systematical rational approaches to its structure function redesign. In this work, we mainly utilized atomistic molecular dynamics simulations to inspect and visualize internal fluctuation and coordination around chromophore inside GFP, from water to nonpolar octane solvent. We found that GFP not only maintains its β-barrel structure well into the octane, but also sustains internal residue and water coordination to position the chromophore stably while suppress dihedral fluctuations of the chromophore, so that functional robustness of GFP is achieved. Our accompanied fluorescence microscope measurements accordingly confirmed the GFP functioning into the octane. Furthermore, we identified that crucial water sites inside GFP along with permeable pores on the β-barrel of the protein are largely preserved from the water to the octane solvent, which allows sufficiently fast exchanges of internal water with the bulk or with the water layer kept on the surface of the protein. By additionally pulling GFP from bulk water to octane, we suggest that the GFP function can be well maintained into the nonpolar solvent as long as, first, the protein does not denature in the nonpolar solvent nor across the polar-nonpolar solvent interface; second, a minimal set of water molecules are in accompany with the protein; third, the nonpolar solvent molecules may need to be large enough to be nonpermeable via the water pores on the β-barrel.     

Molecular dynamics of the salt dependence of a cold-adapted enzyme: endonuclease I

The effects of salt on the stability of globular proteins have been known for a long time. In the present investigations, we shall focus on the effect of the salt ions upon the structure and the activity of the endonuclease I enzyme. In the present work, we shall focus on the relationship between ion position and the structural features of the Vibrio salmonicida (VsEndA) enzyme. We will concentrate on major questions such as: how can salt ions affect the molecular structure? What is the activity of the enzyme and which specific regions are directly involved? For that purpose, we will study the behaviour of the VsEndA over different salt concentrations using molecular dynamics (MD) simulations. We report the results of MD simulations of the endonuclease I enzyme at five different salt concentrations. Analysis of trajectories in terms of the root mean square fluctuation (RMSF), radial distribution function, contact numbers and hydrogen bonding lifetimes, indicate distinct differences when changing the concentration of NaCl. Results are found to be in good agreement with experimental data, where we have noted an optimum salt concentration for activity equal to 425 mM. Under this salt concentration, the VsEndA exhibits two more flexible loop regions, compared to the other salt concentrations. When analysing the RMSF of these two specific regions, three residues were selected for their higher mobility. We find a correlation between the structural properties studied here such as the radial distribution function, the contact numbers and the hydrogen bonding lifetimes, and the structural flexibility of only two polar residues. Finally, in the light of the present work, the molecular basis of the salt adaptation of VsEndA enzyme has been explored by mean of explicit solvent and salt treatment. Our results reveal that modulation of the sodium/chloride ions interaction with some specific loop regions of the protein is the strategy followed by this type of psychrophilic enzyme to enhance catalytic activity at the physiological conditions.     

Dynamics and energetics of water permeation through the aquaporin channel

Structural properties of water inside bovine aquaporin-1 are investigated by molecular simulation. The calculations, which are based on the recently determined X-ray structure at 2.2 A resolution (Sui et al., Nature 2001;414:872-878), are carried out on one monomeric subunit immersed in a water-n-octane-water bilayer. Molecular dynamics (MD) simulations suggest that His182, a fully conserved residue in the channel pore, is protonated in the delta position. Furthermore, they reveal a highly ordered water structure in the channel, induced by the electrostatic properties of the protein. Multiple-steering MD simulations are used to calculate the free-energy of water diffusion. To the best of our knowledge, this represents the first free-energy calculation based on the new, high-resolution structure of the pore. The calculated barrier is 2.5 kcal/mol, and it is associated to water permeation through the Asn-Pro-Ala (NPA) region of the pore, where water molecules are only hydrogen-bonded with themselves. These findings are fully consistent with those based on the previous MD studies on the human protein (de Groot and Grubmüller, Science 2001;294:2353-2357).     

Giant and flux controllable pumping of water molecules in a double-walled carbon nanotube

We designed a water pumping system based on double-walled carbon nanotube. In this system, the inner tube was fixed as the water channel, while the exterior was moved similarly to the piston motion along the axial direction to induce pumping force. Molecular dynamics simulations confirmed that the water flux is sensitive to the motion velocity of the outer tube so that giant and controllable unidirectional water flow can be achieved in this system by varying the velocity. The enhancement of the pumping ability mainly results from the carbon–water van der Waals driving forces of the exterior tube and the osmosis pressure of the water reservoir. This design may open a new way for water pumping in the field of nanodevices.     

Molecular dynamics simulations of interaction between sub-bituminous coal and water

The high moisture content of sub-bituminous coal is associated with the interactions between coal and water. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of sub-bituminous coal according to XPS results. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxy and carbonyl is similar.     

