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At least 37 records · Page 2

Mechanism of unassisted ion transport across membrane bilayers

To establish how charged species move from water to the nonpolar membrane interior and to determine the energetic and structural effects accompanying this process, we performed molecular dynamics simulations of the transport of Na+ and Cl- across a lipid bilayer located between two water lamellae. The total length of molecular dynamics trajectories generated for each ion was 10 ns. Our simulations demonstrate that permeation of ions into the membrane is accompanied by the formation of deep, asymmetric thinning defects in the bilayer, whereby polar lipid head groups and water penetrate the nonpolar membrane interior. Once the ion crosses the midplane of the bilayer the deformation "switches sides"; the initial defect slowly relaxes, and a defect forms in the outgoing side of the bilayer. As a result, the ion remains well solvated during the process; the total number of oxygen atoms from water and lipid head groups in the first solvation shell remains constant. A similar membrane deformation is formed when the ion is instantaneously inserted into the interior of the bilayer. The formation of defects considerably lowers the free energy barrier to transfer of the ion across the bilayer and, consequently, increases the permeabilities of the membrane to ions, compared to the rigid, planar structure, by approximately 14 orders of magnitude. Our results have implications for drug delivery using liposomes and peptide insertion into membranes.

NASA Discipline Exobiology↗

Helicity, membrane incorporation, orientation and thermal stability of the large conductance mechanosensitive ion channel from E. coli

In this report, we present structural studies on the large conductance mechanosensitive ion channel (MscL) from E. coli in detergent micelles and lipid vesicles. Both transmission Fourier transform infrared spectroscopy and circular dichroism (CD) spectra indicate that the protein is highly helical in detergents as well as liposomes. The secondary structure of the proteins was shown to be highly resistant towards denaturation (25-95 degrees C) based on an ellipticity thermal profile. Amide H+/D+ exchange was shown to be extensive (ca. 66%), implying that two thirds of the protein are water accessible. MscL, reconstituted in oriented lipid bilayers, was shown to possess a net bilayer orientation using dichroic ratios measured by attenuated total-reflection Fourier transform infrared spectroscopy. Here, we present and discuss this initial set of structural data on this new family of ion-channel proteins.

NASA Discipline Cell Biology↗

Characterization of individual polynucleotide molecules using a membrane channel

We show that an electric field can drive single-stranded RNA and DNA molecules through a 2.6-nm diameter ion channel in a lipid bilayer membrane. Because the channel diameter can accommodate only a single strand of RNA or DNA, each polymer traverses the membrane as an extended chain that partially blocks the channel. The passage of each molecule is detected as a transient decrease of ionic current whose duration is proportional to polymer length. Channel blockades can therefore be used to measure polynucleotide length. With further improvements, the method could in principle provide direct, high-speed detection of the sequence of bases in single molecules of DNA or RNA.

NASA Discipline Exobiology↗

Permeation of membranes by the neutral form of amino acids and peptides: relevance to the origin of peptide translocation

The flux of amino acids and other nutrient solutes such as phosphate across lipid bilayers (liposomes) is 10(5) slower than facilitated inward transport across biological membranes. This suggest that primitive cells lacking highly evolved transport systems would have difficulty transporting sufficient nutrients for cell growth to occur. There are two possible ways by which early life may have overcome this difficulty: (1) The membranes of the earliest cellular life-forms may have been intrinsically more permeable to solutes; or (2) some transport mechanism may have been available to facilitate transbilayer movement of solutes essential for cell survival and growth prior to the evolution of membrane transport proteins. Translocation of neutral species represents one such mechanism. The neutral forms of amino acids modified by methylation (creating protonated weak bases) permeate membranes up to 10(10) times faster than charged forms. This increased permeability when coupled to a transmembrane pH gradient can result in significantly increased rates of net unidirectional transport. Such pH gradients can be generated in vesicles used to model protocells that preceded and were presumably ancestral to early forms of life. This transport mechanism may still play a role in some protein translocation processes (e.g. for certain signal sequences, toxins and thylakoid proteins) in vivo.

