Computer simulations of NaCl association in polarizable water

Antimicrobial and structural insights of a new snakin-like peptide isolated from Peltophorum dubium (Fabaceae)

Snakins are antimicrobial peptides (AMPs) found, so far, exclusively in plants, and known to be important in the defense against a wide range of pathogens. Like other plant AMPs, they contain several positively charged amino acids, and an even number of cysteine residues forming disulfide bridges which are considered important for their usual function. Despite its importance, studies on snakin tertiary structure and mode of action are still scarce. In this study, a new snakin-like gene was isolated from the native plant Peltophorum dubium, and its expression was verified in seedlings and adult leaves. The deduced peptide (PdSN1) shows 84% sequence identity with potato snakin-1 mature peptide, with the 12 cysteines characteristic from this peptide family at the GASA domain. The mature PdSN1 coding sequence was successfully expressed in Escherichia coli. The purified recombinant peptide inhibits the growth of important plant and human pathogens, like the economically relevant potato pathogen Streptomyces scabies and the opportunistic fungi Candida albicans and Aspergillus niger. Finally, homology and ab initio modeling techniques coupled to extensive molecular dynamics simulations were used to gain insight on the 3D structure of PdSN1, which exhibited a helix-turn-helix motif conserved in both native and recombinant peptides. We found this motif to be strongly coded in the sequence of PdSN1, as it is stable under different patterns of disulfide bonds connectivity, and even when the 12 cysteines are considered in their reduced form, explaining the previous experimental evidences.

Evidence for Reduced Hydrogen-Bond Cooperativity in Ionic Solvation Shells from Isotope-Dependent Dielectric Relaxation

We find that the reduction in dielectric response (depolarization) of water caused by solvated ions is different for H_{2}O and D_{2}O. This isotope dependence allows us to reliably determine the kinetic contribution to the depolarization, which is found to be significantly smaller than predicted by existing theory. The discrepancy can be explained from a reduced hydrogen-bond cooperativity in the solvation shell: we obtain quantitative agreement between theory and experiment by reducing the Kirkwood correlation factor of the solvating water from 2.7 (the bulk value) to ∼1.6 for NaCl and ∼1 (corresponding to completely uncorrelated motion of water molecules) for CsCl.

Enhanced Ion Adsorption on Mineral Nanoparticles

Classical molecular dynamics simulation was used to study the adsorption of Na⁺, Ca²⁺, Ba²⁺, and Cl^- ions on gibbsite edge (1 0 0), basal (0 0 1), and nanoparticle (NP) surfaces. The gibbsite NP consists of both basal and edge surfaces. Simulation results indicate that Na⁺ and Cl^- ions adsorb on both (1 0 0) and (0 0 1) surfaces as inner-sphere species (i.e., no water molecules between an ion and the surface). Outer-sphere Cl^- ions (i.e., one water molecule between an ion and the surface) were also found on these surfaces. On the (1 0 0) edge, Ca²⁺ ions adsorb as inner-sphere and outer-sphere complexes, whereas on the (0 0 1) surface, outer-sphere Ca²⁺ ions are the dominant species. Ba²⁺ ions were found as inner-sphere and outer-sphere complexes on both surfaces. Calculated ion surface coverages indicate that, for all ions, surface coverages are always higher on the basal surface compared to those on the edge surface. More importantly, surface coverages for cations on the gibbsite NP are always higher than those calculated for the (1 0 0) and (0 0 1) surfaces. This enhanced ion adsorption behavior for the NP is due to the significant number of inner-sphere cations found at NP corners. Outer-sphere cations do not contribute to the enhanced surface coverage. In addition, there is no ion adsorption enhancement observed for the Cl^- ion. Our work provides a molecular-scale understanding of the relative significance of ion adsorption onto gibbsite basal versus edge surfaces and demonstrates the corner effect on ion adsorption on NPs.

Structural insights from lipid-bilayer nanodiscs link α-Synuclein membrane-binding modes to amyloid fibril formation

The protein α-Synuclein (αS) is linked to Parkinson’s disease through its abnormal aggregation, which is thought to involve cytosolic and membrane-bound forms of αS. Following previous studies using micelles and vesicles, we present a comprehensive study of αS interaction with phospholipid bilayer nanodiscs. Using a combination of NMR-spectroscopic, biophysical, and computational methods, we structurally and kinetically characterize αS interaction with different membrane discs in a quantitative and site-resolved way. We obtain global and residue-specific αS membrane affinities, and determine modulations of αS membrane binding due to αS acetylation, membrane plasticity, lipid charge density, and accessible membrane surface area, as well as the consequences of the different binding modes for αS amyloid fibril formation. Our results establish a structural and kinetic link between the observed dissimilar binding modes and either aggregation-inhibiting properties, largely unperturbed aggregation, or accelerated aggregation due to membrane-assisted fibril nucleation.

