OrganL: Dynamic triangulation of biomembranes using curved elements.

We describe a method for simulating biomembranes of arbitrary shape. In contrast to other dynamically triangulated surface (DTS) algorithms, our method provides a rich, quasi-tangent-continuous, yet local description of the surface. We use curved Nagata triangles, which we generalize to cubic order to achieve the requisite flexibility. The resulting interpolation can be constructed locally without iterations, at the cost of having only approximate tangent continuity away from the vertices. This allows us to provide a parallelized and fine-tuned Monte Carlo implementation. As a first example of the potential benefits of the enhanced description, our method supports inhomogeneous lipid distributions as well as lipid mixing. It also supports restraints and constraints of various types and is constructed to be as easily extensible as possible. We validate the approach by testing its numerical accuracy, followed by reproducing the known Helfrich solutions for shapes with rotational symmetry. Finally, we present some example applications, including curvature-driven demixing and stylized effects of proteins. Input files for these examples, as well as the implementation itself, are freely available for researchers under the name OrganL (https://zenodo.org/doi/10.5281/zenodo.11204709).

Mitochondrial membrane model: Lipids, elastic properties, and the changing curvature of cardiolipin.

Mammalian and Drosophila melanogaster model mitochondrial membrane compositions are constructed from experimental data. Simplified compositions for inner and outer mitochondrial membranes are provided, including an asymmetric inner mitochondrial membrane. We performed atomistic molecular dynamics simulations of these membranes and computed their material properties. When comparing these properties to those obtained by extrapolation from their constituting lipids, we find good overall agreement. Finally, we analyzed the curvature effect of cardiolipin, considering ion concentration effects, oxidation, and pH. We draw the conclusion that cardiolipin-negative curvature is most likely due to counterion effects, such as cation adsorption, in particular of H3O+. This oft-neglected effect might account for the puzzling behavior of this lipid.

Modulation of Anionic Lipid Bilayers by Specific Interplay of Protons and Calcium Ions.

Biomembranes, important building blocks of living organisms, are often exposed to large local fluctuations of pH and ionic strength. To capture changes in the membrane organization under such harsh conditions, we investigated the mobility and hydration of zwitterionic and anionic lipid bilayers upon elevated H3O+ and Ca2+ content by the time-dependent fluorescence shift (TDFS) technique. While the zwitterionic bilayers remain inert to lower pH and increased calcium concentrations, anionic membranes are responsive. Specifically, both bilayers enriched in phosphatidylserine (PS) and phosphatidylglycerol (PG) become dehydrated and rigidified at pH 4.0 compared to at pH 7.0. However, their reaction to the gradual Ca2+ increase in the acidic environment differs. While the PG bilayers exhibit strong rehydration and mild loosening of the carbonyl region, restoring membrane properties to those observed at pH 7.0, the PS bilayers remain dehydrated with minor bilayer stiffening. Molecular dynamics (MD) simulations support the strong binding of H3O+ to both PS and PG. Compared to PS, PG exhibits a weaker binding of Ca2+ also at a low pH.

Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli.

The bacterial division apparatus catalyses the synthesis and remodelling of septal peptidoglycan (sPG) to build the cell wall layer that fortifies the daughter cell poles. Understanding of this essential process has been limited by the lack of native three-dimensional views of developing septa. Here, we apply state-of-the-art cryogenic electron tomography (cryo-ET) and fluorescence microscopy to visualize the division site architecture and sPG biogenesis dynamics of the Gram-negative bacterium Escherichia coli. We identify a wedge-like sPG structure that fortifies the ingrowing septum. Experiments with strains defective in sPG biogenesis revealed that the septal architecture and mode of division can be modified to more closely resemble that of other Gram-negative (Caulobacter crescentus) or Gram-positive (Staphylococcus aureus) bacteria, suggesting that a conserved mechanism underlies the formation of different septal morphologies. Finally, analysis of mutants impaired in amidase activation (ΔenvC ΔnlpD) showed that cell wall remodelling affects the placement and stability of the cytokinetic ring. Taken together, our results support a model in which competition between the cell elongation and division machineries determines the shape of cell constrictions and the poles they form. They also highlight how the activity of the division system can be modulated to help generate the diverse array of shapes observed in the bacterial domain.

