Membrane potential and dynamics in a ternary lipid mixture: insights from molecular dynamics simulations

Water and ions in electrified silica nano-pores: a molecular dynamics study

Solid-liquid interfaces (SLIs) are ubiquitous in science and technology from the development of energy storage devices to the chemical reactions occurring in the biological milieu. In systems involving aqueous saline solutions as the liquid, both the water and the ions are routinely exposed to an electric field, whether the field is externally applied, or originating from the natural surface charges of the solid. In the current study a molecular dynamics (MD) framework is developed to study the effect of an applied voltage on the behaviour of ionic solutions located in a ∼7 nm pore between two uncharged hydrophilic silica slabs. We systematically investigate the dielectric properties of the solution and the organisation of the water and ions as a function of salt concentration. In pure water, the interplay between interfacial hydrogen bonds and the applied field can induce a significant reorganisation of the water orientation and densification at the interface. In saline solutions, at low concentrations and voltages the interface dominates the whole system due to the extended Debye length resulting in a dielectric constant lower than that for the bulk solution. An increase in salt concentration or voltage brings about more localized interfacial effects resulting in dielectric properties closer to that of the bulk solution. This suggests the possibility of tailoring the system to achieve the desired dielectric properties. For example, at a specific salt concentration, interfacial effects can locally increase the dielectric constant, something that could be exploited for energy storage.

Dynamics of an aqueous suspension of short hyaluronic acid chains near a DPPC bilayer

The synergy between hyaluronic acid (HA) and lipid molecules plays a crucial role in synovial fluids, cell coatings, etc. Diseased cells in cancer and arthritis show changes in HA concentration and chain size, impacting the viscoelastic and mechanical properties of the cells. Although the solution behavior of HA is known in experiments, a molecular-level understanding of the role of HA in the dynamics at the interface of HA-water and the cellular boundary is lacking. Here, we perform atomistic molecular dynamics simulation of short HA chains in an explicit water solvent in the presence of a DPPC bilayer, relevant in pathological cases. We identify a stable interface between HA-water and the bilayer where the water molecules are in contact with the bilayer and the HA chains are located away without any direct contact. Both translation and rotation of the interfacial waters in contact with the lipid bilayer and translation of the HA chains exhibit subdiffusive behavior. The diffusive behavior sets in slightly away from the bilayer, where the diffusion coefficients of water and HA decrease monotonically with increase in HA concentration. On the contrary, the dependence on HA chain size is only marginal due to enhanced chain flexibility as their size increases.

Membrane Domain Anti-Registration Induces an Intrinsic Transmembrane Potential

Plasma membrane segregation into various nanoscale membrane domains is driven by distinct interactions between diverse lipids and proteins. Among them, liquid-ordered (Lo) membrane domains are defined as "lipid rafts" and liquid-disordered (Ld) ones as "lipid non-rafts". Using model membrane systems, both intra-leaflet and inter-leaflet dynamics of these membrane domains are widely studied. Nevertheless, the biological impact of the latter, which is accompanied by membrane domain registration/anti-registration, is far from clear. Hence, in this work, we studied the biological relevance of the membrane domain anti-registration using both all-atom molecular dynamics (MD) simulations and confocal fluorescence microscopy. All-atom MD simulations suggested an intrinsic transmembrane potential for the case of the membrane anti-registration (Lo/Ld). Meanwhile, confocal fluorescence microscopy experiments of HeLa and 293T cell lines indicated that membrane cholesterol depletion could significantly alter the transmembrane potential of cells. Considering differences in the cholesterol content between Lo and Ld membrane domains, our confocal fluorescence microscopy experiments are consistent with our all-atom MD simulations. In short, membrane domain anti-registration induces local membrane asymmetry and, thus, an intrinsic transmembrane potential.

Studying the roles of salt ions in the pore initiation and closure stages in the biomembrane electroporation

Electroporation shows great potential in biology and biomedical applications. However, there is still a lack of reliable protocol for cell electroporation to achieve a high perforation efficiency due to the unclear influence mechanism of various factors, especially the salt ions in buffer solution. The tiny membrane structure of a cell and the electroporation scale make it difficult to monitor the electroporation process. In this study, we used both molecular dynamics (MD) simulation and experimental methods to explore the influence of salt ions on the electroporation process. Giant unilamellar vesicles (GUVs) were constructed as the model, and sodium chloride (NaCl) was selected as the representative salt ion in this study. The results show that the electroporation process follows lag-burst kinetics, where the lag period first appears after applying the electric field, followed by a rapid pore expansion. For the first time, we find that the salt ion plays opposite roles in different stages of the electroporation process. The accumulation of salt ions near the membrane surface provides an extra potential to promote the pore initiation, while the charge screening effect of the ions within the pore increases the line tension of the pore to induce the instability of the pore and lead to the closure. The GUV electroporation experiments obtain qualitatively consistent results with MD simulations. This work can provide guidance for the selection of parameters for cell electroporation process.

