Fink, Lea, Christoph Allolio, Jehuda Feitelson, Carmen Tamburu, Daniel Harries, and Uri Raviv. “Bridges of Calcium Bicarbonate Tightly Couple Dipolar Lipid Membranes.” Langmuir 36, no. 36 (2020): 10715–10724. Publisher's VersionAbstract

The interaction between lipid membranes and ions is associated with a range of key physiological processes. Most earlier studies have focused on the interaction of lipids with cations, while the specific effects of the anions have been largely overlooked. Owing to dissolved atmospheric carbon dioxide, bicarbonate is an important ubiquitous anion in aqueous media. In this paper, we examined the effect of bicarbonate anions on the interactions between dipolar lipid membranes in the presence of previously adsorbed calcium cations. Using a combination of solution X-ray scattering, osmotic stress, and molecular dynamic simulations, we followed the interactions between 1,2-didodecanoyl-sn-glycero-3-phosphocholine (DLPC) lipid membranes that were dialyzed against CaCl2 solutions in the presence and absence of bicarbonate anions. Calcium cations adsorbed onto DLPC membranes charge them and lead to their swelling. In the presence of bicarbonate anions, however, the calcium cations can tightly couple one dipolar DLPC membrane to the other and form a highly condensed and dehydrated lamellar phase with a repeat distance of 3.45±0.02 nm. Similar tight condensation and dehydration has only been observed between charged membranes in the presence of multivalent counterions. Bridging between bilayers by calcium bicarbonate complexes induced this arrangement. Furthermore, in this condensed phase the lipid molecules and the adsorbed ions were arranged in a 2D oblique lattice.


Schachter, Itay, Christoph Allolio, George Khelashvili, and Daniel Harries. “Confinement in Nanodiscs Anisotropically Modifies Lipid Bilayer Elastic Properties.” Journal of Physical Chemistry B 124, no. 33 (2020): 7166–7175. Publisher's VersionAbstract


Lipid nanodiscs are small synthetic lipid bilayer structures that are stabilized in solution by special circumscribing (or scaffolding) proteins or polymers. Because they create native-like environments for transmembrane proteins, lipid nanodiscs have become a powerful tool for structural determination of this class of systems when combined with cryo-electron microscopy or nuclear magnetic resonance. The elastic properties of lipid bilayers determine how the lipid environment responds to membrane protein perturbations, and how the lipid in turn modifies the conformational state of the embedded protein. However, despite the abundant use of nanodiscs in determining membrane protein structure, the elastic material properties of even pure lipid nanodiscs (i.e., without embedded proteins) have not yet been quantitatively investigated. A major hurdle is due to the inherently non-local treatment of the elastic properties of lipid systems implemented by most existing methods, both experimental and computational. In addition, these methods are best suited for very large “infinite” size lipidic assemblies, or ones that contain periodicity, in the case of simulations. We have previously described a computational analysis of molecular dynamics simulations designed to overcome these limitations, so that it allows quantification of the bending rigidity (KC) and tilt moduli (κt) on a local scale even for finite, non-periodic systems, such as lipid nanodiscs. Here we use this computational approach to extract values of KC and κt for a set of lipid nanodisc systems that vary in size and lipid composition. We find that the material properties of lipid nanodiscs are different from those of infinite bilayers of corresponding lipid composition, highlighting the effect of nanodisc confinement. Nanodiscs tend to show higher stiffness than their corresponding macroscopic bilayers, and moreover, their material properties vary spatially within them. For small-size MSP1 nanodiscs, the stiffness decreases radially, from a value that is larger in their center than the moduli of the corresponding bilayers by a factor of ~2-3. The larger nanodiscs (MSP1E3D1 and MSP2N2) show milder spatial changes of moduli that are composition dependent and can be maximal in the center or at some distance from it. These trends in moduli correlate with spatially varying structural properties, including the area per lipid and the nanodisc thickness. Finally, as has previously been reported, nanodiscs tend to show deformations from perfectly flat circular geometries to varying degrees, depending on size and lipid composition. The modulations of lipid elastic properties that we find should be carefully considered when making structural and functional inferences concerning embedded proteins.



