Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature

Phospholipid headgroups govern area per lipid and emergent elastic properties of bilayers

Phospholipid bilayers are liquid-crystalline materials whose intermolecular interactions at mesoscopic length scales have key roles in the emergence of membrane physical properties. Here we investigated the combined effects of phospholipid polar headgroups and acyl chains on biophysical functions of membranes with solid-state 2H NMR spectroscopy. We compared the structural and dynamic properties of phosphatidylethanolamine and phosphatidylcholine with perdeuterated acyl chains in the solid-ordered (so) and liquid-disordered (ld) phases. Our analysis of spectral lineshapes of 1,2-diperdeuteriopalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE-d62) and 1,2-diperdeuteriopalmitoyl-sn-glycero-3-phosphocholine (DPPC-d62) in the so (gel) phase indicated an all-trans rotating chain structure for both lipids. Greater segmental order parameters (SCD) were observed in the ld (liquid-crystalline) phase for DPPE-d62 than for DPPC-d62 membranes, while their mixtures had intermediate values irrespective of the deuterated lipid type. Our results suggest the SCD profiles of the acyl chains are governed by methylation of the headgroups and are averaged over the entire system. Variations in the acyl chain molecular dynamics were further investigated by spin-lattice (R1Z) and quadrupolar-order relaxation (R1Q) measurements. The two acyl-perdeuterated lipids showed distinct differences in relaxation behavior as a function of the order parameter. The R1Z rates had a square-law dependence on SCD, implying collective mesoscopic dynamics, with a higher bending rigidity for DPPE-d62 than for DPPC-d62 lipids. Remodeling of lipid average and dynamic properties by methylation of the headgroups thus provides a mechanism to control the actions of peptides and proteins in biomembranes.

Small-Angle Neutron Scattering for Studying Lipid Bilayer Membranes

Small-angle neutron scattering (SANS) is a powerful tool for studying biological membranes and model lipid bilayer membranes. The length scales probed by SANS, being from 1 nm to over 100 nm, are well-matched to the relevant length scales of the bilayer, particularly when it is in the form of a vesicle. However, it is the ability of SANS to differentiate between isotopes of hydrogen as well as the availability of deuterium labeled lipids that truly enable SANS to reveal details of membranes that are not accessible with the use of other techniques, such as small-angle X-ray scattering. In this work, an overview of the use of SANS for studying unilamellar lipid bilayer vesicles is presented. The technique is briefly presented, and the power of selective deuteration and contrast variation methods is discussed. Approaches to modeling SANS data from unilamellar lipid bilayer vesicles are presented. Finally, recent examples are discussed. While the emphasis is on studies of unilamellar vesicles, examples of the use of SANS to study intact cells are also presented.

Change in Morphology of Dimyristoylphosphatidylcholine/Bile Salt Derivative Bicelle Assemblies with Dodecylmaltoside in the Disk and Ribbon Phases

Bicelles, composed of a mixture of long and short chain lipids, form nanostructured molecular assemblies that are attractive lipid-membrane mimics for in vitro studies of integral membrane proteins. Here we study the effect of a third component, the single chain detergent n-dodecyl-β-d-maltoside (DDM) on the morphology of bicelles composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO) below (10 °C) and above (38 °C) the phase transition. In the absence of DDM, bicelles convert from ellipsoidal disks at 10 °C to extended ribbon-like structures at 38 °C. The addition of DDM reshapes the ellipsoidal disc to a circular one and the flattened ribbon to a circular-cylinder worm-like micelle. Knowledge of the influence of the single chain detergent DDM on bicelle nanoscale morphology contributes toward comprehending lipid membrane self-organization and to the goal of optimizing lipid mimics for membrane biology research.

