Publications

2022
Speer, Shannon L., Claire J. Stewart, Liel Sapir, Daniel Harries, and Gary J. Pielak. “Macromolecular Crowding Is More than Hard-Core Repulsions.” Annual Review of Biophysics 51 (2022). Publisher's VersionAbstract

Cells are crowded, but proteins are almost always studied in dilute aqueous buffer. We review the experimental evidence that crowding affects the equilibrium thermodynamics of protein stability and protein association and discuss the theories employed to explain these observations. In doing so, we highlight differences between synthetic polymers and biologically relevant crowders. Theories based on hard-core interactions predict only crowding-induced entropic stabilization. However, experiment-based efforts conducted under physiologically relevant conditions show that crowding can destabilize proteins and their complexes. Furthermore, quantification of the temperature dependence of crowding effects produced by both large and small cosolutes, including osmolytes, sugars, synthetic polymers, and proteins, reveals enthalpic effects that stabilize or destabilize proteins. Crowding-induced destabilization and the enthalpic component point to the role of chemical interactions between and among the macromolecules, cosolutes, and water. We conclude with suggestions for future studies.

Elimelech, Orian, Omer Aviv, Meirav Oded, Xiaogang Peng, Daniel Harries, and Uri Banin. “Entropy of Branching Out: Linear versus Branched Alkylthiols Ligands on CdSe Nanocrystals.” ACS Nano (2022). Publisher's VersionAbstract

Surface ligands of semiconductor nanocrystals (NCs) play key roles in determining their colloidal stability and physicochemical properties and are thus enablers also for the NCs flexible manipulation toward numerous applications. Attention is usually paid to the ligand binding group, while the impact of the ligand chain backbone structure is less discussed. Using isothermal titration calorimetry (ITC), we studied the effect of structural changes in the ligand chain on the thermodynamics of the exchange reaction for oleate coated CdSe NCs, comparing linear and branched alkylthiols. The investigated alkylthiol ligands differed in their backbone length, branching position, and branching group length. Compared to linear ligands, lower exothermicity and entropy loss were observed for an exchange with branched ligands, due to steric hindrance in ligand packing, thereby justifying their previous classification as “entropic ligands”. Mean-field calculations for ligand binding demonstrate the contribution to the overall entropy originating from ligand conformational entropy, which is diminished upon binding mainly by packing of NC-bound ligands. Model calculations and the experimental ITC data both point to an interplay between the branching position and the backbone length in determining the entropic nature of the branched ligand. Our findings suggest that the most entropic ligand should be a short, branched ligand with short branching group located toward the middle of the ligand chain. The insights provided by this work also contribute to a future smarter NC surface design, which is an essential tool for their implementation in diverse applications.

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2021
Maor, Inbar, Naama Koifman, Ellina Kesselman, Pnina Matsanov, Ilan Shumilin, Daniel Harries, and Iris Sonia Weitz. “Molecular Self-Assembly under Nanoconfinement: Indigo Carmine Scroll Structures Entrapped Within Polymeric Capsules.” Nanoscale 13 (2021): 20462-20470. Publisher's VersionAbstract

Molecular self-assembly forms structures of well-defined organization that allow control over material properties, affording many advanced technological applications. Although the self-assembly of molecules is seemingly spontaneous, the structure into which they assemble can be altered by carefully modulating the driving forces. Here we study the self-assembly within the constraints of nanoconfined closed spherical volumes of polymeric nanocapsules, whereby a mixture of polyester-polyether block copolymer and methacrylic acid methyl methacrylate copolymer forms the entrapping capsule shell of nanometric dimensions. We follow the organization of the organic dye indigo carmine that serves as a model building unit due to its tendency to self-assemble into flat lamellar molecular sheets. Analysis of the structures formed inside the nanoconfined space using cryogenic-transmission electron microscopy (cryo-TEM) and cryogenic-electron tomography (cryo-ET) reveal that confinement drives the self-assembly to produce tubular scroll-like structures of the dye. Combined continuum theory and molecular modeling allow us to estimate the material properties of the confined nanosheets, including their elasticity and brittleness. Finally, we comment on the formation mechanism and forces that govern self-assembly under nanoconfinement.