NASA Discipline Exobiology↗

Energetic and spatial parameters for gating of the bacterial large conductance mechanosensitive channel, MscL

MscL is multimeric protein that forms a large conductance mechanosensitive channel in the inner membrane of Escherichia coli. Since MscL is gated by tension transmitted through the lipid bilayer, we have been able to measure its gating parameters as a function of absolute tension. Using purified MscL reconstituted in liposomes, we recorded single channel currents and varied the pressure gradient (P) to vary the tension (T). The tension was calculated from P and the radius of curvature was obtained using video microscopy of the patch. The probability of being open (Po) has a steep sigmoidal dependence on T, with a midpoint (T1/2) of 11.8 dyn/cm. The maximal slope sensitivity of Po/Pc was 0.63 dyn/cm per e-fold. Assuming a Boltzmann distribution, the energy difference between the closed and fully open states in the unstressed membrane was DeltaE = 18.6 kBT. If the mechanosensitivity arises from tension acting on a change of in-plane area (DeltaA), the free energy, TDeltaA, would correspond to DeltaA = 6.5 nm2. MscL is not a binary channel, but has four conducting states and a closed state. Most transition rates are independent of tension, but the rate-limiting step to opening is the transition between the closed state and the lowest conductance substate. This transition thus involves the greatest DeltaA. When summed over all transitions, the in-plane area change from closed to fully open was 6 nm2, agreeing with the value obtained in the two-state analysis. Assuming a cylindrical channel, the dimensions of the (fully open) pore were comparable to DeltaA. Thus, the tension dependence of channel gating is primarily one of increasing the external channel area to accommodate the pore of the smallest conducting state. The higher conducting states appear to involve conformational changes internal to the channel that don't involve changes in area.

Non-NASA Center↗

Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness

Two mechanisms have been proposed to account for solute permeation of lipid bilayers. Partitioning into the hydrophobic phase of the bilayer, followed by diffusion, is accepted by many for the permeation of water and other small neutral solutes, but transient pores have also been proposed to account for both water and ionic solute permeation. These two mechanisms make distinctively different predictions about the permeability coefficient as a function of bilayer thickness. Whereas the solubility-diffusion mechanism predicts only a modest variation related to bilayer thickness, the pore model predicts an exponential relationship. To test these models, we measured the permeability of phospholipid bilayers to protons, potassium ions, water, urea, and glycerol. Bilayers were prepared as liposomes, and thickness was varied systematically by using unsaturated lipids with chain lengths ranging from 14 to 24 carbon atoms. The permeability coefficient of water and neutral polar solutes displayed a modest dependence on bilayer thickness, with an approximately linear fivefold decrease as the carbon number varied from 14 to 24 atoms. In contrast, the permeability to protons and potassium ions decreased sharply by two orders of magnitude between 14 and 18 carbon atoms, and leveled off, when the chain length was further extended to 24 carbon atoms. The results for water and the neutral permeating solutes are best explained by the solubility-diffusion mechanism. The results for protons and potassium ions in shorter-chain lipids are consistent with the transient pore model, but better fit the theoretical line predicted by the solubility-diffusion model at longer chain lengths.

NASA Program Exobiology↗

Purification of the small mechanosensitive channel of Escherichia coli (MscS): the subunit structure, conduction, and gating characteristics in liposomes

The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic downshift. It has been identified in Escherichia coli as a product of the orphan yggB gene, now called mscS (Levina et al., 1999, EMBO J. 18:1730). Here I show that that the isolated 31-kDa MscS protein is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. MscS-6His complexes purified in the presence of octylglucoside and lipids migrate in a high-resolution gel-filtration column as particles of approximately 200 kDa. Consistent with that, the protein cross-linking patterns predict a hexamer. The channel reconstituted in soybean asolectin liposomes was activated by pressures of 20-60 mm Hg and displayed the same asymmetric I-V curve and slight anionic preference as in situ. At the same time, the single-channel conductance is proportional to the buffer conductivity in a wide range of salt concentrations. The rate of channel activation in response to increasing pressure gradient across the patch was slower than the rate of closure in response to decreasing steps of pressure gradient. Therefore, the open probability curves were recorded with descending series of pressures. Determination of the curvature of patches by video imaging permitted measurements of the channel activity as a function of membrane tension (gamma). Po(gamma) curves had the midpoint at 5.5 +/- 0.1 dyne/cm and gave estimates for the energy of opening DeltaG = 11.4 +/- 0.5 kT, and the transition-related area change DeltaA = 8.4 +/- 0.4 nm(2) when fitted with a two-state Boltzmann model. The correspondence between channel properties in the native and reconstituted systems is discussed.