Thibault Viennet and colleagues gain structural insight into amyloid fibril formation from their innovative use of lipid bilayer nanodiscs. This study connects α-Synuclein membrane binding modes to its aggregation properties, furthering our understanding of the cause of neurodegerative diseases.

Atomic-scale investigation of physical adsorption of water molecules and aggressive ions to ettringite's surfaces

The strength and durability of cementitious composite materials are adversely affected by the ingress of water molecules and aggressive ions into their intrinsic meso- and nano-pore spaces. Among various phases of hydrated cement paste (HCP), aluminum-rich phases play an important role in controlling the diffusivity of aqueous solutions, which can contain aggressive ions. To this date, however, there has been no systematic study to understand the adsorption mechanisms and chloride binding capacity of the aluminum-rich phases of HCP. This research gap has been the motivation of the current study to investigate the physical adsorption characteristics of ettringite as the main aluminum-rich phase of HCP and the primary hydrated product of calcium sulfoaluminate cement. Through a set of Molecular Dynamics simulations supported by macro-scale experimental tests, a fundamental insight into the molecular origins of the diffusion of water molecules, as well as sodium and chloride ions, in contact with ettringite is provided. As the primary objective of this study is to evaluate the transport properties at and near solution/solid interfaces, the molecular adsorption mechanisms are characterized for inner- and outer-sphere distances from the solid substrate. With an in-depth understanding of the structure and dynamics of water molecules and aggressive ions in contact with ettringite's surfaces, the outcome of this study provides reliable measures of physical adsorption, binding capacity, and self-diffusion coefficient, which can be further employed to introduce strategies to avoid the degradation of a wide variety of cementitious materials exposed to harsh environmental conditions.

The catalytic inactivation of the N-half of human hexokinase 2 and structural and biochemical characterization of its mitochondrial conformation

The high proliferation rate of tumor cells demands high energy and metabolites that are sustained by a high glycolytic flux known as the 'Warburg effect'. The activation and further metabolism of glucose is initiated by hexokinase, a focal point of metabolic regulation. The human hexokinase 2 (HK2) is overexpressed in all aggressive tumors and predominantly found on the outer mitochondrial membrane, where interactions through its N-terminus initiates and maintains tumorigenesis. Here, we report the structure of HK2 in complex with glucose and glucose-6-phosphate (G6P). Structural and biochemical characterization of the mitochondrial conformation reveals higher conformational stability and slow protein unfolding rate (k_u) compared with the cytosolic conformation. Despite the active site similarity of all human hexokinases, the N-domain of HK2 is catalytically active but not in hexokinase 1 and 3. Helix-α₁₃ that protrudes out of the N-domain to link it to the C-domain of HK2 is found to be important in maintaining the catalytic activity of the N-half. In addition, the N-domain of HK2 regulates the stability of the whole enzyme in contrast with the C-domain. Glucose binding enhanced the stability of the wild-type (WT) enzyme and the single mutant D657A of the C-domain, but it did not increase the stability of the D209A mutant of the N-domain. The interaction of HK2 with the mitochondria through its N-half is proposed to facilitate higher stability on the mitochondria. The identification of structural and biochemical differences between HK2 and other human hexokinase isozymes could potentially be used in the development of new anticancer therapies.

Binding of Divalent Cations to Insulin: Capillary Electrophoresis and Molecular Simulations

In the present study, we characterize the binding of divalent cations to insulin in aqueous salt solutions by means of capillary electrophoresis and molecular dynamics simulations. The results show a strong pH dependence. At low pH, at which all the carboxylate groups are protonated and the protein has an overall positive charge, all the cations exhibit only weak and rather unspecific interactions with insulin. In contrast, at close to neutral pH, when all the carboxylate groups are deprotonated and negatively charged, the charge-neutralizing effect of magnesium, calcium, and zinc, in particular, on the electrophoretic mobility of insulin is significant. This is also reflected in the results of molecular dynamics simulations showing accumulation of cations at the protein surface, which becomes smaller in magnitude upon effective inclusion of electronic polarization via charge rescaling.

