Surface viscosities of lipid bilayers determined from equilibrium molecular dynamics simulations

Molecular Mechanisms of Perfluoroalkyl Substances Integration into Phospholipid Membranes

Understanding the molecular interactions of per- and polyfluoroalkyl substances (PFAS) with phospholipids is crucial for elucidating their pathological mechanisms and developing PFAS remediation strategies. In this study, we employ atomistic molecular dynamics simulations to examine PFAS insertion into phospholipid bilayers, including anionic perfluorooctanesulfonic acid (PFOS), perfluorobutanoic acid (PFBA), perfluorooctanoic acid (PFOA), and perfluorododecanoic acid (PFDoA), as well as neutral polytetrafluoroethylene (PTFE). Our study shows that PFAS insertion into lipid bilayers is driven by the free energy gradient between bulk water and the lipid membrane. Positively charged trimethylammonium groups of phospholipids attract negatively charged PFAS, overcoming the surface hydration barrier. Hydrophobic interactions between PFAS fluoroalkyl tails and lipid chains generate a significant driving force for PFAS reorientation and insertion. The increase in electrostatic potential across the lipid surface aids anionic PFAS insertion, but their dehydration hinders further movement. PFAS insertion enhances membrane ordering and decreases lipid fluidity, potentially affecting cellular functions by modifying membrane rigidity. The extended chain length of PFAS facilitates its interactions with the lipid membrane, resulting in a more pronounced influence on altering its structural and dynamic properties.

Sphingomyelin slows interfacial hydrogen-bonding dynamics in lipid membranes

Interfacial hydrogen bonding (H-bonding) partly determines membrane structure, heterogeneity, and dynamics. Given the chemical diversity of lipids, it is important to understand how composition determines lipid-lipid interactions and how those are translated to H-bond populations and dynamics. Here, we investigate the role of palmitoyl sphingosylphosphorylcholine (PSM) in modulating lipid H-bond networks in combination with dipalmitoyl phosphatidylcholine (DPPC) using ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics simulations. We report composition-dependent H-bond ensembles for ester and amide carbonyls, with increased H-bond populations and slower dynamics with higher PSM concentrations. Specifically, amide carbonyl 2D IR spectra indicate that PSM, acting as an H-bond donor, partially replaces water-mediated interactions, with the number of direct lipid-lipid H-bonds constituting up to 20% of the total. These interactions create comparatively stable H-bond networks that significantly slow interfacial dynamics. 2D IR spectra show an H-bond lifetime slowdown of 45% in an equimolar mixture of the two lipids compared to DPPC alone. This study highlights PSM's dual role in H-bonding, which increases membrane viscosity and stabilizes lipid interfaces, providing molecular insights into the role of sphingolipids in cell membranes. The findings further emphasize the synergy of experimental and computational approaches for extracting molecular-level insights into interfacial lipid-lipid and lipid-water interactions in heterogeneous membranes.

Effects of a Polarizable Force Field on Membrane Dynamics: Surface Viscosity, Lipid Diffusion, and Peptide Induced Pore Formation

The effects of the newly developed CHARMM polarizable lipid force field (FF), Drude2023, on selected lipid dynamical properties are compared with the additive CHARMM36 (C36), and an extension of C36, termed C36/LJ-PME, which includes long-range Lennard-Jones (LJ) interactions. Polarizability and long-range LJ interactions increase the membrane surface viscosity, which decreases the translational diffusion constants. Simulated diffusion constants for dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC) extrapolated to infinite system size agree well with experiment for Drude2023, but overestimate experiment by 60% (on average) and a factor of 2.5 for C36/LJ-PME and C36, respectively. The relaxation time of lipid wobble is described about equally well by C36/LJ-PME and Drude2023, as consistent with the hexadecane viscosity for the FF, and both are more accurate than C36. Hence, physical improvements in the FF, which slowed down these dynamic processes led to better agreement with experiment. Lastly, bilayers containing 10 influenza fusion peptides and high fractions of lysolipids (which are known to accelerate pore formation) were simulated with C36 and Drude2023. Pore formation rates were comparable for the two FF for the bilayers with 80% and 90% lysolipid. However, while no pores formed in 24 μs (including a single 20 μs trajectory) in the 70% lysolipid with C36, 4 of 15 replicates formed pores in less than 1 μs with Drude. While the pathway to poration is qualitatively similar for the additive and polarizable FF for the systems studied, Drude2023 should be considered for quantitative studies of pore formation, and, in some cases, will accelerate the process.