Calcium Ions Promote Membrane Fusion by Forming Negative-Curvature Inducing Clusters on Specific Anionic Lipids.

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.

Bridges of Calcium Bicarbonate Tightly Couple Dipolar Lipid Membranes.

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 report on 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 dynamics 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, lipid molecules and adsorbed ions were arranged in a two-dimensional oblique lattice.

Heterogeneous Electrofreezing of Super-Cooled Water on Surfaces of Pyroelectric Crystals is Triggered by Trigonal Planar Ions.

Electrofreezing experiments of super-cooled water (SCW) with different ions, performed directly on the charged hemihedral faces of pyroelectric LiTaO3 and AgI crystals, in the presence and in the absence of pyroelectric charge are reported. It is demonstrated that bicarbonate (HCO3 - ) ions elevate the icing temperature near the positively charged faces. In contrast, the hydronium (H3 O+ ) slightly reduces the icing temperature. Molecular dynamics simulations suggest that the hydrated trigonal planar HCO3 - ions self-assemble with water molecules near the surface of the AgI crystal as clusters of slightly different configuration from those of the ice-like hexagons. These clusters, however, have a tendency to serve as embryonic nuclei for ice crystallization. Consequently, we predicted and experimentally confirmed that the trigonal planar ions of NO3 - and guanidinium (Gdm+ ), at appropriate concentrations, elevate the icing temperature near the positive and negative charged surfaces, respectively. On the other hand, the Cl- and SO4 2- ions of different configurations reduce the icing temperature.

Confinement in Nanodiscs Anisotropically Modifies Lipid Bilayer Elastic Properties.

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 nonlocal 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 it allows quantification of the bending rigidity (KC) and tilt modulus (κt) on a local scale even for finite, nonperiodic 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.

How Sugars Modify Caffeine Self-Association and Solubility: Resolving a Mechanism of Selective Hydrotropy.

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.

Arginine-rich cell-penetrating peptides induce membrane multilamellarity and subsequently enter via formation of a fusion pore.

Arginine-rich cell-penetrating peptides do not enter cells by directly passing through a lipid membrane; they instead passively enter vesicles and live cells by inducing membrane multilamellarity and fusion. The molecular picture of this penetration mode, which differs qualitatively from the previously proposed direct mechanism, is provided by molecular dynamics simulations. The kinetics of vesicle agglomeration and fusion by an iconic cell-penetrating peptide-nonaarginine-are documented via real-time fluorescence techniques, while the induction of multilamellar phases in vesicles and live cells is demonstrated by a combination of electron and fluorescence microscopies. This concert of experiments and simulations reveals that the identified passive cell penetration mechanism bears analogy to vesicle fusion induced by calcium ions, indicating that the two processes may share a common mechanistic origin.

H-Aggregation Effects between π-Conjugated Chromophores in Cofacial Dimers and Trimers: Comparison of Theory and Single-Molecule Experiment.

Excited-state interchromophoric couplings in π-conjugated polymers present a daunting challenge to study as their spectroscopic signatures are difficult to separate from structure-dependent intrachromophoric spectral characteristics. Using custom-designed molecular model systems in combination with single-molecule spectroscopy, a controlled coupling of the excited states between cofacially arranged π-conjugated oligomers is shown to be possible. Multiscale molecular dynamics simulations allow us to generate a representative ensemble of molecular structures of the model molecule embedded in a polymer matrix and examine the connection between structural fluctuations of the molecule with theoretically predicted and measured spectral signatures. The single molecules in the embedding matrix polymer can be assigned to specific conformational features with the help of computer-based "virtual spectroscopy". By combining a quantum chemical approach with an analytical approach, we show that the coupling between the chromophores is well-described by transition dipole coupling above an interchromophoric separation of ∼4.5 Å. Even for aligned chromophores, however, twisting between repeat units of the π-system and bending of the individual π-systems can lead to a decoupling of the chromophores to a degree far beyond what their equilibrium structures would suggest: tiny displacements of the molecular constituents can dramatically impact excited-state interactions. This observation has profound implications for the design of future tunable organic optoelectronic materials.