NASA Discipline Cell Biology↗

Computer Simulation Studies of Ion Channel Gating: Characteristics of the M2 Channel of Influenza-A Virus in a Phospholipid Bilayer

The 25 amino acids long, transmembrane fragment of the Influenza virus M2 protein forms a homotetrameric channel that transports protons across lipid bilayers. It has been postulated that high efficiency and selectivity of this process is due to gating by four histidine residues that occlude the channel lumen in the closed state. Two mechanisms of gating have been postulated. In one mechanism, the proton is "shuttled" through the gate by attaching to the delta nitrogen atom on the extracellular side of the imidazole ring, followed by the release of the proton attached to the epsilon nitrogen atom on the opposite side. In the second mechanism, the four histidines move away from each other due to electrostatic repulsion upon protonation, thus opening the gate sufficiently that a wire of water molecules can penetrate the gate. Then, protons are transported by "hopping" along the wire. In this paper, both mechanisms are evaluated in a series of molecular dynamics simulations by investigating stability of different protonation states of the channel that are involved in these mechanisms. For the shuttle mechanism, these are states with all epsilon protonated histidines, one biprotonated residue or one histidine protonated in the delta position. For the gate opening mechanism, this is the state in which all four histidines are biprotonated. In addition, a state with two biprotonated histidines is considered. For each system, composed of the protein channel embedded in phospholipid bilayer located between two water lamellae, a molecular dynamics trajectory of approximately 1.3 ns (after equilibration) was obtained. It is found that the states involved in the shuttle mechanism are stable during the simulations. Furthermore, the orientations and dynamics of water molecules near the gate are conducive to proton transfers involved in the shuttle. In contract, the fully biprotonated state, implicated in the gate opening mechanism, is not stable and the channel looses its structural integrity. If only two histidines are biprotonated the channel deforms but remains intact with the gate mostly closed. In summary, the results of this study lend support to the shuttle mechanism but not to the gate opening mechanism of proton gating in M2.

Schweighofer, Karl J.↗

Curvature Memory in Electrically Stimulated Lipid Membranes

Here, we demonstrate, using non-equilibrium molecular dynamics simulations, that lipid membrane capacitance varies with surface charge accumulation linked to membrane shape and curvature changes. Specifically, we show that lipid membranes exhibit a hysteretic response when exposed to oscillatory electric fields. The electromechanical coupling in these membranes leads to hysteretic buckling, in which the membrane can spontaneously buckle in one of two distinct directions along the electric field, even for the same ionic charge accumulation at the water–membrane interface. In this regard, these binary buckled membrane states suggest potential applications in neuromorphic computing. Their bistable nature, characterized by two distinct and stable configurations, could serve as a foundation for implementing memory storage systems and logic operations. Furthermore, we introduce a circuit model that captures these dynamic effects, offering insights into emergent memory effects in electrically stimulated lipid membranes. Finally, this work presents lipid bilayers as dynamic, adaptable elements and suggests a new platform for exploring energy storage, information processing, and memory encoding at the lipid membrane level.