Curland, Sofia, Christoph Allolio, Leah Javitt, Shiri Dishon, Isabelle Weissbuch, David Ehre, Daniel Harries, Meir Lahav, and Igor Lubomirsky. “Heterogeneous Electrofreezing of Super Cooled Water on Surfaces of Pyroelectric Crystals is Trigered by Planar-Trigonal Ions.” Angewandte Chemie International Edition 59 (2020): 15575–15579. Publisher's VersionAbstract





Shumilin, Ilan, Benny Bogoslavsky, and Daniel Harries. “Stressing Crystals With Solutes: Effects of Added Solutes on Crystalline Caffeine and their Relevance to Determining Transfer Free Energies.” Colloids and Surfaces A: Physicochemical and Engineering Aspects 599 (2020): 124889. Publisher's VersionAbstract

In calculating transfer free energies of solvated substances, the coexisting crystal state is often taken as the reference. Furthermore, the free energy of this reference state is often assumed to remain constant upon changes made in solution. Yet little is known about the way added cosolutes impact the thermodynamic stability of the out-of-solution crystal phase. To provide insight into the changes in the activity of the coexisting solid state, we used caffeine, a well-studied hydrophobic compound that forms a hydrated crystal in saturated aqueous solutions. By using X-ray powder diffraction, we found that cosolutes, such as trehalose, sucrose, sodium sulfate, and polyethylene glycol (PEG) alter the unit cell volume of crystalline caffeine, in a concentration dependent manner. The dehydration of solid caffeine translates into an overall increase in its free energy, which can be directly calculated as the reversible ΠV work required to compress the crystal. We determined that trehalose, sucrose, and sodium sulfate increase the free energy of the solid, while PEG decreases it. For 2 mol/kg trehalose, this change in free energy corresponds to 17 % of the total change in solvation free energy of monomeric caffeine. Although our results indicate that cosolutes modify the free energy of the solid less than that of the solvated state, this effect is non negligible and measurable, suggesting that it should generally be taken into account as a contribution to changes in solubility, particularly whenever the solid phase is hydrated.

graphical abstract

Sapir, Liel, and Daniel Harries. “Restructuring a Deep Eutectic Solvent by Water: The Nanostructure of Hydrated Choline Chloride/Urea.” Journal of Chemical Theory and Computation 16 (2020): 3335-3342. Publisher's VersionAbstract

Deep eutectic mixtures are a promising sustainable and diverse class of tunable solvents that hold great promise for various green chemical and technological processes. Many deep eutectic solvents (DES) are hygroscopic and find use in applications with varying extents of hydration, hence urging a profound understanding of changes in the nanostructure of DES with water content. Here, we report on molecular dynamics simulations of the quintessential choline chloride–urea mixture, using a newly parametrized force field with scaled charges to account for physical properties of hydrated DES mixtures. These simulations indicate that water changes the nanostructure of solution even at very low hydration. We present a novel approach that uses convex constrained analysis to dissect radial distribution functions into base components representing different modes of local association. Specifically, DES mixtures can be deconvoluted locally into two dominant competing nanostructures, whose relative prevalence (but not their salient structural features) change with added water over a wide concentration range, from dry up to ∼30 wt % hydration. Water is found to be associated strongly with several DES components but remarkably also forms linear bead-on-string clusters with chloride. At high water content (beyond ∼50 wt % of water), the solution changes into an aqueous electrolyte-like mixture. Finally, the structural evolution of the solution at the nanoscale with extent of hydration is echoed in the DES macroscopic material properties. These changes to structure, in turn, should prove important in the way DES acts as a solvent and to its interactions with additive components.


Olgenblum, Gil I., Liel Sapir, and Daniel Harries. “Properties of Aqueous Trehalose Mixtures: Glass Transition and Hydrogen Bonding.” Journal of Chemical Theory and Computation 16 (2020): 1249-1262. Publisher's VersionAbstract

Trehalose is a naturally occurring disaccharide known to remarkably stabilize biomacromolecules in the biologically active state. The stabilizing effect is typically observed over a large concentration range and affects many macromolecules including proteins, lipids, and DNA. Of special interest is the transition from aqueous solution to the dense and highly concentrated glassy state of trehalose that has been implicated in bioadaptation of different organisms toward desiccation stress. Although several mechanisms have been suggested to link the structure of the low water content glass with its action as an exceptional stabilizer, studies are ongoing to resolve which are most pertinent. Specifically, the role that hydrogen bonding plays in the formation of the glass is not well resolved. Here we model aqueous trehalose mixtures over a wide concentration range, using molecular dynamics simulations with two available force fields. Both force fields indicate glass transition temperatures and osmotic pressures that are close to experimental values, particularly at high trehalose contents. We develop and employ a methodology that allows us to analyze the thermodynamics of hydrogen bonds in simulations at different water contents and temperatures. Remarkably, this analysis is able to link the liquid to glass transition with changes in hydrogen bond characteristics. Most notably, the onset of the glassy state can be quantitatively related to the transition from weakly to strongly correlated hydrogen bonds. Our findings should help resolve the properties of the glass and the mechanisms of its formation in the presence of added macromolecules.