Molecular View on the Impact of DHA Molecules on the Physical Properties of a Model Cell Membrane

Docosahexaenoic acid (DHA) is a ω-3 polyunsaturated fatty acid, which can be uptaken by cells and is essential for proper neuronal and retinal function. However, the detailed physical impact of DHA molecules on the plasma membrane is still unclear. Hence, in this work, we carried out μs-scale coarse-grained molecular dynamics (MD) simulations to reveal the interactions between DHA molecules and a model cell membrane. As is known, the cell membrane can segregate into liquid-ordered (L_o) and liquid-disordered (L_d) membrane domains due to the differential interactions between lipids and proteins. In order to capture this feature, we adopted the three-component phase-separated lipid membranes and considered both anionic and neutral DHA molecules in the current work. Our results showed that DHA molecules can spontaneously self-assemble into nanoclusters, fuse with lipid membranes, and localize preferably in L_d membrane domains. During the membrane fusion process, DHA molecules can change the intrinsic transmembrane potential of the lipid membrane, and the effects of anionic DHA molecules are much more significant. Besides, the presence of DHA molecules mainly in the L_d membrane domains could regulate the differences in the lipid chain order, membrane thickness, cholesterol preference, and cholesterol flip-flop basically in a concentration-dependent manner, which further promote the stability of the intraleaflet dynamics and inhibit the interleaflet dynamics (or promote membrane domain registration) of the membrane domains. In short, the impact of DHA molecules on the physical properties of a model cell membrane on the molecular level revealed in our work will provide useful insights for understanding the biological functions of DHA molecules.

Design of Lipid-Based Nanocarriers via Cation Modulation of Ethanol-Interdigitated Lipid Membranes

Short-chain alcohols (i.e., ethanol) can induce membrane interdigitation in saturated-chain phosphatidylcholines (PCs). In this process, alcohol molecules intercalate between phosphate heads, increasing lateral separation and favoring hydrophobic interactions between opposing acyl chains, which interpenetrate forming an interdigitated phase. Unraveling mechanisms underlying the interactions between ethanol and model lipid membranes has implications for cell biology, biochemistry, and for the formulation of lipid-based nanocarriers. However, investigations of ethanol-lipid membrane systems have been carried out in deionized water, which limits their applicability. Here, using a combination of small- and wide-angle X-ray scattering, small-angle neutron scattering, and all-atom molecular dynamics simulations, we analyzed the effect of varying CaCl₂ and NaCl concentrations on ethanol-induced interdigitation. We observed that while ethanol addition leads to the interdigitation of bulk phase 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers in the presence of CaCl₂ and NaCl regardless of the salt concentration, the ethanol-induced interdigitation of vesicular DPPC depends on the choice of cation and its concentration. These findings unravel a key role for cations in the ethanol-induced interdigitation of lipid membranes in either bulk phase or vesicular form.

Effects of applied surface-tension on membrane-assisted Aβ aggregation

Accumulation of protein-based (Aβ) aggregates on cellular membranes with varying structural properties is commonly recognized as the key step in Alzheimer's pathogenesis. But experimental and computational challenges have made this biophysical characterization difficult. In particular, studies connecting biological membrane organization and Aβ aggregation are limited. While experiments have suggested that an increased membrane curvature results in faster Aβ peptide aggregation in the context of Alzheimer's disease, a mechanistic explanation for this relation is missing. In this work, we are leveraging molecular simulations with a physics-based coarse grained model to address and understand the relationships between curved cellular membranes and aggregation of a model template peptide Aβ 16-22. In agreement with experimental results, our simulations also suggest a positive correlation between increased peptide aggregation and membrane curvature. More curved membranes have higher lipid packing defects that engage peptide hydrophobic groups and promote faster diffusion leading to peptide fibrillar structures. In addition, we curated the effects of peptide aggregation on the membrane's structure and organization. Interfacial peptide aggregation results in heterogeneous headgroup-peptide interactions and an induced crowding effect at the lipid headgroup region, leading to a more ordered headgroup region and disordered lipid-tails at the membrane core. This work presents a mechanistic and morphological overview of the relationships between the biomembrane local structure and organization, and Aβ peptide aggregation.