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Allolio, Christoph, and Daniel Harries. “Calcium Ions Promote Membrane Fusion by Forming Negative-Curvature Inducing Clusters on Specific Anionic Lipids.” ACS Nano 15, no. 8 (2021): 12880–12887. Publisher's VersionAbstract

Vesicles enriched in certain negatively charged lipids, such as phosphatidylserine and PIP2, are known to undergo fusion in the presence of calcium ions without assistance from protein assemblies. Other lipids do not exhibit this propensity, even if they are negatively charged. Using our recently developed methodology, we extract elastic properties of a representative set of lipids. This allows us to trace the origin of lipid-calcium selectivity in membrane fusion to the formation of lipid clusters with long-range correlations that induce negative curvature on the membrane surface. Furthermore, the clusters generate lateral tension in the headgroup region at the membrane surface, concomitantly also stabilizing negative Gaussian curvature. Finally, calcium binding also reduces the orientational polarization of water around the membrane head groups, potentially reducing the hydration force acting between membranes. Binding calcium only weakly increases membrane bending rigidity and tilt moduli, in agreement with experiments. We show how the combined effects of calcium binding to membranes lower the barriers along the fusion pathway that lead to the formation of the fusion stalk as well as the fusion pore.

Olgenblum, Gil I., Liel Sapir, Frank Wien, and Daniel Harries. “β-Hairpin Miniprotein Stabilization in Trehalose Glass Is Facilitated by an Emergent Compact Non-Native State.” The Journal of Physical Chemistry Letters 12, no. 32 (2021): 7659–7664. Publisher's VersionAbstract

From stem cell freeze-drying to organ storage, considerable recent efforts have been directed toward the development of new preservation technologies. A prominent protein stabilizing strategy involves vitrification in glassy matrices, most notably those formed of sugars such as the biologically relevant preservative trehalose. Here, we compare the folding thermodynamics of a model miniprotein in solution and in the glassy state of the sugars trehalose and glucose. Using synchrotron radiation circular dichroism (SRCD), we find that the same native structure persists in solution and glass. However, upon transition to the glass, a completely different, conformationally restricted unfolded state replaces the disordered denatured state found in solution, potentially inhibiting misfolding. Concomitantly, a large exothermic contribution is observed in glass, exposing the stabilizing effect of interactions with the sugar matrix on the native state. Our results shed light on the mechanism of protein stabilization in sugar glass and should aid in future preservation technologies.

Shumilin, Ilan, and Daniel Harries. “Cyclodextrin solubilization in hydrated reline: Resolving the unique stabilization mechanism in a deep eutectic solvent.” The Journal of Chemical Physics 154, no. 22 (2021): 224505. Publisher's VersionAbstract

By complexing with hydrophobic compounds, cyclodextrins afford increased solubility and thermodynamic stability to hardly soluble compounds, thereby underlining their invaluable applications in pharmaceutical and other industries. However, common cyclodextrins such as β-cyclodextrin, suffer from limited solubility in water, which often leads to precipitation and formation of unfavorable aggregates, driving the search for better solvents. Here, we study the solvation of cyclodextrin in deep eutectic solvents (DESs), environmentally friendly media that possess unique properties. We focus on reline, the DES formed from choline chloride and urea, and resolve the mechanism through which its constituents elevate β-cyclodextrin solubility in hydrated solutions compared to pure water or dry reline. Combining experiments and simulations, we determine that the remarkable solubilization of β-cyclodextrin in hydrated reline is mostly due to the inclusion of urea inside β-cyclodextrin’s cavity and at its exterior surfaces. The role of choline chloride in further increasing solvation is twofold. First, it increases urea’s solubility beyond the saturation limit in water, ultimately leading to much higher β-cyclodextrin solubility in hydrated reline in comparison to aqueous urea solutions. Second, choline chloride increases urea’s accumulation in β-cyclodextrin’s vicinity. Specifically, we find that the accumulation of urea becomes stronger at high reline concentrations, as the solution transitions from reline-in-water to water-in-reline, where water alone cannot be regarded as the solvent. Simulations further suggest that in dry DES, the mechanism of β-cyclodextrin solvation changes so that reline acts as a quasi-single component solvent that lacks preference for the accumulation of urea or choline chloride around β-cyclodextrin.