Sukenik, Shahar, Daniel Harries, and Assaf Friedler. “Biophysical Chemistry.” In Elsevier Reference Module in Chemistry, Molecular Sciences and Chemical Engineering. Waltham, MA: Elsevier, 2019. Publisher's VersionAbstract

Biophysical chemistry is a branch of the multidisciplinary study of biophysics. The field is devoted to a quantitative analysis of biological systems using experimental, theoretical, and computational tools. In contrast to a physics-centered approach for biophysics that deals with forces and scaling laws, or a biology-centered view that deals with the phenotype of the studied system, biophysical chemistry focuses on the molecular level. Unlike biochemistry, which often focuses on chemical reactions driving biological systems, biophysical chemistry is aimed at the collection and analysis of quantitative data to provide predictive physical models describing biological phenomena occurring at the molecular level. Biophysical chemistry aims to bridge the physical and biological disciplines: in biological systems physical forces and interactions are mediated through molecules, which ultimately
determine phenotype. The experimental and theoretical tools of biophysical chemistry have demonstrated significant success in unraveling multiple basic molecular mechanisms that govern biological processes. Here we highlight some of the important contemporary areas and questions currently studied in the field of biophysical chemistry. Since molecules are at the center of this study, we focus our discussion on three classes of molecules essential for all living organisms: proteins, nucleic acids, and lipids.

Shumilin, Ilan, Christoph Allolio, and Daniel Harries. “How Sugars Modify Caffeine Self-Association and Solubility: Resolving a Mechanism of Selective Hydrotropy.” Journal of the American Chemical Society 141, no. 45 (2019): 18056-18063. Publisher's VersionAbstract

The aggregation of drugs and nutraceuticals in aqueous media is an outstanding problem for their efficacy and bioavailability. A common solution is to add excipients or hydrotropes that increase solubility and limit aggregation. Here we study caffeine, a widely consumed drug that undergoes oligomerization and aggregation in aqueous solutions. Combining partition and solubility experiments with molecular dynamics simulations, we determined the effect of sugars (mono- and disaccharides) on caffeine self-association and solubility. We find that sugars selectively increase the concentration of caffeine in its monomeric state, but decrease its solubility in all oligomeric forms. Thus we determine that, in contrast to common hydrotropes, sugars act as selective hydrotropes toward caffeine, since they differentially act on specific solvated forms of the drug. We furthermore unravel the molecular mechanism for this selectivity, and comment on the general design principles that should help develop targeted excipients for bioavailability and taste modification in drugs and foods.

Mentions in scientific media: herehere, and here


Allolio, Christoph, Amir Haluts, and Daniel Harries. “A local instantaneous surface method for extracting membrane elastic moduli from simulation: Comparison with other strategies.” Chemical Physics 514 (2018): 31-43. Publisher's VersionAbstract

Advances over the past decade have made it possible to extract elastic constants of lipid assemblies from molecular dynamics simulations. We summarize existing strategies for obtaining membrane elastic moduli and clarify the differences in the underlying approaches. We analyze these strategies in depth, including several important advantages and limitations. By addressing these limitations, we obtain a newly formulated spatially local methodology for extracting bending and tilt moduli: The Real Space Instantaneous Surface Method (ReSIS). With its freely available implementation, this method is designed for highly dynamic systems with arbitrary interface geometries. We demonstrate how the method provides consistent results for membranes of arbitrary size. In addition, we describe alternative implementations of various Fourier-space methods, and use these to compare the results from the different available methods and from published computational data. We specifically focus on the tilt modulus, where very large differences between Fourier and real-space based methods are observed, including those derived using ReSIS. These discrepancies are likely due to the known difference between model moduli and thermodynamic moduli that are derived from the corresponding response functions. In addition, we reexamine the issue of angular degeneracy and its effect on conformational ensembles. Finally, a van ’t Hoff analysis of the tilt and bending moduli reveals that both modes act as entropic springs and that enthalpy favors nonzero tilt, perhaps heralding the spontaneous lipid chain tilt of the gel phase at lower temperatures.

Additional information and implementation available here


Ben-Abu, Natalie, Daniel Harries, Hillary Voet, and Masha Y. Niv. “The taste of KCl - what a difference a sugar makes.” Food Chemistry 255 (2018): 165-173. Publisher's VersionAbstract

Dramatic increase in NaCl consumption lead to sodium intake beyond health guidelines. KCl substitution helps reduce sodium intake but results in a bitter-metallic off-taste. Two disaccharides, trehalose and sucrose, were tested in order to untangle the chemical (increase in effective concentraion of KCl due to sugar addition) from the sensory effects. The bitter-metallic taste of KCl was reduced by these sugars, while saltiness was enhanced or unaltered. The perceived sweetness of sugar, regardless of its type and concentration, was an important factor in KCl taste modulation. Though KCl was previously shown to increase the chemical activity of trehalose but not of sucrose, we found that it suppressed the perceived sweetness of both sugars. Therefore, sensory integration was the dominant factor in the tested KCl-sugar combinations.