59 BASIC BIOLOGICAL SCIENCES↗

Excipient screening by lyophilization provides insights into spray drying formulations for nanoparticle vaccines

Nanoparticles have shown great promise as delivery platforms in the development of tunable and safe vaccines. Nanolipoprotein particles (NLPs), also known as nanodiscs, are discoidal nanoparticles composed of a lipid bilayer stabilized at their periphery by apolipoproteins. Under the right conditions, the NLP self-assembly process is highly customizable in terms of lipids and apolipoprotein constituents, allowing for tunable physical and chemical characteristics. This flexibility allows a wide range of vaccine antigens and adjuvants to be incorporated onto the NLP platform for tailored vaccine design. The stability of NLPs during long term storage is a very important factor in developing a vaccine delivery platform suitable for widespread global use. When stored in a solution for extended periods of time, NLPs dissociate into their corresponding lipids and protein constituents, leading to particle degradation. Proper stabilization of NLPs can often be achieved by lyophilization (i.e. freeze-drying), a method widely used for various applications including pharmaceuticals. This process, however, can be damaging to particles without the presence of lyoprotectants or excipients that help maintain particle stability during lyophilization. Another method used to stabilize vaccines and pharmaceuticals is spray drying, a process that converts liquid formulations into dry powders through controlled heating and airflow. While spray drying is rapid, scalable, and cost-effective, lyophilization is typically a gentler process that better retains biomolecule structure and function. Both processes use excipients for particle stabilization, so lyophilization can be used as a surrogate to test stability of NLPs, to down-select formulations that may withstand the harsher conditions of spray drying. To screen different formulations, NLPs were synthesized and purified to homogeneity by size exclusion chromatography (SEC) and samples were prepared with a wide range of lyoprotectants and/or excipients. To assess the protective effects of excipients on NLPs upon spray drying, both pre- and post-lyophilized samples were analyzed by SEC. To assess the protective effects upon heating (encountered during the spray drying process), NLP samples were incubated at elevated temperatures prior to SEC analysis. The lyoprotectants and excipients evaluated in this study had different efficiencies in protecting NLPs during lyophilization and heating tests. Trehalose, for example, exhibits stabilization on NLPs both upon lyophilization and heating whereas leucine accelerated NLP dissociation. Although some lyoprotectants are effective by themselves, different combinations can decrease the stabilization of NLPs. Shelf-stable vaccines that do not require cold-chain storage are essential for global accessibility and our findings provide fundamental insight into how to advance NLP-based vaccines for these applications.

Serrano, Litzay J [Lawrence Livermore National Lab↗

Molecular Modeling of Surfactant Interaction on Phospholipid Bilayers Mimicking Corneal Epithelium

Surfactants found in consumer products can compromise eye corneal membrane integrity upon accidental exposure. Traditional in vitro and in vivo approaches to evaluate membrane–surfactant interaction pose experimental limitations such as species variability, reproducibility, and most often do not provide the overall picture. These limitations motivate the use of in silico models to study phenomena like cellular disruption assays caused by surfactants at the molecular scale. In this work, coarse-grained molecular dynamics simulations have been employed to investigate how nonionic alcohol ethoxylate (AE) and anionic surfactant alcohol ethoxy sulfate (AES) interact with lipid bilayer liposomes that mimic corneal epithelial cell membranes. The spherical liposome is composed of 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-di(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-di(9Z-octadecenoyl)-sn-glycero-3-phospho-l-serine (DOPS), and cholesterol, resembling the composition of the corneal epithelial cells’ membrane bilayer. The simulation consisted of varying degrees of representative surfactant compositions and two initial types of surfactant configurations within or outside the liposome. Our results reveal that both surfactants induce outer leaflet bulging, agreeing with membrane solubilization models. The more highly ethoxylated surfactant, AE, caused more consistent inner leaflet disruption than AES, resulting in significantly more water permeation and membrane thinning. In addition, both surfactants increase the lateral diffusion of lipids within the membrane layers, with higher ethoxylated AE showing a stronger effect than AES. This study demonstrates how surfactant structure and localization influence bilayer membrane integrity, offering mechanistic insights into the irritation potential, thus guiding the rational design of effective surfactant-based formulations.