Robust water desalination membranes against degradation using high loads of carbon nanotubes

Chlorine resistant reverse osmosis (RO) membranes were fabricated using a multi-walled carbon nanotube-polyamide (MWCNT-PA) nanocomposite. The separation performance of these membranes after chlorine exposure (4800 ppm·h) remained unchanged (99.9%) but was drastically reduced to 82% in the absence of MWCNT. It was observed that the surface roughness of the membranes changed significantly by adding MWCNT. Moreover, membranes containing MWCNT fractions above 12.5 wt.% clearly improved degradation resistance against chlorine exposure, with an increase in water flux while maintaining salt rejection performance. Molecular dynamics and quantum chemical calculations were performed in order to understand the high chemical stability of the MWCNT-PA nanocomposite membranes, and revealed that high activation energies are required for the chlorination of PA. The results presented here confirm the unique potential of carbon nanomaterials embedded in polymeric composite membranes for efficient RO water desalination technologies.

Thermal Polarization of Water Influences the Thermoelectric Response of Aqueous Solutions

Aqueous solutions under thermal gradients feature thermodiffusion (Ludwig-Soret) and thermoelectric (Seebeck) effects, whereby the thermal fields build concentration and charge density gradients. Recently, it has been shown that thermal gradients induce polarization fields in water. We use non-equilibrium molecular simulations to quantify the thermoelectric Seebeck coefficient of alkali halide aqueous solutions. We examine the dependence of the coefficient on temperature and salt concentration and show that the thermal polarization of water plays a key role in determining the magnitude of the thermoelectric behavior of the solution.

The Water-Alkane Interface at Various NaCl Salt Concentrations: A Molecular Dynamics Study of the Readily Available Force Fields

In this study, classical molecular dynamic simulations have been used to examine the molecular properties of the water-alkane interface at various NaCl salt concentrations (up to 3.0 mol/kg). A variety of different force field combinations have been compared against experimental surface/interfacial tension values for the water-vapour, decane-vapour and water-decane interfaces. Six different force fields for water (SPC, SPC/E, TIP3P, TIP3Pcharmm, TIP4P & TIP4P2005), and three further force fields for alkane (TraPPE-UA, CGenFF & OPLS) have been compared to experimental data. CGenFF, OPLS-AA and TraPPE-UA all accurately reproduce the interfacial properties of decane. The TIP4P2005 (four-point) water model is shown to be the most accurate water model for predicting the interfacial properties of water. The SPC/E water model is the best three-point parameterisation of water for this purpose. The CGenFF and TraPPE parameterisations of oil accurately reproduce the interfacial tension with water using either the TIP4P2005 or SPC/E water model. The salinity dependence on surface/interfacial tension is accurately captured using the Smith & Dang parameterisation of NaCl. We observe that the Smith & Dang model slightly overestimates the surface/interfacial tensions at higher salinities (>1.5 mol/kg). This is ascribed to an overestimation of the ion exclusion at the interface.

Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations

Long-range Lennard-Jones (LJ) interactions have a significant impact on the structural and thermodynamic properties of nonpolar systems. While several methods have been introduced for the treatment of long-range LJ interactions in molecular dynamics (MD) simulations, increased accuracy and extended applicability is required for anisotropic systems such as lipid bilayers. The recently refined Lennard-Jones particle-mesh Ewald (LJ-PME) method extends the particle-mesh Ewald (PME) method to long-range LJ interactions and is suitable for use with anisotropic systems. Implementation of LJ-PME with the CHARMM36 (C36) additive and CHARMM Drude polarizable force fields improves agreement with experiment for density, isothermal compressibility, surface tension, viscosity, translational diffusion, and ¹³C T₁ relaxation times of pure alkanes. Trends in the temperature dependence of the density and isothermal compressibility of hexadecane are also improved. While the C36 additive force field with LJ-PME remains a useful model for liquid alkanes, the Drude polarizable force field with LJ-PME is more accurate for nearly all quantities considered. LJ-PME is also preferable to the isotropic long-range correction for hexadecane because the molecular order extends to nearly 20 Å, well beyond the usual 10-12 Å cutoffs used in most simulations.

All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies

Prediction of motional EPR spectra of spin labelled DNA structures from fully atomistic MD simulations.

How abasic sites impact hole transfer dynamics in GC-rich DNA sequences

Hole transfer dynamics through GC-rich DNA duplexes containing abasic sites is strongly modulated by the nature of the unpaired nucleobase.