Permeability Benchmarking: Guidelines for Comparing in Silico, in Vitro, and in Vivo Measurements

Permeability is a measure of the degree to which cells can transport molecules across biological barriers. Units of permeability are distance per unit time (typically cm/s), where accurate measurements are needed to define drug delivery in homeostasis and to model dysfunction occurring during disease. This perspective offers a set of community-led guidelines to benchmark permeability data across multidisciplinary approaches and different biological contexts. First, we lay out the analytical framework for three methodologies to calculate permeability: in silico assays using either transition-based counting or the inhomogeneous-solubility diffusion approaches, in vitro permeability assays using cells cultured in 2D or 3D geometries, and in vivo assays utilizing in situ brain perfusion or multiple time-point regression analysis. Then, we demonstrate a systematic benchmarking of in silico to both in vitro and in vivo, depicting the ways in which each benchmarking is sensitive to the choices of assay design. Finally, we outline seven recommendations for best practices in permeability benchmarking and underscore the significance of tailored permeability assays in driving advancements in drug delivery research and development. Our exploration encompasses a discussion of "generic" and tissue-specific biological barriers, including the blood-brain barrier (BBB), which is a major hurdle for the delivery of therapeutic agents into the brain. By addressing challenges in reconciling simulated data with experimental assays, we aim to provide insights essential for optimizing accuracy and reliability in permeability modeling.

Phonons reveal coupled cholesterol-lipid dynamics in ternary membranes

Experimental studies of collective dynamics in lipid bilayers have been challenging due to the energy resolution required to observe these low-energy phonon-like modes. However, inelastic x-ray scattering (IXS) measurements-a technique for probing vibrations in soft and biological materials-are now possible with sub-meV resolution, permitting direct observation of low-energy, phonon-like modes in lipid membranes. Here, IXS measurements with sub-meV energy resolution reveal a low-energy optic-like phonon mode at roughly 3 meV in the liquid-ordered (Lo) and liquid-disordered phases of a ternary lipid mixture. This mode is only observed experimentally at momentum transfers greater than 5 nm-1 in the Lo system. A similar gapped mode is also observed in all-atom molecular dynamics (MD) simulations of the same mixture, indicating that the simulations accurately represent the fast, collective dynamics in the Lo phase. Its optical nature and the Q range of the gap together suggest that the observed mode is due to the coupled motion of cholesterol-lipid pairs, separated by several hydrocarbon chains within the membrane plane. Analysis of the simulations provides molecular insight into the origin of the mode in transient, nanoscale substructures of hexagonally packed hydrocarbon chains. This nanoscale hexagonal packing was previously reported based on MD simulations and, later, by NMR measurements. Here, however, the integration of IXS and MD simulations identifies a new signature of the Lo substructure in the collective lipid dynamics, thanks to the recent confluence of IXS sensitivity and MD simulation capabilities.

Curvature fluctuations of fluid vesicles reveal hydrodynamic dissipation within the bilayer

The biological function of membranes is closely related to their softness, which is often studied through the membranes' thermally driven fluctuations. Typically, the analysis assumes that the relaxation rate of a pure bending deformation is determined by the competition between membrane bending rigidity and viscous dissipation in the surrounding medium. Here, we reexamine this assumption and demonstrate that viscous flows within the membrane dominate the dynamics of bending fluctuations of nonplanar membranes with a radius of curvature smaller than the Saffman-Delbrück length. Using flickering spectroscopy of giant vesicles made of dipalmitoylphosphatidylcholine, DPPC:cholesterol mixtures and pure diblock-copolymer membranes, we experimentally detect the signature of membrane dissipation in curvature fluctuations. We show that membrane viscosity can be reliably obtained from the short time behavior of the shape time correlations. The results indicate that the DPPC:cholesterol membranes behave as a Newtonian fluid, while the polymer membranes exhibit more complex rheology. Our study provides physical insights into the time scales of curvature remodeling of biological and synthetic membranes.