TMAO mediates effective attraction between lipid membranes by partitioning unevenly between bulk and lipid domain
Sukenik, Shahar, Shaked Dunsky, Avishai Barnoy, Ilan Shumilin, and Daniel Harries. “TMAO mediates effective attraction between lipid membranes by partitioning unevenly between bulk and lipid domain.” Physical Chemistry Chemical Physics 19 (2017): 29862-29871. Publisher's VersionAbstract

Under environmental duress, many organisms accumulate large amounts of osmolytes – molecularly small organic solutes. Osmolytes are known to counteract stress, driving proteins to their compact native states by their exclusion from protein surfaces. In contrast, the effect of osmolytes on lipid membranes is poorly understood and widely debated. Many fully membrane-permeable osmolytes exert an apparent attractive force between lipid membranes, yet all proposed models fail to fully account for the origin of this force. We follow the quintessential osmolyte trimethylamine N-oxide (TMAO) and its interaction with dimyristoyl phosphatidylcholine (DMPC) membranes in aqueous solution. We find that by partitioning away from the inter-bilayer space, TMAO pushes adjacent membranes closer together. Experiments and simulations further show that the partitioning of TMAO away from the volume between bilayers stems from its exclusion from the lipid–water interface, similar to the mechanism of protein stabilization by osmolytes. We extend our analysis to show that the preferential interaction of other physiologically relevant solutes (including sugars and DMSO) also correlates with their effect on membrane bilayer interactions. Our study resolves a long-standing puzzle, explaining how osmolytes can increase membrane– membrane attraction or repulsion depending on their preferential interactions with lipids.

This article is part of the themed collection: 2017 PCCP HOT Articles

Poplinger, Michal, Ilan Shumilin, and Daniel Harries. “Impact of trehalose on the activity of sodium and potassium chloride in aqueous solutions: why trehalose is worth its salt.” Food Chemistry 237 (2017): 1209-1215. Publisher's Version
Wisdom of the crowd
Sapir, Liel, and Daniel Harries. “Wisdom of the crowd.” Bunsen-Magazin 19, no. 4 (2017): 152-162. Sapir&Harries_BM_2017.pdf
Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations
Doktorova, Milka, Daniel Harries, and George Khalashvili. “Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations.” Physical Chemistry Chemical Physics 19 (2017): 16806-16818. Publisher's Version
Revisiting hydrogen bond thermodynamics in molecular simulations
Sapir, Liel, and Daniel Harries. “Revisiting hydrogen bond thermodynamics in molecular simulations.” Journal of Chemical Theory and Computation 13, no. 6 (2017): 2851–2857. Publisher's Version
Hu, Yuwei, Jason S Kahn, Weiwei Guo, Fujian Huang, Michael Fadeev, Daniel Harries, and Itamar Willner. “Reversible modulation of DNA-based hydrogel shapes by internal stress interactions.” Journal of the American Chemical Society 138, no. 49 (2016): 16112-16119. Publisher's Version
Competing processes of micellization and fibrillization in native and reduced casein proteins
Portnaya, Irina, Sharon Avni, Ellina Kesselman, Yoav Boyarski, Shahar Sukenik, Daniel Harries, Nily Dan, Uri Cogan, and Dganit Danino. “Competing processes of micellization and fibrillization in native and reduced casein proteins.” Physical Chemistry Chemical Physics 18, no. 32 (2016): 22516-22525. Publisher's Version
Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations
Johner, Niklaus, Daniel Harries, and George Khelashvili. “Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations.” BMC bioinformatics 17, no. 1 (2016): 1. Publisher's Version
Macromolecular compaction by mixed solutions: Bridging versus depletion attraction
Sapir, Liel, and Daniel Harries. “Macromolecular compaction by mixed solutions: Bridging versus depletion attraction.” Current Opinion in Colloid & Interface Science 22 (2016): 80-87. Publisher's Version
Nonclassical Crystal Growth as Explanation for the Riddle of Polarity in Centrosymmetric Glycine Crystals
Meirzadeh, Elena, Liel Sapir, Hagai Cohen, Sidney R Cohen, David Ehre, Daniel Harries, Meir Lahav, and Igor Lubomirsky. “Nonclassical Crystal Growth as Explanation for the Riddle of Polarity in Centrosymmetric Glycine Crystals.” Journal of the American Chemical Society 138, no. 44 (2016): 14756-14763. Publisher's Version