Density Fluctuation in Aqueous Solutions and Molecular Origin of Salting-Out Effect for CO2

Using molecular dynamics simulation, we studied the density fluctuations and cavity formation probabilities in aqueous solutions and their effect on the hydration of CO₂. With increasing salt concentration, we report an increased probability of observing a larger than the average number of species in the probe volume. Our energetic analyses indicate that the van der Waals and electrostatic interactions between CO₂ and aqueous solutions become more favorable with increasing salt concentration, favoring the solubility of CO₂ (salting in). However, due to the decreasing number of cavities forming when salt concentration is increased, the solubility of CO₂ decreases. The formation of cavities was found to be the primary control on the dissolution of gas, and is responsible for the observed CO₂ salting-out effect. Our results provide the fundamental understanding of the density fluctuation in aqueous solutions and the molecular origin of the salting-out effect for real gas.

Behavior of BsoBI endonuclease in the presence and absence of DNA

BsoBI is a type II restriction endonuclease belonging to the EcoRI family. There is only one previously published X-ray structure for this endonuclease: it shows a homodimer of BsoBI completely encircling DNA in a tunnel. In this work, molecular dynamics simulations were employed to elucidate possible ways in which DNA is loaded into this complex prior to its cleavage. We found that the dimer does not open spontaneously when DNA is removed from the complex on the timescale of our simulations (~ 0.5 μs). A biased simulation had to be used to facilitate the opening, which revealed a possible way for the two catalytic domains to separate. The α-helices connecting the catalytic and helical domains were found to act as a hinge during the separation. In addition, we found that the opening of the BsoBI dimer was influenced by the type of counterions present in the environment. A reference simulation of the BsoBI/DNA complex further showed spontaneous reorganization of the active sites due to the binding of solvent ions, which led to an active-site structure consistent with other experimental structures of type II restriction endonucleases determined in the presence of metal ions.

Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance, and Analysis

While DNA supercoiling is ubiquitous in vivo, the structure of supercoiled DNA is more challenging to study experimentally than simple linear sequences because the DNA must have a closed topology in order to sustain superhelical stress. DNA minicircles, which are closed circular double-stranded DNA sequences typically containing between 60 and 500 base pairs, have proven to be useful biochemical tools for the study of supercoiled DNA mechanics. We present detailed protocols for constructing models of DNA minicircles in silico, for performing atomistic molecular dynamics (MD) simulations of supercoiled minicircle DNA, and for analyzing the results of the calculations. These simulations are computationally challenging due to the large system sizes. However, improvements in parallel computing software and hardware promise access to improve conformational sampling and simulation timescales. Given the concurrent improvements in the resolution of experimental techniques such as atomic force microscopy (AFM) and cryo-electron microscopy, the study of DNA minicircles will provide a more complete understanding of both the structure and the mechanics of supercoiled DNA.

How accurate are accurate force-fields for B-DNA?

Last generation of force-fields are raising expectations on the quality of molecular dynamics (MD) simulations of DNA, as well as to the belief that theoretical models can substitute experimental ones in several cases. However these claims are based on limited benchmarks, where MD simulations have shown the ability to reproduce already existing ‘experimental models’, which in turn, have an unclear accuracy to represent DNA conformation in solution. In this work we explore the ability of different force-fields to predict the structure of two new B-DNA dodecamers, determined herein by means of ¹H nuclear magnetic resonance (NMR). The study allowed us to check directly for experimental NMR observables on duplexes previously not solved, and also to assess the reliability of ‘experimental structures’. We observed that technical details in the annealing procedures can induce non-negligible local changes in the final structures. We also found that while not all theoretical simulations are equally reliable, those obtained using last generation of AMBER force-fields (BSC1 and BSC0_OL15) show predictive power in the multi-microsecond timescale and can be safely used to reproduce global structure of DNA duplexes and fine sequence-dependent details.

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes

G-quadruplexes (GQs) are key noncanonical DNA and RNA architectures stabilized by desolvated monovalent cations present in their central channels. We analyze extended atomistic molecular dynamics simulations (∼580 μs in total) of GQs with 11 monovalent cation parametrizations, assessing GQ overall structural stability, dynamics of internal cations, and distortions of the G-tetrad geometries. Majority of simulations were executed with the SPC/E water model; however, test simulations with TIP3P and OPC water models are also reported. The identity and parametrization of ions strongly affect behavior of a tetramolecular d[GGG]₄ GQ, which is unstable with several ion parametrizations. The remaining studied RNA and DNA GQs are structurally stable, though the G-tetrad geometries are always deformed by bifurcated H-bonding in a parametrization-specific manner. Thus, basic 10-μs-scale simulations of fully folded GQs can be safely done with a number of cation parametrizations. However, there are parametrization-specific differences and basic force-field errors affecting the quantitative description of ion-tetrad interactions, which may significantly affect studies of the ion-binding processes and description of the GQ folding landscape. Our d[GGG]₄ simulations indirectly suggest that such studies will also be sensitive to the water models. During exchanges with bulk water, the Na⁺ ions move inside the GQs in a concerted manner, while larger relocations of the K⁺ ions are typically separated. We suggest that the Joung-Cheatham SPC/E K⁺ parameters represent a safe choice in simulation studies of GQs, though variation of ion parameters can be used for specific simulation goals.

