Erik Wernersson

Mechanisms of Acceleration and Retardation of Water Dynamics by Ions

There are fundamental and not yet fully resolved questions concerning the impact of solutes, ions in particular, on the structure and dynamics of water, which can be formulated as follows: Are the effects of ions local or long-ranged? Is the action of cations and anions on water cooperative or not? Here, we investigate how the reorientation and hydrogen-bond dynamics of water are affected by ions in dilute and concentrated aqueous salt solutions. By combining simulations and analytic modeling, we first show that ions have a short-ranged influence on the reorientation of individual water molecules and that depending on their interaction strength with water, they may accelerate or slow down water dynamics. A simple additive picture combining the effects of the cations and anions is found to provide a good description in dilute solutions. In concentrated solutions, we show that the average water reorientation time ceases to scale linearly with salt concentration due to overlapping hydration shells and structural rearrangements which reduce the translational displacements induced by hydrogen-bond switches and increase the solution viscosity. This effect is not ion-specific and explains why all concentrated salt solutions slow down water dynamics. Our picture, which is demonstrated to be robust vis-a-vis a change in the force-field, reconciles the seemingly contradictory experimental results obtained by ultrafast infrared and NMR spectroscopies, and suggests that there are no long-ranged cooperative ion effects on the dynamics of individual water molecules in dilute solutions.

Effect of Water Polarizability on the Properties of Solutions of Polyvalent Ions: Simulations of Aqueous Sodium Sulfate with Different Force Fields

We show that aqueous sodium sulfate solutions exhibit an unrealistically large degree of ion pairing and clustering when modeled using nonpolarizable force fields, with clusters resembling precipitate readily forming in a 0.5 m solution at ambient conditions. This aggregation behavior was found to be persistent in nonpolarizable water for a range of parameters of the sulfate anion. In contrast, a polarizable potential performs satisfactorily, producing a well dissolved salt with a degree of association that is consistent with activity data for real solutions. Most of this improvement is due to polarization of water molecules in the vicinity of the divalent sulfate anion, which enhances its solvation.

Solvation and ion-pairing properties of the aqueous sulfate anion: explicit versus effective electronic polarization

We assessed the relative merits of two approaches for including polarization effects in classical force fields for the sulfate anion. One of the approaches is the explicit shell model for atomic polarization and the other is an implicit dielectric continuum representation of the electronic polarization, wherein the polarizability density is spatially uniform. Both the solvation and ion association properties of sulfate were considered. We carried out an ab initio molecular dynamics simulation for a single sulfate anion in aqueous solution to obtain a benchmark for the solvation structure. For the ion-pairing properties, the models were compared to experimental thermodynamic data through Kirkwood-Buff theory, which relates the integrals of the pair correlation functions to measurable properties. While deficiencies were found for both of the approaches, the continuum polarization model was not systematically worse than the shell model. The shell model was found to give a more structured solution than the continuum polarization model, both with respect to solvation and ion pairing.

Effect of association with sulfate on the electrophoretic mobility of polyarginine and polylysine.

Domains rich in cationic amino acids are ubiquitous in peptides with the ability to cross cell membranes, which is likely related to the binding of such polypeptides to anionic groups on the membrane surface. To shed more light on these interactions, we investigated specific interactions between basic amino acids and oligopeptides thereof and anions by means of electrophoretic experiments and molecular dynamics simulations. To this end, we measured the electrophoretic mobilities of arginine, lysine, tetraarginine, and tetralysine in sodium chloride and sodium sulfate electrolytes as a function of ionic strength. The mobility was found to be consistently lower in sodium sulfate than in sodium chloride at the same ionic strength. The decrease in mobility in sodium sulfate was greater for tetraarginine than for tetralysine and was larger for tetrapeptides compared to the corresponding free amino acids. On the basis of molecular dynamics simulations and Bjerrum theory, we rationalize these results in terms of enhanced association between the amino acid side chains and sulfate. Simulations also predict a greater affinity of sulfate to the guanidinium side chain groups of arginine than to the ammonium groups of lysine, as the planar guanidinium geometry allows simultaneous strong hydrogen bonding to two sulfate oxygens. We show that the sulfate binding to arginine, but not to lysine, is cooperative. These results are consistent with the greater decrease in the mobility of arginine compared to that of lysine upon addition of sulfate salt. The nonspecific mobility retardation by sulfate is ascribed to its electrostatic interaction with the cationic amino acid side chain groups.

Field-induced assembly of colloidal ellipsoids into well-defined microtubules

Current theoretical attempts to understand the reversible formation of stable microtubules and virus shells are generally based on shape-specific building blocks or monomers, where the local curvature of the resulting structure is explicitly built-in via the monomer geometry. Here we demonstrate that even simple ellipsoidal colloids can reversibly self-assemble into regular tubular structures when subjected to an alternating electric field. Supported by model calculations, we discuss the combined effects of anisotropic shape and field-induced dipolar interactions on the reversible formation of self-assembled structures. Our observations show that the formation of tubular structures through self-assembly requires much less geometrical and interaction specificity than previously thought, and advance our current understanding of the minimal requirements for self-assembly into regular virus-like structures.

Accurate description of aqueous carbonate ions: an effective polarization model verified by neutron scattering.

