Tetraspanner-based nanodomains modulate BAR domain-induced membrane curvature.

The topography of biological membranes is critical for formation of protein and lipid microdomains. One prominent example in the yeast plasma membrane (PM) are BAR domain-induced PM furrows. Here we report a novel function for the Sur7 family of tetraspanner proteins in the regulation of local PM topography. Combining TIRF imaging, STED nanoscopy, freeze-fracture EM and membrane simulations we find that Sur7 tetraspanners form multimeric strands at the edges of PM furrows, where they modulate forces exerted by BAR domain proteins at the furrow base. Loss of Sur7 tetraspanners or Sur7 displacement due to altered PIP2 homeostasis leads to increased PM invagination and a distinct form of membrane tubulation. Physiological defects associated with PM tubulation are rescued by synthetic anchoring of Sur7 to furrows. Our findings suggest a key role for tetraspanner proteins in sculpting local membrane domains. The maintenance of stable PM furrows depends on a balance between negative curvature at the base which is generated by BAR domains and positive curvature at the furrows' edges which is stabilized by strands of Sur7 tetraspanners.

Electron transfer reaction of TEMPO-based organic radical batteries in different solvent environments: comparing quantum and classical approaches.

In this study, we delve into the complex electron transfer reactions associated with the redox-active (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO), a common component in organic radical batteries (ORBs). Our approach estimates quantum electron-transfer (ET) energies using Density Functional Theory (DFT) calculations by sampling from structures simulated classically. This work presents a comparative study of reorganization energies in ET reactions across different solvents. Furthermore, we investigate how changes in the electrolyte environment can modify the reorganization energy and, consequently, impact ET dynamics. We also explore the relationship between classical and quantum vertical energies using linear regression models. Importantly, this comparison between quantum and classical vertical energies underscores the role of quantum effects, like charge delocalization, in offering added stabilization post-redox reactions. These effects are not adequately represented by the classical vertical energy distribution. Our study shows that, although we find a significant correlation between the vertical energies computed by DFT and the classical force field, the regression parameters depend on the solvent, highlighting that classical methods should be benchmarked by DFT before applying them to novel electrolyte materials.

Photo-Responsive Control of Adsorption and Structure Formation at the Air-Water Interface with Arylazopyrazoles.

Smart interfaces that are responsive to external triggers such as light are of great interest for the development of responsive or adaptive materials and interfaces. Using alkyl-arylazopyrazole butyl sulfonate surfactants (alkyl-AAP) that can undergo E/Z photoisomerization when irradiated with green (E) and UV (Z) lights, we demonstrate through a combination of experiments and computer simulations that there can be surprisingly large changes in surface tension and in the molecular structure and order at air-water interfaces. Surface tensiometry, vibrational sum-frequency generation (SFG) spectroscopy, and neutron reflectometry (NR) are applied to the study of custom-synthesized AAP surfactants with octyl- and H-terminal groups at air-water interfaces as a function of their bulk concentration and E/Z configuration. Upon photoswitching, a drastic influence of the alkyl chain on both the surface activity and the responsiveness of interfacial surfactants is revealed from changes in the surface tension, γ, where the largest changes in γ are observed for octyl-AAP (Δγ ∼ 23 mN/m) in contrast to H-AAP with Δγ < 10 mN/m. Results from vibrational SFG spectroscopy and NR show that the interfacial composition and the molecular order of the surfactants drastically change with E/Z photoisomerization and surface coverage. Indeed, from analysis of the S-O (head group) and C-H vibrational bands (hydrophobic tail), a qualitative analysis of orientational and structural changes of interfacial AAP surfactants is provided. The experiments are complemented by resolution of thermodynamic parameters such as equilibrium constants from ultra-coarse-grained simulations, which also capture details like island formation and interaction parameters of interfacial molecules. Here, the interparticle interaction ("stickiness") and the interaction with the surface are adjusted, closely reflecting experimental conditions.