Lipids↗

Nonstereotypical Distribution and Effect of Ergosterol in Lipid Membranes

Ergosterol, found in fungi and some protist membranes, is understudied compared with cholesterol from animal membranes. Generally, ergosterol is assumed to modulate membranes in the same manner as cholesterol, based on their similar chemical structures. Here we reveal some fundamental structural and dynamical differences between them. Neutron diffraction shows that ergosterol is embedded in the lipid bilayer much shallower than cholesterol. Further, ergosterol does not change the membrane thickness as much as cholesterol does, indicating little condensation effect. Neutron spin echo shows that ergosterol can rigidify and soften membranes at different concentrations. The lateral lipid diffusion measured by quasielastic neutron scattering indicates that ergosterol promotes a jump diffusion of the lipid, whereas cholesterol keeps the same continuous lateral diffusion as the pure lipid membrane. Our results point to quite distinct interactions of ergosterol with membranes compared with cholesterol. These insights provide a basic understanding of membranes containing ergosterol with implications for phenomena such as lipid rafts and drug interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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, in this study, IXS measurements with sub-meV energy resolution reveal a low-energy optic-like phonon mode at roughly 3 meV in the liquid-ordered (L o ) and liquid-disordered (L d ) phases of a ternary lipid mixture. This mode is only observed experimentally at momentum transfers greater than 5 nm -1 in the L o system. A similar gapped mode is also observed in all-atom molecular dynamics (MD) simulations of the same mixture, indicating that the simulations accurately represnt the fast, collective dynamics in the L o phase. It’s 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 provide 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 molecular dynamics simulations and later by NMR measurements. Here, however, the integration of IXS and MD simulations identifies a new signature of the L o substructure in the collective lipid dynamics, thanks to the recent confluence of IXS sensitivity and MD simulation capabilities.

36 MATERIALS SCIENCE↗

Assembly of small silica nanoparticles using lipid-tethered DNA ‘bonds’

Single-stranded DNA molecules modified with cholesterol functional groups are physically tethered to silica nanoparticles (diameter 25 nm) that are encapsulated in a lipid bilayer. Such tethering increases the azimuthal mobility of the DNA molecules across the nanoparticle surface and enables nonspecific bonding, eliminating the need for specialized surface chemistries (such as silane or thiol ligands). To induce assembly, double-stranded DNA ‘bridge’ molecules are then added with complementary nucleotides to the DNA ‘anchor’ molecules that are physically tethered to the lipids on the surface of the particles. Assembly is observed to occur at room temperature and without the need for temperature annealing. Using automated liquid handling tools, assemblies are created in high throughput and rapidly characterized using SAXS. It is determined that the relative concentration of DNA-to-silica and the ionic strength of the solution are important parameters that affect the resulting assembly. Analysis of SAXS data is performed using coarse-grained particle dynamics simulations. The results support the spontaneous formation of semi-crystalline particle assemblies by particle condensation, where the interparticle distance is tuned by the sequence of the DNA ‘bridge’ used to link the particles. Crystallinity analysis performed on the resulting simulations, optimized to match SAXS observations, suggest that particle clusters display increased crystallinity in the center of the clusters, but their maximum size remains relatively small (sub-micron) before settling occurs, which limits the extent of crystallization.

Chiang, Huat Thart [Univ. of Washington, Seattle, ↗

Neutrons reveal the dynamics of leaf thylakoids in living plants

The study is the first known exploration of photosynthetic membranes dynamics in living plants by high resolution quasielastic neutron scattering spectroscopy. We investigated the mobility and flexibility of thylakoid membranes in common duckweed (Landoltia punctata) and identified dynamics across various length scales corresponding to individual membranes and membranes stack. We employed classical models typically used to study lipid bilayers to characterize the undulation modes and rigidity of the membranes and reveal how structural variations influence the observed complex dynamics. Our findings show that the stacks of thylakoids in duckweed behave as rigid systems, exhibiting an effective bending coefficient in the lower range associated with surfactant membranes. In contrast, the single thylakoid leaflets display greater apparent flexibility and are well situated within the bi-continuous surfactant phase dynamics. While our observations enhance the understanding of the intricate architecture and mobility of photosynthetic cellular machinery, they also highlight the limitations of applying ideal lipid membranes models to describe complex biological systems. This work opens more questions and the need for further investigations across extended length and time scales, as well as the importance of rigorous sample preparation and experimental control.