Ion Distribution and Hydration Structure in the Stern Layer on Muscovite Surface

Based on molecular dynamics simulations of eight ions (Na⁺, K⁺, Rb⁺, Cs⁺, Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺) on muscovite mica surfaces in water, we demonstrate that experimental data on the muscovite mica surface can be rationalized through a unified picture of adsorption structures including the hydration structure, cation heights from the muscovite surface, and state stability. These simulations enable us to categorize the inner-sphere surface complex into two different species: an inner-sphere surface complex in a ditrigonal cavity (IS1) and that on top of Al (IS2). By considering the presence of the two inner-sphere surface complexes, the experimental finding that the heights of adsorbed cations from the muscovite surface are proportional to the ionic radius for K⁺ and Cs⁺ but inversely proportional to the ionic radius for Ca²⁺ and Ba²⁺ was explained. We find that Na⁺, Ca²⁺, Sr²⁺, and Ba²⁺ can form both IS1 and IS2; K⁺, Rb⁺, and Cs⁺ can form only IS1; and Mg²⁺ can form only IS2. It is suggested that the formation of IS1 and IS2 is governed by the charge density of the ions. Among the eight ions, we also find that the hydration structure for the outer-sphere surface complexes of divalent cations differs from that of the monovalent cations by one adsorbed water molecule (i.e., a water molecule located in a ditrigonal cavity).

Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.

A computational approach to calculate the heat of transport of aqueous solutions

Thermal gradients induce concentration gradients in alkali halide solutions, and the salt migrates towards hot or cold regions depending on the average temperature of the solution. This effect has been interpreted using the heat of transport, which provides a route to rationalize thermophoretic phenomena. Early theories provide estimates of the heat of transport at infinite dilution. These values are used to interpret thermodiffusion (Soret) and thermoelectric (Seebeck) effects. However, accessing heats of transport of individual ions at finite concentration remains an outstanding question both theoretically and experimentally. Here we discuss a computational approach to calculate heats of transport of aqueous solutions at finite concentrations, and apply our method to study lithium chloride solutions at concentrations >0.5 M. The heats of transport are significantly different for Li⁺ and Cl⁻ ions, unlike what is expected at infinite dilution. We find theoretical evidence for the existence of minima in the Soret coefficient of LiCl, where the magnitude of the heat of transport is maximized. The Seebeck coefficient obtained from the ionic heats of transport varies significantly with temperature and concentration. We identify thermodynamic conditions leading to a maximization of the thermoelectric response of aqueous solutions.

Evidence of Structure-Performance Relation for Surfactants Used as Antiagglomerants for Hydrate Management

Molecular dynamics simulations were employed to study the structure of molecularly thin films of antiagglomerants adsorbed at the interface between sII methane hydrates and a liquid hydrocarbon. The liquid hydrocarbon was composed of dissolved methane and higher-molecular-weight alkane such as n-hexane, n-octane, and n-dodecane. The antiagglomerants considered were surface-active compounds with three hydrophobic tails and a complex hydrophilic head that contains both amide and tertiary ammonium cation groups. The length of the hydrophobic tails and the surface density of the compounds were changed systematically. The results were analyzed in terms of the preferential orientation of the antiagglomerants, density distributions of various molecular compounds, and other molecular-level properties. At low surface densities, the hydrophobic tails do not show preferred orientation, irrespectively of the tail length. At sufficiently high surface densities, our simulations show pronounced differences in the structure of the interfacial film depending on the molecular features and on the type of hydrocarbons present in the system. Some antiagglomerants are found to pack densely at the interface and exclude methane from the interfacial region. Under these conditions, the antiagglomerant film resembles a frozen interface. The hydrophobic tails of the antiagglomerants that show this feature has a length comparable to that of the n-dodecane in the liquid phase. It is possible that the structured interfacial layer is in part responsible for determining the performance of antiagglomerants in flow-assurance applications. The simulation results are compared against experimental data obtained with the rocking cell apparatus. It was found that the antiagglomerants for which our simulations suggest evidence of a frozen interface at sufficiently high surface densities are those that show better performance in rocking cell experiments.