Dehydration induced dynamical heterogeneity and ordering mechanism of lipid bilayers

Understanding the influence of dehydration on the membrane structure is crucial to control membrane functionality related to domain formation and cell fusion under anhydrobiosis conditions. To this end, we perform all-atom molecular dynamic simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dimyristoylphosphatidylcholine lipid membranes at different hydration levels at 308 K. As dehydration increases, the lipid area per head group decreases with an increase in bilayer thickness and lipid order parameters indicating bilayer ordering. Concurrently, translational and rotational dynamics of interfacial water (IW) molecules near membranes slow down. On the onset of bilayer ordering, the IW molecules exhibit prominent features of dynamical heterogeneity evident from non-Gaussian parameters and one-dimensional van Hove correlation functions. At a fully hydrated state, diffusion constants (D) of the IW follow a scaling relation, D∼τ_α ^-1, where the α relaxation time (τ_α) is obtained from self-intermediate scattering functions. However, upon dehydration, the relation breaks and the D of the IW follows a power law behavior as D∼τ_α ^-0.57, showing the signature of glass dynamics. τ_α and hydrogen bond lifetime calculated from intermittent hydrogen bond auto-correlation functions undergo a similar crossover in association with bilayer ordering on dehydration. The bilayer ordering is accompanied with an increase in fraction of caged lipids spanned over the bilayer surface and a decrease in fraction of mobile lipids due to the non-diffusive dynamics. Our analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity. The fundamental understanding from this study can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature.

Binding of Inhibitors to BACE1 Affected by pH-Dependent Protonation: An Exploration from Multiple Replica Gaussian Accelerated Molecular Dynamics and MM-GBSA Calculations

To date, inhibiting the activity of β-amyloid cleaving enzyme 1 (BACE1) has been considered an efficient approach for treating Alzheimer's disease (AD). In the current work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations and the molecular mechanics general Born surface area (MM-GBSA) method were combined to investigate the effect of pH-dependent protonation on the binding of the inhibitors CS9, C6U, and 6WE to BACE1. Dynamic analyses based on the MR-GaMD trajectory show that pH-dependent protonation strongly affects the structural flexibility, correlated motions, and dynamic behavior of inhibitor-bound BACE1. According to the constructed free energy profiles, in the protonated state at low pH, inhibitor-bound BACE1 tends to populate at more conformations than in high pH. The binding free energies calculated by MM-GBSA suggest that inhibitors possess stronger binding abilities under the protonation conditions at high pH than under the protonation conditions at low pH. Moreover, pH-dependent protonation exerts a significant effect on the hydrogen bonding interactions of CS9, C6U, and 6WE to BACE1, which correspondingly alters the binding abilities of the three inhibitors to BACE1. Furthermore, in different protonated environments, three inhibitors share common interaction clusters and similar binding sites in BACE1, which are reliably used as efficient targets for the design of potent inhibitors of BACE1.

Transmembrane potential of physiologically relevant model membranes: Effects of membrane asymmetry

Transmembrane potential difference (V_m) plays important roles in regulating various biological processes. At the macro level, V_m can be experimentally measured or calculated using the Nernst or Goldman-Hodgkin-Katz equation. However, the atomic details responsible for its generation and impact on protein and lipid dynamics still need to be further elucidated. In this work, we performed a series of all-atom molecular dynamics (MD) simulations of symmetric model membranes of various lipid compositions and cation contents to evaluate the relationship between membrane asymmetry and V_m. Specifically, we studied the impact of the asymmetric distribution of POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine), PIP2 (phosphatidylinositol 4,5-bisphosphate), as well as Na⁺ and K⁺ on V_m using atomically detailed MD simulations of symmetric model membranes. The results suggest that, for an asymmetric POPC-POPC/POPS bilayer in the presence of NaCl, the presence of the monovalent anionic lipid POPS in the inner leaflet polarizes the membrane (ΔV_m < 0). Intriguingly, replacing a third of the POPS lipids by the polyvalent anionic signaling lipid PIP2 counteracts this effect, resulting in a smaller negative membrane potential. We also found that replacing Na⁺ ions in the inner region by K⁺ depolarizes the membrane (ΔV_m > 0). These divergent effects arise from variations in the strength of cation-lipid interactions and are correlated with changes in lipid chain order and head-group orientation.

Dynamic coupling of a hydration layer to a fluid phospholipid membrane: intermittency and multiple time-scale relaxations

Understanding the coupling of a hydration layer and a lipid membrane is crucial to gaining access to membrane dynamics and understanding its functionality towards various biological processes.