The carbonate ion plays a central role in the biochemical formation of the shells of aquatic life, which is an important path for carbon dioxide sequestration. Given the vital role of carbonate in this and other contexts, it is imperative to develop accurate models for such a high charge density ion. As a divalent ion, carbonate has a strong polarizing effect on surrounding water molecules. This raises the question whether it is possible to describe accurately such systems without including polarization. It has recently been suggested the lack of electronic polarization in nonpolarizable water models can be effectively compensated by introducing an electronic dielectric continuum, which is with respect to the forces between atoms equivalent to rescaling the ionic charges. Given how widely nonpolarizable models are used to model electrolyte solutions, establishing the experimental validity of this suggestion is imperative. Here, we examine a stringent test for such models: a comparison of the difference of the neutron scattering structure factors of K2CO3 vs KNO3 solutions and that predicted by molecular dynamics simulations for various models of the same systems. We compare standard nonpolarizable simulations in SPC/E water to analogous simulations with effective ion charges, as well as simulations in explicitly polarizable POL3 water (which, however, has only about half the experimental polarizability). It is found that the simulation with rescaled charges is in a very good agreement with the experimental data, which is significantly better than for the nonpolarizable simulation and even better than for the explicitly polarizable POL3 model.

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

Precisely measuring the location and frequency of DNA double-strand breaks (DSBs) along the genome is instrumental to understanding genomic fragility, but current methods are limited in versatility, sensitivity or practicality. Here we present Breaks Labeling In Situ and Sequencing (BLISS), featuring the following: (1) direct labelling of DSBs in fixed cells or tissue sections on a solid surface; (2) low-input requirement by linear amplification of tagged DSBs by in vitro transcription; (3) quantification of DSBs through unique molecular identifiers; and (4) easy scalability and multiplexing. We apply BLISS to profile endogenous and exogenous DSBs in low-input samples of cancer cells, embryonic stem cells and liver tissue. We demonstrate the sensitivity of BLISS by assessing the genome-wide off-target activity of two CRISPR-associated RNA-guided endonucleases, Cas9 and Cpf1, observing that Cpf1 has higher specificity than Cas9. Our results establish BLISS as a versatile, sensitive and efficient method for genome-wide DSB mapping in many applications.

Orientational Dependence of the Affinity of Guanidinium Ions to the Water Surface

The behavior of guanidinium chloride at the surface of aqueous solutions is investigated using classical molecular dynamics (MD) simulations. It is found that the population of guanidinium ions oriented parallel to the interface is greater in the surface region than in bulk. The opposite is true for ions in other orientations. Overall, guanidinium chloride is depleted in the surface region, in agreement with the fact that the addition of guanidinium chloride increases the surface tension of water. The orientational dependence of the surface affinity of the guanidinium cation is related to its anisotropic hydration. To bring the ion to the surface in the parallel orientation does not require hydrogen bonds to be broken, in contrast to other orientations. The surface enrichment of parallel-oriented guanidinium indicates that its solvation is more favorable near the surface than in bulk solution for this orientation. The dependence of the bulk and surface properties of guanidinium on the force field parameters is also investigated. Despite significant quantitative differences between the force fields, the surface behavior is qualitatively robust. The implications for the orientations of the guanidinium groups of arginine side chains on protein surfaces are also outlined.

Aggregation of oligoarginines at phospholipid membranes: molecular dynamics simulations, time-dependent fluorescence shift, and biomimetic colorimetric assays.

A time-dependent fluorescence shift method, biomimetic colorimetric assays, and molecular dynamics simulations have been performed in search of explanations why arginine rich peptides with intermediate lengths of about 10 amino acids translocate well through cellular membranes, while analogous lysine rich peptides do not. First, we demonstrate that an important factor for efficient peptide adsorption, as the first prerequisite for translocation across the membrane, is the presence of negatively charged phospholipids in the bilayer. Second, we observe a strong tendency of adsorbed arginine (but not lysine) containing peptides to aggregate at the bilayer surface. We suggest that this aggregation of oligoarginines leads to partial disruption of the bilayer integrity due to the accumulated large positive charge at its surface, which increases membrane-surface interactions due to the increased effective charge of the aggregates. As a result, membrane penetration and translocation of medium length oligoarginines becomes facilitated in comparison to single arginine and very long polyarginines, as well as to lysine containing peptides.

Surface Behavior of Hydrated Guanidinium and Ammonium Ions: A Comparative Study by Photoelectron Spectroscopy and Molecular Dynamics

Through the combination of surface sensitive photoelectron spectroscopy and molecular dynamics simulation, the relative surface propensities of guanidinium and ammonium ions in aqueous solution are characterized. The fact that the N 1s binding energies differ between these two species was exploited to monitor their relative surface concentration through their respective photoemission intensities. Aqueous solutions of ammonium and guanidinium chloride, and mixtures of these salts, have been studied in a wide concentration range, and it is found that the guanidinium ion has a greater propensity to reside at the aqueous surface than the ammonium ion. A large portion of the relative excess of guanidinium ions in the surface region of the mixed solutions can be explained by replacement of ammonium ions by guanidinium ions in the surface region in combination with a strong salting-out effect of guanidinium by ammonium ions at increased concentrations. This interpretation is supported by molecular dynamics simulations, which reproduce the experimental trends very well. The simulations suggest that the relatively higher surface propensity of guanidinium compared with ammonium ions is due to the ease of dehydration of the faces of the almost planar guanidinium ion, which allows it to approach the water-vapor interface oriented parallel to it.