Improved chemical and isotopic labeling of biomembranes in Bacillus subtilis by leveraging CRISPRi inhibition of beta-ketoacyl-ACP synthase (fabF)

Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure-and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct in vivo structural studies of the cell membrane in the Gram-positive bacterium, Bacillus subtilis, using small-angle neutron scattering. This was accomplished through a genetic inhibition of fatty acid (FA) degradation (ΔfadN) and a chemical inhibition of FA biosynthesis using cerulenin, an irreversible inhibitor of type II fatty acid synthases. Here, we improve upon the previous system by introducing a dCas9/sgRNA-fabF complex that blocks transcription of the essential fabF gene when under xylose induction. This leads to greater sensitivity to cerulenin in the mutant strain (JEBS102) and more robust cell growth when supplementary FAs are introduced to the culture medium. A subtle change in FA uptake is noted when compared to the prior labeling strategy. This is seen in the gas chromatography/mass spectrometry (GC/MS) data as a higher ratio of n16:0 to a15:0, and manifests in an apparent increase in the membrane thickness determined via neutron scattering. This represents an improved method of isotopic labeling for the cell membrane of Bacillus subtilis; enabling improved investigations of cellular uptake and utilization of FAs, cell membrane structure and organization as a phenotypic response to metabolic and environmental changes.

Emerging Diamond Quantum Sensing in Bio-Membranes

Bio-membranes exhibit complex but unique mechanical properties as communicative regulators in various physiological and pathological processes. Exposed to a dynamic micro-environment, bio-membranes can be seen as an intricate and delicate system. The systematical modeling and detection of their local physical properties are often difficult to achieve, both quantitatively and precisely. The recent emerging diamonds hosting quantum defects (i.e., nitrogen-vacancy (NV) center) demonstrate intriguing optical and spin properties, together with their outstanding photostability and biocompatibility, rendering them ideal candidates for biological applications. Notably, the extraordinary spin-based sensing enable the measurements of localized nanoscale physical quantities such as magnetic fields, electrical fields, temperature, and strain. These nanoscale signals can be optically read out precisely by simple optical microscopy systems. Given these exclusive properties, NV-center-based quantum sensors can be widely applied in exploring bio-membrane-related features and the communicative chemical reaction processes. This review mainly focuses on NV-based quantum sensing in bio-membrane fields. The attempts of applying NV-based quantum sensors in bio-membranes to investigate diverse physical and chemical events such as membrane elasticity, phase change, nanoscale bio-physical signals, and free radical formation are fully overviewed. We also discuss the challenges and future directions of this novel technology to be utilized in bio-membranes.

Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes

Antimicrobial peptides (AMPs) can be directed to specific membranes based on differences in lipid composition. In this study, we performed atomistic and coarse-grained simulations of different numbers of the designed AMP adepantin-1 with a eukaryotic membrane, cytoplasmic Gram-positive and Gram-negative membranes, and an outer Gram-negative membrane. At the core of adepantin-1's behavior is its amphipathic α-helical structure, which was implemented in its design. The amphipathic structure promotes rapid self-association of peptide in water or upon binding to bacterial membranes. Aggregates initially make contact with the membrane via positively charged residues, but with insertion, the hydrophobic residues are exposed to the membrane's hydrophobic core. This adaptation alters the aggregate's stability, causing the peptides to diffuse in the polar region of the membrane, mostly remaining as a single peptide or pairing up to form an antiparallel dimer. Thus, the aggregate's proposed role is to aid in positioning the peptide into a favorable conformation for insertion. Simulations revealed the molecular basics of adepantin-1 binding to various membranes, and highlighted peptide aggregation as an important factor. These findings contribute to the development of novel anti-infective agents to combat the rapidly growing problem of bacterial resistance to antibiotics.

Structural and mechanical properties of the red blood cell's cytoplasmic membrane seen through the lens of biophysics

Red blood cells (RBCs) are the most abundant cell type in the human body and critical suppliers of oxygen. The cells are characterized by a simple structure with no internal organelles. Their two-layered outer shell is composed of a cytoplasmic membrane (RBC cm ) tethered to a spectrin cytoskeleton allowing the cell to be both flexible yet resistant against shear stress. These mechanical properties are intrinsically linked to the molecular composition and organization of their shell. The cytoplasmic membrane is expected to dominate the elastic behavior on small, nanometer length scales, which are most relevant for cellular processes that take place between the fibrils of the cytoskeleton. Several pathologies have been linked to structural and compositional changes within the RBC cm and the cell's mechanical properties. We review current findings in terms of RBC lipidomics, lipid organization and elastic properties with a focus on biophysical techniques, such as X-ray and neutron scattering, and Molecular Dynamics simulations, and their biological relevance. In our current understanding, the RBC cm 's structure is patchy, with nanometer sized liquid ordered and disordered lipid, and peptide domains. At the same time, it is surprisingly soft, with bending rigidities κ of 2-4 kBT. This is in strong contrast to the current belief that a high concentration of cholesterol results in stiff membranes. This extreme softness is likely the result of an interaction between polyunsaturated lipids and cholesterol, which may also occur in other biological membranes. There is strong evidence in the literature that there is no length scale dependence of κ of whole RBCs.