Dynamic ejection behaviour of water molecules passing through a nano-aperture nozzle

This study used molecular dynamics (MD) simulation to investigate the passage of water molecules through a composite graphene/Au nano-nozzle. Our focus was on the degree to which system temperature, extrusion speed, and nozzle diameter affect jet dynamics and the associated transient phenomena. Our findings show that high pressure and spatial confinement cause the nanojet from a small nozzle diameter (1.0?nm) to bend and twist, whereas the jets from a nozzle with a diameter of 1.5?nm present columns of greater stability. At 100?K, the H₂O nanojet froze at the outlet of the nozzle in the form of condensed icicles. At 500?K, the H₂O nanojet formed a loose spray and gaseous clusters. High extrusion speed of 55.824?m/s produced recirculating flow downstream from the nanojet with the appearance of an erupting volcano, which further prompted the jet column to thicken. Lower extrusion speeds produced jets with flow velocity insufficient to overcome the capillary force at the outlet of the nozzle, which subsequently manifests as unstable fluctuations in the flow rate.

• HIGHLIGHTS

• Water molecules through a composite graphene/Au nano-nozzle forming a nanojet is investigated.

• High pressure and spatial confinement cause the nanojet from a small nozzle diameter (≤1.0?nm) to bend and twist.

• High extrusion speed (≧55.824?m/s) produced recirculating flow downstream from the nanojet.

• Figure abstract: Schematic of the H₂O nano-jet through a nano-nozzle of graphene/Au

     

基于ESTDA模型的中国水生态足迹及水生态压力评价

基于水足迹视角,测度了中国31个省份2000-2018年的水生态足迹广度、深度及水生态压力,采用ESTDA框架对其时空动态特征进行分析。结果表明：①研究期内,中国水生态足迹总量呈波动上升态势;水生态承载力波动幅度较大,空间分布格局整体呈现自东南向西北逐渐较少的趋势。②水生态足迹广度与水生态承载力呈同步变化趋势,整体上已接近水资源可提供的流量资本上限,各省市水生态足迹深度差异较大。③研究期内,水生态压力指数小于1的区域与水生态足迹深度为1的区域相吻合,水生态压力指数大于1的区域主要分布在华北及西北地区。④LISA时间路径表明,水生态足迹广度、深度及水生态压力的整体空间格局均具有较强的稳定性;三者的局部空间结构在空间依赖方向上的稳定性依次加强;空间格局演化的空间整合性呈现水生态足迹深度 > 水生态压力 > 水生态足迹广度,空间上,水生态足迹广度正向协同增长省份主要集中于南方省份,而水生态足迹深度和水生态压力正向协同增长区则分布于华北、西北地区;各要素的空间分布格局表现出较强的路径依赖及锁定特征。     

Thermodynamic analysis of the physical state of water during freezing in plant tissue, based on the temperature dependence of proton spin-spin relaxation

Multi-proton spin-echo images were collected from cold-acclimated winter wheat crowns (Triticum aestivum L.) cv. Cappelle Desprez at 400 MHz between 4 and ?4 °C. Water proton relaxation by the spin-spin (T2) mechanism from individual voxels in image slices was found to be mono-exponential. The temperature dependence of these relaxation rates was found to obey Arrhenius or absolute rate theory expressions relating temperature, activation energies and relaxation rates, Images whose contrast is proportional to the Arrhenius activation energy (E_a), Gibb's free energy of activation (ΔG^?), and the entropy of activation (ΔS^?) for water relaxation on a voxel basis were constructed by post-image processing. These new images exhibit contrast based on activation energies rather than rules of proton relaxation. The temperature dependence of water proton T₂ relaxation rates permits prediction of changes in the physical state of water in this tissue over modest temperature ranges. A simple model is proposed to predict the freezing temperature kof various tissue in wheat crowns. The average E_a and ΔH^? for water proton T₂ relaxation over the above temperature range in winter wheat tissue were ?6.4 ± 14.8 and ?8.6 ± 14.8kj mol^?1, respectively. This barrier is considerably lower than the E_a for proton translation in ice at 0°C, which is reported to be between 46.0 and 56.5 kj mol^?1     

Base water potential of Picea abies as a characteristic of the soil water status

Variation in base water potential (Ψ_b, a daily maximum level of plant water potential, which is presumed to correspond to the condition of equilibrium between the soil and plant water potentials) was examined in shoots of Norway spruce trees growing in well-drained and waterlogged soils. The influence of soil water content, air temperature, and vapour pressure deficit of the atmosphere on Ψ_b was studied using the pressure chamber technique. Maximum daily water potentials were not always observable before dawn; some were registered up to two hours later. This tendency being characteristic of trees growing under stress (shade, waterlogging) conditions, increased with declining soil water availability. In trees growing in well-drained soil, Ψ_b depended asymptotically on the available soil water storage (R²=0.73), while the values were slightly influenced by vapour pressure deficit of the atmosphere as well. In trees growing in waterlogged soil, Ψ_b was independent of the soil water storage, but sensitive to the vapour pressure deficit.