Applied physics↗

Reparameterizing a Lipid Force Field Using Small-Angle X-ray Scattering to Improve Predictions of Multicomponent Membranes under Organic Solvent Stress

Understanding and predicting properties of lipid-bilayer membranes are essential to elucidating organismal physiology and pathophysiology. Therefore, substantial efforts have been undertaken to derive accurate molecular-mechanics force fields (FF) to allow simulation of their properties; however, much of these past efforts focused on tuning force fields to accurately reproduce the properties of model single-component membranes and not multicomponent or stressed membranes. Here, we tuned the CHARMM36 FF for a simple 2-component model of a Gram-positive bacterium. This updated force field is parametrized against a single condensed-phase property, the small-angle X-ray scattering (SAXS) intensities of the 2-component lipid system, using a version of ForceBalance implemented previously (named ForceBalance-SAS) with SAXS and small-angle neutron scattering (SANS) intensities as optimization targets. After tuning, we observe improved agreement with the experimental SAXS of the membrane under 1-butanol and tetrahydrofuran solvent stresses, with a factor of 10.0 and 7.5 reduction, respectively, in χ 2 , the measure of the discrepancy between experimental and computed SAXS intensities. Furthermore, this reparametrized force field yielded improved agreement between experimental and simulated membrane thicknesses for the pure lipid systems. However, we note limitations in transferability and diagnose the source of such limitations, particularly the need for SANS in addition to SAXS.

Demerdash, Omar N. A. [Oak Ridge National Laborato↗

A Pseudo‐Surfactant Chemical Permeation Enhancer to Treat Otitis Media via Sustained Transtympanic Delivery of Antibiotics

Abstract Chemical permeation enhancers (CPEs) represent a prevalent and safe strategy to enable noninvasive drug delivery across skin‐like biological barriers such as the tympanic membrane (TM). While most existing CPEs interact strongly with the lipid bilayers in the stratum corneum to create defects as diffusion paths, their interactions with the delivery system, such as polymers forming a hydrogel, can compromise gelation, formulation stability, and drug diffusion. To overcome this challenge, differing interactions between CPEs and the hydrogel system are explored, especially those with sodium dodecyl sulfate (SDS), an ionic surfactant and a common CPE, and those with methyl laurate (ML), a nonionic counterpart with a similar length alkyl chain. Notably, the use of ML effectively decouples permeation enhancement from gelation, enabling sustained delivery across TMs to treat acute otitis media (AOM), which is not possible with the use of SDS. Ciprofloxacin and ML are shown to form a pseudo‐surfactant that significantly boosts transtympanic permeation. The middle ear ciprofloxacin concentration is increased by 70‐fold in vivo in a chinchilla AOM model, yielding superior efficacy and biocompatibility than the previous highest‐performing formulation. Beyond improved efficacy and biocompatibility, this single‐CPE formulation significantly accelerates its progression toward clinical deployment.

Engineering↗

Shape‐Evolving Structured Liquids

Migration, division, and reconfiguration - functions essential to living systems - are driven by active processes. Developing synthetic mimics is an outstanding challenge. Lipid bilayers that bound natural systems are locally deformed by active species, e.g., microtubules, but the resulting non-equilibrium shapes relax when active species motion ceases, and the shape changes lack immediate control. A fully synthetic system is described, driven by active particles encapsulated by a reconfigurable nanoparticle-surfactant membrane that undergoes shape fluctuations reminiscent of living cells. These shape changes are preserved after particle activity stops. Surfactant concentration tunes the interfacial tension over three orders of magnitude, making on-demand shape evolution possible. Directional migration, division, and reconfiguration across multiple scales are possible, leading to a new class of biomimetic, reconfigurable, and responsive materials, paving the way for autonomous synthetic machines.

Kim, Paul Y↗