Peptide-membrane binding is not enough to explain bioactivity: A case study

Membrane-active peptides are a promising class of antimicrobial and anticancer therapeutics. For this reason, their molecular mechanisms of action are currently actively investigated. By exploiting Electron Paramagnetic Resonance, we study the membrane interaction of two spin-labeled analogs of the antimicrobial and cytotoxic peptide trichogin GA IV (Tri), with opposite bioactivity: Tri(Api⁸), able to selectively kill cancer cells, and Tri(Leu⁴), which is completely nontoxic. In our attempt to determine the molecular basis of their different biological activity, we investigate peptide impact on the lateral organization of lipid membranes, peptide localization and oligomerization, in the zwitter-ionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) model membrane We show that, despite their divergent bioactivity, both peptide analogs (i) are membrane-bound, (ii) display a weak tendency to oligomerization, and (iii) do not induce significant lipid rearrangement. Conversely, literature data show that the parent peptide trichogin, which is cytotoxic without any selectivity, is strongly prone to dimerization and affects the reorganization of POPC membranes. Its dimers are involved in the rotation around the peptide helix, as observed at cryogenic temperatures in the millisecond timescale. Since this latter behavior is not observed for the inactive Tri(Leu⁴), we propose that for short-length peptides as trichogin oligomerization and molecular motions are crucial for bioactivity, and membrane binding alone is not enough to predict or explain it. We envisage that small changes in the peptide sequence that affect only their ability to oligomerize, or their molecular motions inside the membrane, can tune the peptide activity on membranes of different compositions.

Dielectric dispersion characteristics of the phospholipid bilayer with subnanometer resolution from terahertz to mid-infrared

There is growing interest in whether the myelinated nerve fiber acts as a dielectric waveguide to propagate terahertz to mid-infrared electromagnetic waves, which are presumed stable signal carrier for neurotransmission. The myelin sheath is formed as a multilamellar biomembrane structure, hence insights into the dielectric properties of the phospholipid bilayer is essential for a complete understanding of the myelinated fiber functioning. In this work, by means of atomistic molecular dynamics simulations of the dimyristoylphosphatidylcholine (DMPC) bilayer in water and numerical calculations of carefully layered molecules along with calibration of optical dielectric constants, we for the first time demonstrate the spatially resolved (in sub-nm) dielectric spectrum of the phospholipid bilayer in a remarkably wide range from terahertz to mid-infrared. More specifically, the membrane head regions exhibit both larger real and imaginary permittivities than that of the tail counterparts in the majority of the 1–100 THz band. In addition, the spatial variation of dielectric properties suggests advantageous propagation characteristics of the phospholipid bilayer in a relatively wide band of 55–85 THz, where the electromagnetic waves are well confined within the head regions.

Partial Volumes of Phosphatidylcholines and Vitamin E: α-Tocopherol Prefers Disordered Membranes

Despite its discovery over 95 years ago, the biological and nutritional roles of vitamin E remain subjects of much controversy. Though it is known to possess antioxidant properties, recent assertions have implied that vitamin E may not be limited to this function in living systems. Through densitometry measurements and small-angle X-ray scattering we observe favorable interactions between α-tocopherol and unsaturated phospholipids, with more favorable interactions correlating to an increase in lipid chain unsaturation. Our data provide evidence that vitamin E may preferentially associate with oxygen sensitive lipids─an association that is considered innate for a viable membrane antioxidant.