By complexing with hydrophobic compounds, cyclodextrins afford increased solubility and thermodynamic stability to hardly soluble compounds, thereby underlining their invaluable applications in pharmaceutical and other industries. However, common cyclodextrins such as β-cyclodextrin, suffer from limited solubility in water, which often leads to precipitation and formation of unfavorable aggregates, driving the search for better solvents. Here, we study the solvation of cyclodextrin in deep eutectic solvents (DESs), environmentally friendly media that possess unique properties. We focus on reline, the DES formed from choline chloride and urea, and resolve the mechanism through which its constituents elevate β-cyclodextrin solubility in hydrated solutions compared to pure water or dry reline. Combining experiments and simulations, we determine that the remarkable solubilization of β-cyclodextrin in hydrated reline is mostly due to the inclusion of urea inside β-cyclodextrin’s cavity and at its exterior surfaces. The role of choline chloride in further increasing solvation is twofold. First, it increases urea’s solubility beyond the saturation limit in water, ultimately leading to much higher β-cyclodextrin solubility in hydrated reline in comparison to aqueous urea solutions. Second, choline chloride increases urea’s accumulation in β-cyclodextrin’s vicinity. Specifically, we find that the accumulation of urea becomes stronger at high reline concentrations, as the solution transitions from reline-in-water to water-in-reline, where water alone cannot be regarded as the solvent. Simulations further suggest that in dry DES, the mechanism of β-cyclodextrin solvation changes so that reline acts as a quasi-single component solvent that lacks preference for the accumulation of urea or choline chloride around β-cyclodextrin.

 

Cyclodextrin in DES

Garfagnini, Tommaso, Yael Levi-Kalisman, Daniel Harries, and Assaf Friedler. “Osmolytes and crowders regulate aggregation of the cancer-related L106R mutant of the Axin protein.” Biophysical J. 120, no. 16 (2021): 3455-3469. Publisher's VersionAbstract

Protein aggregation is involved in a variety of diseases, including neurodegenerative diseases and cancer. The cellular environment is crowded by a plethora of cosolutes comprising small molecules and biomacromolecules at high concentrations, which may influence the aggregation of proteins in vivo. To account for the effect of cosolutes on cancer-related protein aggregation, we studied their effect on the aggregation of the cancer-related L106R mutant of the Axin protein. Axin is a key player in the Wnt signaling pathway, and the L106R mutation in its RGS domain results in a native molten globule that tends to form native-like aggregates. This results in uncontrolled activation of the Wnt signaling pathway, leading to cancer. We monitored the aggregation process of Axin RGS L106R in vitro in the presence of a wide ensemble of cosolutes including polyols, amino acids, betaine and polyethylene glycol (PEG) crowders. Except myo-inositol, all polyols decreased RGS L106R aggregation, with carbohydrates exerting the strongest inhibition. Conversely, betaine and PEGs enhanced aggregation. These results are consistent with the reported effects of osmolytes and crowders on the stability of molten globular proteins and with both amorphous and amyloid aggregation mechanisms. We suggest a model of Axin L106R aggregation in vivo, whereby molecularly small osmolytes keep the protein as a free solublemolecule but the increased crowding of the bound state by macromolecules induces its aggregation at the nano-scale. To our knowledge, this is the first systematic study on the effect of osmolytes and crowders on a process of native-like aggregation involved in pathology, as it sheds light on the contribution of cosolutes to the onset of cancer as a protein misfolding disease, and on the relevance of aggregation in the molecular aetiology of cancer.

osmolyte-protein

Shakhman, Y., and D. Harries. “How Glycine Betaine Modifies Lipid Membrane Interactions.” ChemSystemsChem 3 (2021): e2100010. Publisher's VersionAbstract

Ubiquitous in the cellular milieu, small organic compounds termed osmolytes help to regulate the response to environmental stress. Elasmobranchii, such as sharks, accumulate high concentrations of several osmolytes, most notably urea, trimethylamine N‐oxide (TMAO), and glycine betaine (GB). These three compounds are used to osmoregulate the organism's body fluids, so that they counteract seawater salinity, as well as the destabilizing effects of hydrostatic pressure on cells and their molecular components. Herein we focus on glycine betaine and show how it modifies interactions between lipid membranes. We find that the addition of GB exerts an apparent attractive force that draws neighboring membranes toward one another. We show that, at the molecular level, this apparent attraction between membranes in the presence of GB is due to its preferential exclusion from the space between adjacent membranes, which thereby exerts an osmotic pressure that brings membranes closer together. This action is similar to the one we have previously reported for TMAO. However, we find that the net effect of GB is significantly smaller than that of TMAO, because GB concomitantly significantly weakens van der Waals attractions between membranes by changing the dielectric properties of the intervening solution. Finally, we show how GB acts in combination with urea. At high total concentrations and over a wide range of GB‐to‐urea ratios, urea counteracts the effect of GB, so that the equilibrium separation between membranes is close to their values in pure water. This finding supports the prevailing idea that mixtures of several osmolytes can achieve minimal net impact on biomacromolecular stability while also counteracting osmotic stress.

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2020
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.

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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.

 

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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

 

 

 

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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.

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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.

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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.

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2019
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

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2018
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

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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.

2017
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

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