Systematic analysis of curvature-dependent lipid dynamics in a stochastic 3D membrane model.

To minimize the free energy of the system, lipid membranes display curvature-dependent rearrangements at the local and global scale. The optimal membrane shape is generally approximated by averaging the curvature preference of individual lipids across the whole surface. Potential stress due to imperfections in lipid packing caused by local lipid inhomogeneities, however, is frequently neglected. Here, we developed a stochastic 3D membrane model to investigate the relevance of this parameter for shape-dependent lipid and membrane dynamics. A systematic analysis of the discretized Helfrich type Hamiltonian indicates that stress-energy arising from imperfections in packing is analogous to van der Waals interactions, jointly determining membrane shape and localization of curvature-sensitive lipids based on their relative strengths. Insights from this work can be used to characterize natural and design synthetic agents for membrane-shape changes.

The impact of bilayer composition on the dimerization properties of the Slg1 stress sensor TMD from a multiscale analysis.

The impact of mutual interactions between the transmembrane domains of membrane proteins and lipids on bilayer properties has gained major attraction. Most simulation studies of membranes rely on the Martini force field, which has proven extremely helpful in providing molecular insights into realistic systems. Accordingly, an evaluation of the accuracy of the Martini force field is crucial to be able to correctly interpret the reported data. In this study, we combine atomistic and coarse-grained Martini simulations to investigate the properties of transmembrane domains (TMDs) in a model yeast membrane. The results show that the TMD binding state (monomeric and dimeric with positive or negative crossing angle) and the membrane composition significantly influence the properties around the TMDs and change TMD-TMD and TMD-lipid affinities. Furthermore, ergosterol (ERG) exhibits a strong affinity to TMD dimers. Importantly, the right-handed TMD dimer configuration is stabilized via TMD-TMD contacts by the addition of asymmetric anionic phosphatidylserine (PS). The coarse-grained simulations corroborate many of these findings, with two notable exceptions: a systematic overestimation of TMD-ERG interaction and lack of stabilization of the right-handed TMD dimers with the addition of PS.

Polypropylene carbonate-based electrolytes as model for a different approach towards improved ion transport properties for novel electrolytes.

Linear poly(alkylene carbonates) such as polyethylene carbonate (PEC) and polypropylene carbonate (PPC) have gained increasing interest due to their remarkable ion transport properties such as high Li+ transference numbers. The cause of these properties is not yet fully understood which makes it challenging to replicate them in other polymer electrolytes. Therefore, it is critical to understand the underlying mechanisms in polycarbonate electrolytes such as PPC. In this work we present insights from impedance spectroscopy, transference number measurements, PFG-NMR, IR and Raman spectroscopy as well as molecular dynamics simulations to address this issue. We find that in addition to plasticization, the lithium ion coordination by the carbonate groups of the polymer is weakened upon gelation, leading to a rapid exhange of the lithium ion solvation shell and consequently a strong increase of the conductivity. Moreover, we study the impact of the anions by employing different conducting salts. Interestingly, while the total conductivity decreases with increasing anion size, the reverse trend can be observed for the lithium ion transference numbers. Via our holistic approach, we demonstrate that this behavior can be attributed to differences in the collective ion dynamics.

Mechanistic understanding of the correlation between structure and dynamics of liquid carbonate electrolytes: impact of polarization.