Arginine "Magic": Guanidinium Like-Charge Ion Pairing from Aqueous Salts to Cell Penetrating Peptides.

It is a textbook knowledge that charges of the same polarity repel each other. For two monovalent ions in the gas phase at a close contact this repulsive interaction amounts to hundreds of kilojoules per mole. In aqueous solutions, however, this Coulomb repulsion is strongly attenuated by a factor equal to the dielectric constant of the medium. The residual repulsion, which now amounts only to units of kilojoules per mole, may be in principle offset by attractive interactions. Probably the smallest cationic pair, where a combination of dispersion and cavitation forces overwhelms the Coulomb repulsion, consists of two guanidinium ions in water. Indeed, by a combination of molecular dynamics with electronic structure calculations and electrophoretic, as well as spectroscopic, experiments, we have demonstrated that aqueous guanidinium cations form (weakly) thermodynamically stable like-charge ion pairs. The importance of pairing of guanidinium cations in aqueous solutions goes beyond a mere physical curiosity, since it has significant biochemical implications. Guanidinium chloride is known to be an efficient and flexible protein denaturant. This is due to the ability of the orientationally amphiphilic guanidinium cations to disrupt various secondary structural motifs of proteins by pairing promiscuously with both hydrophobic and hydrophilic groups, including guanidinium-containing side chains of arginines. The fact that the cationic guanidinium moiety forms the dominant part of the arginine side chain implies that the like-charge ion pairing may also play a role for interactions between peptides and proteins. Indeed, arginine-arginine pairing has been frequently found in structural protein databases. In particular, when strengthened by a presence of negatively charged glutamate, aspartate, or C-terminal carboxylic groups, this binding motif helps to stabilize peptide or protein dimers and is also found in or near active sites of several enzymes. The like-charge pairing of the guanidinium side-chain groups may also hold the key to the understanding of the arginine "magic", that is, the extraordinary ability of arginine-rich polypeptides to passively penetrate across cellular membranes. Unlike polylysines, which are also highly cationic but lack the ease in crossing membranes, polyarginines do not exhibit mutual repulsion. Instead, they accumulate at the membrane, weaken it, and might eventually cross in a concerted, "train-like" manner. This behavior of arginine-rich cell penetrating peptides can be exploited when devising smart strategies how to deliver in a targeted way molecular cargos into the cell.

Orientation-Induced Adsorption of Hydrated Protons at the Air-Water Interface.

The surface tension of the air-water interface increases upon addition of inorganic salts, implying a negative surface excess of ionic species. Most acids, however, induce a decrease in surface tension, indicating a positive surface excess of hydrated protons. In combination with the apparent negative charge at pure air-water interfaces derived from electrokinetic experiments, this experimental observation has been a source of intense debate since the mid-19th century. Herein, we calculate surface tensions and ionic surface propensities at air-water interfaces from classical, thermodynamically consistent molecular dynamics simulations. The surface tensions of NaOH, HCl, and NaCl solutions show outstanding quantitative agreement with experiment. Of the studied ions, only H3 O+ adsorbs to the air-water interface. The adsorption is explained by the deep potential well caused by the orientation of the H3 O+ dipole in the interfacial electric field, which is confirmed by ab initio simulations.

Increased Binding of Calcium Ions at Positively Curved Phospholipid Membranes.

Calcium ion is the ubiquitous messenger in cells and plays a key role in neuronal signaling and fusion of synaptic vesicles. These vesicles are typically ∼20-50 nm in diameter, and thus their interaction with calcium ions cannot be modeled faithfully with a conventional flat membrane bilayer setup. Within our newly developed molecular dynamics simulations setup, we characterize here interactions of the calcium ion with curved membrane interfaces with atomistic detail. The present molecular dynamics simulations together with time-dependent fluorescence shift experiments suggest that the mode and strength of interaction of calcium ion with a phospholipid bilayer depends on its curvature. Potential of mean force calculations demonstrate that the binding of calcium ion to the positively curved side of the bilayer is significantly stronger compared with that to a flat membrane.

Dynamical Dimension to the Hofmeister Series: Insights from First-Principles Simulations.