Quantitative Comparison against Experiments Reveals Imperfections in Force Fields' Descriptions of POPC-Cholesterol Interactions

Cholesterol is a central building block in biomembranes, where it induces orientational order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular dynamics (MD) simulations have played a crucial role in resolving these effects at the molecular level; yet, it has recently become evident that different MD force fields predict quantitatively different behavior. Although easily neglected, identifying such limitations is increasingly important as the field rapidly progresses toward simulations of complex membranes mimicking the in vivo conditions: pertinent multicomponent simulations must capture accurately the interactions between their fundamental building blocks, such as phospholipids and cholesterol. Here, we define quantitative quality measures for simulations of binary lipid mixtures in membranes against the C-H bond order parameters and lateral diffusion coefficients from NMR spectroscopy as well as the form factors from X-ray scattering. Based on these measures, we perform a systematic evaluation of the ability of commonly used force fields to describe the structure and dynamics of binary mixtures of palmitoyloleoylphosphatidylcholine (POPC) and cholesterol. None of the tested force fields clearly outperforms the others across the tested properties and conditions. Still, the Slipids parameters provide the best overall performance in our tests, especially when dynamic properties are included in the evaluation. The quality evaluation metrics introduced in this work will, particularly, foster future force field development and refinement for multicomponent membranes using automated approaches.

Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids

Accurate empirical force fields of lipid molecules are a critical component of molecular dynamics simulation studies aimed at investigating properties of monolayers, bilayers, micelles, vesicles, and liposomes, as well as heterogeneous systems, such as protein-membrane complexes, bacterial cell walls, and more. While the majority of lipid force field-based simulations have been performed using pairwise-additive nonpolarizable models, advances have been made in the development of the polarizable force field based on the classical Drude oscillator model. In the present study, we undertake further optimization of the Drude lipid force field, termed Drude2023, including improved treatment of the phosphate and glycerol linker region of PC and PE headgroups, additional optimization of the alkene group in monounsaturated lipids, and inclusion of long-range Lennard-Jones interactions using the particle-mesh Ewald method. Initial optimization targeted quantum mechanical (QM) data on small model compounds representative of the linker region. Subsequent optimization targeted QM data on larger model compounds, experimental data, and dihedral potentials of mean force from the CHARMM36 additive lipid force field using a parameter reweighting protocol. The use of both experimental and QM target data during the reweighting protocol is shown to produce physically reasonable parameters that reproduce a collection of experimental observables. Target data for optimization included surface area/lipid for DPPC, DSPC, DMPC, and DLPC bilayers and nuclear magnetic resonance (NMR) order parameters for DPPC bilayers. Validation data include prediction of membrane thickness, scattering form factors, electrostatic potential profiles, compressibility moduli, surface area per lipid, water permeability, NMR T1 relaxation times, diffusion constants, and monolayer surface tensions for a variety of saturated and unsaturated lipid mono- and bilayers. Overall, the agreement with experimental data is quite good, though the results are less satisfactory for the NMR T1 relaxation times for carbons near the ester groups. Notable improvements compared to the additive C36 force field were obtained for membrane dipole potentials, lipid diffusion coefficients, and water permeability with the exception of monounsaturated lipid bilayers. It is anticipated that the optimized polarizable Drude2023 force field will help generate more accurate molecular simulations of pure bilayers and heterogeneous systems containing membranes, advancing our understanding of the role of electronic polarization in these systems.