Liquid electrolyte design and modelling is an essential part of the development of improved lithium ion batteries. For mixed organic carbonates (ethylene carbonate (EC) and ethyl-methyl carbonate (EMC) mixtures)-based electrolytes with LiPF6 as salt, we have compared a polarizable force field with the standard non-polarizable force field with and without charge rescaling to model the structural and dynamic properties. The result of our molecular dynamics simulations shows that both polarizable and non-polarizable force fields have similar structural factors, which are also in agreement with X-ray diffraction experimental results. In contrast, structural differences are observed for the lithium neighborhood, while the lithium-anion neighbourhood is much more pronounced for the polarizable force field. Comparison of EC/EMC coordination statistics with Fourier transformed infrared spectroscopy (FTIR) shows the best agreement for the polarizable force field. Also for transport quantities such as ionic conductivities, transference numbers, and viscosities, the agreement with the polarizable force field is by far better for a large range of salt concentrations and EC : EMC ratios. In contrast, for the non-polarizable variants, the dynamics are largely underestimated. The excellent performance of the polarizable force field is explored in different ways to pave the way to a realistic description of the structure-dynamics relationships for a wide range of salt and solvent compositions for this standard electrolyte. In particular, we can characterize the distinct correlation terms between like and unlike ions, relate them to structural properties, and explore to which degree the transport in this electrolyte is mass or charge limited.

Hydrodynamic interactions in ion transport-Theory and simulation.

We present a hydrodynamic theory describing pair diffusion in systems with periodic boundary conditions, thereby generalizing earlier work on self-diffusion [B. Dünweg and K. Kremer, J. Chem. Phys. 99, 6983-6997 (1993) and I.-C. Yeh and G. Hummer, J. Phys. Chem. B 108, 15873-15879 (2004)]. Its predictions are compared with Molecular Dynamics simulations for a liquid carbonate electrolyte and two ionic liquids, for which we characterize the correlated motion between distinct ions. Overall, we observe good agreement between theory and simulation data, highlighting that hydrodynamic interactions universally dictate ion correlations. However, when summing over all ion pairs in the system to obtain the cross-contributions to the total cationic or anionic conductivity, the hydrodynamic interactions between ions with like and unlike charges largely cancel. Consequently, significant conductivity contributions only arise from deviations from a hydrodynamic flow field of an ideal fluid, which is from the local electrolyte structure as well as the relaxation processes in the subdiffusive regime. In the case of ionic liquids, the momentum-conservation constraint additionally is vital, which we study by employing different ionic masses in the simulations. Our formalism will likely also be helpful to estimate finite-size effects of the conductivity or of Maxwell-Stefan diffusivities in simulations.

Wettability gradient-driven droplets with an applied external force.

On homogeneous substrates, droplets can slide due to external driving forces, such as gravity, whereas in the presence of wettability gradients, sliding occurs without external forces since this gradient gives rise to an internal driving force. Here, we study via molecular dynamics simulations the more complex behavior when droplets are driven under the combined influence of an external and internal driving force. For comparison, the limiting cases of a single driving force are studied as well. During a large part of the sliding process over the borderline of both substrates, separating both wettabilities, the velocity is nearly constant. When expressing it as the product of the effective mobility and the effective force, the effective mobility mainly depends on the mobility of the initial substrate, experienced by the receding contact line. This observation can be reconciled with the properties of the flow pattern, indicating that the desorption of particles at the receding contact line is the time-limiting step. The effective force is the sum of the external force and a renormalized internal force. This renormalization can be interpreted as stronger dissipation effects when driving occurs via wettability gradients.

Dynamic Wetting of Photoresponsive Arylazopyrazole Monolayers is Controlled by the Molecular Kinetics of the Monolayer.

Smart surfaces that can change their wettability on demand are interesting for applications such as self-cleaning surfaces or lab-on-a-chip devices. We have synthesized arylazopyrazole (AAP) phosphonic acids as a new class of photoswitchable molecules for functionalization of aluminum oxide surfaces. AAP monolayers were deposited on α-Al2O3(0001) and showed reversible E/Z photoswitching that can trigger contact angle changes of up to ∼10°. We monitored these changes on the macroscopic level by recording the contact angle while the monolayer was switched in situ. On the molecular level, time-dependent vibrational sum-frequency generation (SFG) spectroscopy provided information on the kinetic changes within the AAP monolayer and the characteristic times for E/Z switching. In addition, vibrational SFG at different relative humidity indicates that the thermal stability of the Z configuration is largely influenced by the presence of water which can stabilize the Z state and hinder E → Z switching of the AAP monolayer when it is wetted with H2O. Having established the switching times on the molecular scale, we additionally measured the dynamic contact angle and show that the time scales of the substrate and droplet dynamics can be extracted individually. For that, we report on a relaxation model that is solved analytically and is verified via a comparison with simulations of a Lennard-Jones system and with experimental data. The slower E to Z switching in the presence of the droplet as compared to the vapor phase is rationalized in terms of specific interactions of water with the exposed AAP moieties.