A systematic characterization of the competing kosmotropic and chaotropic effects of a series of divalent salts on the aqueous H-bonding structure by means of first-principles molecular dynamics simulations is presented. The structural properties are quantified by means of experimental and computed (1) H NMR chemical shifts, whereby the local environments of cations and anions can be discriminated. Complementary to the well-established structural features, a dynamical aspect is added to the concept of kosmotropes and chaotropes. The H-bond dynamics, quantified in terms of the H-bonding autocorrelation functions, shows a good correlation with the structural kosmotropic and chaotropic modifications, which are commonly referred to as the Hofmeister series. The considerably enhanced (reduced) fluctuations of the H-bonding network in the hydration shells around the anions (cations) are a complementary dynamical dimension to the concept of kosmotropic/chaotropic behavior of solvated ions.

Guanidinium Pairing Facilitates Membrane Translocation.

Ab initio free energy calculations of guanidinium pairing in aqueous solution confirm the counterintuitive conjecture that the like-charge ion pair is thermodynamically stable. Transferring the guanidinium pair to the inside of a POPC lipid bilayer, like-charge ion pairing is found to occur also inside the membrane defect. It is found to contribute to the nonadditivity of ion transfer, thereby facilitating the presence of ions inside the bilayer. The effect is quantified by free energy decomposition and comparison with ammonium ions, which do not form a stable pair. The presence of two charges inside the center of the bilayer leads to the formation of a pore. Potential consequences for cell penetrating peptides and ion conduction are drawn.

Water wires in aqueous solutions from first-principles calculations.

We elucidate the concept of water wires in aqueous solutions in view of their structural and dynamical properties by means of first-principles molecular dynamics simulations. We employ a specific set of hydroxyquinoline derivatives (heteroaromatic fluorescent dyes) as probe molecules that provide a well-defined initial and final coordinate for possible water wires by means of their photoacid and photobase functionalities. Besides the geometric structure of the hydrogen bond network connecting these functional sites, we focus on the dependence of the length of the resulting water wire on the initial/final coordinates determined by the chromophore. Special attention is devoted to the persistence of the wires on the picosecond time scale and their capability of shifting the nature of the proton transfer process from a concerted to a stepwise mechanism. Our results shed light on the long debate on whether water wires represent characteristic structural motifs or transient phenomena.

Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system.

We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.

Palladium complexes with chelating bis-NHC ligands in the Mizoroki-Heck reaction­mechanism and electronic effects, a DFT study.

Experimental results have shown that palladium complexes with chelating aryl- and alkyl-substituted bis-NHC ligands, including [(H3C-Im)2CH2]PdBr2, [(C6H5-Im)2CH2]PdBr2, and [(H3CO-C6H4-Im)2CH2]PdBr2 are excellent catalysts for the Mizoroki-Heck reaction. To better understand and improve the catalysts, a density functional theory (DFT) study of the Heck reaction has been performed at the B3LYP/6-31G* level of theory, complemented by M06/def2-TZVP single-point calculations. Different mechanistic pathways have been investigated and compared to available experimental results. The most likely mechanism is a cationic catalytic cycle involving the palladium oxidation states 0 and +II. We also looked at other oxidation states, but on the basis of the calculated Gibbs free energy a +II/+IV mechanism can be excluded. Aryl substitution with electron-donating groups at the para position (e.g., the methoxy group in [(H3CO-C6H4-Im)2CH2]PdBr2) was found to reduce the reaction barrier of the rate-determining step. This is in agreement with the experimental findings for the catalysts. The experimentally observed cis selectivity could also be explained by the DFT study.

Ab initio H2O in realistic hydrophilic confinement.

A protocol for the ab initio construction of a realistic cylindrical pore in amorphous silica, serving as a geometric nanoscale confinement for liquids and solutions, is presented. Upon filling the pore with liquid water at different densities, the structure and dynamics of the liquid inside the confinement can be characterized. At high density, the pore introduces long-range oscillations into the water density profile, which makes the water structure unlike that of the bulk across the entire pore. The tetrahedral structure of water is also affected up to the second solvation shell of the pore wall. Furthermore, the effects of the confinement on hydrogen bonding and diffusion, resulting in a weakening and distortion of the water structure at the pore walls and a slowdown in diffusion, are characterized.