Wetting dynamics under periodic switching on different scales: characterization and mechanisms.

The development of substrates with a switchable wettability is proceeding and the limit of switching frequencies and contact angle differences between substrate states has developed in the past years. In this paper we investigate the behavior of a droplet on a homogeneous substrate, which is switched between two wettabilities for a large range of switching frequencies. Here, we are particularly interested in the dependence of the wetting behavior on the switching frequency. We show that results obtained on the particle level via molecular dynamics simulations and on the continuum level via the thin-film model are consistent. Predictions of simple models as the molecular theory of wetting (MKT) and analytical calculations based on the MKT also show good agreement and offer deeper insights into the underlying mechanisms.

Controlling Li+ transport in ionic liquid electrolytes through salt content and anion asymmetry: a mechanistic understanding gained from molecular dynamics simulations.

In this work, we report the results from molecular dynamics simulations of lithium salt-ionic liquid electrolytes (ILEs) based either on the symmetric bis[(trifluoromethyl)sulfonyl]imide (TFSI-) anion or its asymmetric analogue 2,2,2-(trifluoromethyl)sulfonyl-N-cyanoamide (TFSAM-). Relating lithium's coordination environment to anion mean residence times and diffusion constants confirms the remarkable transport behaviour of the TFSAM--based ILEs that has been observed in recent experiments: for increased salt doping, the lithium ions must compete for the more attractive cyano over oxygen coordination and a fragmented landscape of solvation geometries emerges, in which lithium appears to be less strongly bound. We present a novel, yet statistically straightforward methodology to quantify the extent to which lithium and its solvation shell are dynamically coupled. By means of a Lithium Coupling Factor (LCF) we demonstrate that the shell anions do not constitute a stable lithium vehicle, which suggests for this electrolyte material the commonly termed "vehicular" lithium transport mechanism could be more aptly pictured as a correlated, flow-like motion of lithium and its neighbourhood. Our analysis elucidates two separate causes why lithium and shell dynamics progressively decouple with higher salt content: on the one hand, an increased sharing of anions between lithium limits the achievable LCF of individual lithium-anion pairs. On the other hand, weaker binding configurations naturally entail a lower dynamic stability of the lithium-anion complex, which is particularly relevant for the TFSAM--containing ILEs.

Frame-guided assembly from a theoretical perspective.

The molecular self-assembly of various structures such as micelles and vesicles has been the subject of comprehensive studies. Recently, a new approach to design these structures, the frame-guided assembly, has been developed to progress toward fabrics of predefined shape and size, following an initially provided frame of guiding elements. Here, we study the frame-guided assembly in a two-dimensional membrane via computer simulations based on a single-bead coarse grained surfactant model in continuous space. In agreement with the experiment, the assembly process already starts for surfactant concentrations below the critical micelle concentration. Furthermore, upon increasing temperature, the formation process gets more delocalized. Additionally, the assembly process of the resulting membrane plane is modeled by a lattice gas model. It displays a similar phenomenology but additionally allows for the derivation of analytical mean-field predictions. In this way, a fundamental understanding of frame-guided assembly can be gained.

Influence of the coordination defects on the dynamics and the potential energy landscape of two-dimensional silica.

The main cause of the fragile-to-strong crossover of 3D silica was previously attributed to the presence of a low-energy cutoff in the potential energy landscape. An important question emerges about the microscopic origin of this crossover and its generalizibility to other glass-formers. In this work, the fragile-to-strong crossover of a model two-dimensional (2D) glassy system is analyzed via molecular dynamics simulation, which represents 2D-silica. By separating the sampled defect and defect-free inherent structures, we are able to identify their respective density of state distributions with respect to energy. A low energy cutoff is found in both distributions. It is shown that the fragile-to-strong crossover can be quantitatively related to the parameters of the energy landscape, involving, in particular, the low-energy cutoff of the energy distribution. It is also shown that the low-energy cutoff of the defect-states is determined by the formation energy of a specific defect configuration, involving two silicon and no oxygen defects. The low-temperature behavior of 2D silica is quantitatively compared with that of 3D silica, showing surprisingly similar behavior.

Chain ordering of phospholipids in membranes containing cholesterol: what matters?

Cholesterol (CHOL) drives lipid segregation and is thus a key player for the formation of lipid rafts and followingly for the ability of a cell to, e.g., enable selective agglomeration of proteins. The lipid segregation is driven by cholesterol's affinity for saturated lipids, which stands directly in relation to the ability of cholesterol to order the individual phospholipid (PL) acyl chains. In this work, molecular dynamics simulations of DPPC (dipalmitoylphosphatidylcholine, saturated lipid) and DLiPC (dilineoylphosphatidylcholine, unsaturated lipid) mixtures with cholesterol are used to elucidate the underlying mechanisms of the cholesterol ordering effect. To this end, all enthalpic contributions, experienced by the PL molecules, are recorded as a function of the PL's acyl chain order. This involves the PL-PL, the PL-cholesterol interaction, the interaction of the PLs with water, and the interleaflet interaction. This systematic analysis allows one to unravel differences of saturated and unsaturated lipids in terms of the different interaction factors. It turns out that cholesterol's impact on chain ordering stems not only from direct interactions with the PLs but is also indirectly present in the other energy contributions. Furthermore, the analysis sheds light on the relevance of the entropic contributions, related to the degrees of freedom of the acyl chain.

Stabilization of DPPC lipid bilayers in the presence of co-solutes: molecular mechanisms and interaction patterns.

We study the interactions between dipalmitoylphosphatidylcholine (DPPC) lipid bilayers in the gel and the fluid phase with ectoine, amino ectoine and water molecules by means of atomistic molecular dynamics (MD) simulations and conceptual density functional theory (DFT) calculations. Our results reveal a pronounced preferential exclusion of both co-solutes from the DPPC lipid bilayer which is stronger for the fluid phase. The corresponding outcomes can be brought into relation with the Kirkwood-Buff theory of solutions in order to provide a thermodynamic rationale for the experimentally observed stabilization of the gel phase. Closely related to preferential exclusion of both co-solutes, our simulations also highlight a preferential hydration behavior as manifested by an increased number of hydrogen bonds between water and DPPC molecules. All results are rationalized by conceptual DFT calculations with regard to differences in the electronic properties between ectoine and amino ectoine.

Connecting the quantum and classical mechanics simulation world: Applications of reactive step molecular dynamics simulations.

This article presents the application of the reactive step molecular dynamics simulation method [M. Biedermann, D. Diddens, and A. Heuer, J. Chem. Theory Comput. 17, 1074 (2021)] toward two different atomistic, chemically reactive systems. During reactive steps, transitions from reactant to product molecules are modeled according to physically correct transition probabilities based on quantum chemical information about the reactions such as molecular reaction rates via instant exchange of the employed force field and a subsequent, short relaxation of the structure. In the first application, we study the follow-up reactions of singly reduced ethylene carbonate (EC) radicals in EC solution, first, via extensive ab initio molecular dynamics simulations and, second, with the reactive step algorithm. A direct comparison of both simulation methods shows excellent agreement. Then, we employ the reactive step algorithm to simulate the enolate formation of 2-methylcyclopropanone with the base lithium diisopropylamine. Thereby, we can demonstrate that the reactive step algorithm is also capable of capturing effects from kinetic vs thermodynamic control of chemical reactions during simulation.

Insights into the Microscopic Structure of RNF4-SIM-SUMO Complexes from MD Simulations.

Post-translational modification with one of the isoforms of the small ubiquitin-like modifier (SUMO) affects thousands of proteins in the human proteome. The binding of SUMO to SUMO interacting motifs (SIMs) can translate the SUMOylation event into functional consequences. The E3 ubiquitin ligase RNF4 contains multiple SIMs and connects SUMOylation to the ubiquitin pathway. SIM2 and SIM3 of RNF4 were shown to be the most important motifs to recognize SUMO chains. However, the study of SIM-SUMO complexes is complicated by their typically low affinity and variable binding of the SIMs in parallel and antiparallel orientations. We investigated properties of complexes formed by SUMO3 with peptides containing either SIM2 or SIM3 using molecular dynamics simulations. The affinities of the complexes were determined using a state-of-the-art free energy protocol and were found to be in good agreement with experimental data, thus corroborating our method. Long unrestrained simulations allowed a new interpretation of experimental results regarding the structure of the SIM-SUMO interface. We show that both SIM2 and SIM3 bind SUMO3 in parallel and antiparallel orientations and identified main interaction sites for acidic residues flanking the SIM. We noticed unusual SIM-SUMO interfaces in a previously reported NMR structure (PDB: 2mp2) of a complex formed by a SUMO3 dimer with the bivalent SIM2-SIM3 peptide. Computational determination of the individual SIM-SUMO affinities based on these structural arrangements yielded significantly higher dissociation constants. To our knowledge, our approach adds new opportunities to characterize individual SIM-SUMO complexes and suggests that further studies will be necessary to understand these interactions when occurring in multivalent form.

Molecular barcoding of viral vectors enables mapping and optimization of mRNA trans-splicing.

Genome editing has proven to be highly potent in the generation of functional gene knockouts in dividing cells. In the CNS however, efficient technologies to repair sequences are yet to materialize. Reprogramming on the mRNA level is an attractive alternative as it provides means to perform in situ editing of coding sequences without nuclease dependency. Furthermore, de novo sequences can be inserted without the requirement of homologous recombination. Such reprogramming would enable efficient editing in quiescent cells (e.g., neurons) with an attractive safety profile for translational therapies. In this study, we applied a novel molecular-barcoded screening assay to investigate RNA trans-splicing in mammalian neurons. Through three alternative screening systems in cell culture and in vivo, we demonstrate that factors determining trans-splicing are reproducible regardless of the screening system. With this screening, we have located the most permissive trans-splicing sequences targeting an intron in the Synapsin I gene. Using viral vectors, we were able to splice full-length fluorophores into the mRNA while retaining very low off-target expression. Furthermore, this approach also showed evidence of functionality in the mouse striatum. However, in its current form, the trans-splicing events are stochastic and the overall activity lower than would be required for therapies targeting loss-of-function mutations. Nevertheless, the herein described barcode-based screening assay provides a unique possibility to screen and map large libraries in single animals or cell assays with very high precision.

Solvate ionic liquids based on lithium bis(trifluoromethanesulfonyl)imide-glyme systems: coordination in MD simulations with scaled charges.

Equimolar mixtures of lithium bis(trifluoromethanesulfonyl)imide (Li[NTf2]) with triglyme or tetraglyme (small oligoethers) are regarded as a new class of ionic liquids, the so-called solvate ionic liquids. In these mixtures, the glyme molecules wrap around the lithium ions forming crown-ether like [Li(glyme)1]+ complex cations. New molecular dynamics (MD) simulations suggest that the lithium-glyme coordination is stronger than that predicted in a former MD study [K. Shimizu, et al., Phys. Chem. Chem. Phys., 2015, 17, 22321-22335], whereas lithium-NTf2 connections are weaker. The differences between the present and the previous study arise from different starting conditions. Both studies employed charges scaled by a factor of 0.8. As shown by the comparison of MD simulations with and without reduced charges to experiments, charge scaling is necessary in order to obtain data close to experimental results.