Passive Macromolecular Translocation Mechanism through Lipid Membranes

The translocation of biologically active macromolecules through cell membranes is of vital importance for cells and is a key process for drug delivery. Proteins exploit specific conformational changes in their secondary structure to facilitate membrane translocation. For the large class of biological and synthetic macromolecules, where such conformational adaptions are not possible, guidelines to tailor the structure of monomers and macromolecules to aid membrane translocation and cross-membrane drug delivery would be highly desirable. Here, we use alternating amphiphilic macromolecules to systematically investigate the relation between polarity, polymer chain length, lipid chain length, polymer concentration, and temperature on membrane partition and translocation rate. We employed pulse field gradient NMR and confocal fluorescence microscopy to determine membrane adsorption and desorption rate constants and partitioning coefficients. We find that translocation is a two-step process involving a fast adsorption and membrane insertion process and a slower desorption process. Membrane insertion is a key step that determines the molecular weight, concentration, and temperature dependences. Passive translocation is possible on time scales from minutes to hours. Macromolecules with different adapted hydrophilic/hydrophobic comonomer sequences show the same translocation rate, indicating that common optimized translocation conditions can be realized with a variety of monomer chemical structures. The investigated copolymers are biocompatible, biodegradable, and capable of transporting a hydrophobic payload through the lipid membrane. This detailed understanding of the macromolecular translocation mechanism enables to better tailor the delivery of active agents using macromolecular carriers.

Generation and Computational Characterization of a Complex Staphylococcus aureus Lipid Bilayer

Studies indicate a crucial cell membrane role in the antibiotic resistance of Staphylococcus aureus. To simulate its membrane structure and dynamics, a complex molecular-scale computational representation of the S. aureus lipid bilayer was developed. Phospholipid types and their amounts were optimized by reverse Monte Carlo to represent characterization data from the literature, leading to 19 different phospholipid types that combine three headgroups [phosphatidylglycerol, lysyl-phosphatidylglycerol (LPG), and cardiolipin] and 10 tails, including iso- and anteiso-branched saturated chains. The averaged lipid bilayer thickness was 36.7 Å, and area per headgroup was 67.8 Ų. Phosphorus and nitrogen density profiles showed that LPG headgroups tended to be bent and oriented more parallel to the bilayer plane. The water density profile showed that small amounts reached the membrane center. Carbon density profiles indicated hydrophobic interactions for all lipids in the middle of the bilayer. Bond vector order parameters along each tail demonstrated different C-H ordering even within distinct lipids of the same type; however, all tails followed similar trends in average order parameter. These complex simulations further revealed bilayer insights beyond those attainable with monodisperse, unbranched lipids. Longer tails often extended into the opposite leaflet. Carbon at and beyond a branch showed significantly decreased ordering compared to carbon in unbranched tails; this feature arose in every branched lipid. Diverse tail lengths distributed these disordered methyl groups throughout the middle third of the bilayer. Distributions in mobility and ordering reveal diverse properties that cannot be obtained with monodisperse lipids.

Salt effects on mixed composition membranes containing an antioxidant lipophilic edaravone derivative: a computational-experimental study

The protection of lipid membranes against oxidation avoids diseases associated with oxidative stress. As a strategy to contrast it, functionalized lipids with antioxidant activity are used to become part of membranes thus protecting them. For this purpose, a lipophilic edaravone derivative has been synthesized, adding a C18 saturated chain to the original structure. The antioxidant activity of C18-Edv has been demonstrated in our previous work. In this study, molecular dynamics simulations have been performed to define the effects of NaCl, MgCl₂, KCl, and CaCl₂ salts on a palmitoyl-oleoyl-sn-glycero-phosphocholine (POPC) lipid bilayer encapsulating C18-Edv. The results showed how different salts influence POPC lateral diffusion, and the movements of C18-Edv heads, which are antioxidant moieties, were correlated to the ability of C18-Edv molecules to protect membranes. MgCl₂ showed a negative impact leading to C18-Edv clusterization and membrane stretching, while KCl and NaCl showed a moderate influence on the mixed lipid membrane structure. CaCl₂ increased the exposure of the C18-Edv heads to the lipid-water interface, resulting in the salt with a higher propensity to guarantee protection against radicals in the aqueous phase. Finally, C18-Edv-POPC liposomes have been prepared following the simulation conditions, and then an experimental Oxygen Radical Absorbance Capacity (ORAC) assay has been performed to confirm the in silico predicted results.

Extreme Membrane Tensile Loads Induce Half-Activation of the Thermosensitive TRPV1 Channel

Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels convert a wide range of physical and chemical stimuli into channel opening is essential to understanding their normal function. Here, half-activation of thermosensitive TRPV1 channel under extreme membrane stretching from blast loads was provided by molecular dynamics simulations. The results show that such extreme membrane stretch loading will only lead to half-activation of the TRPV1 channel: that is, the upper gate is open for high-speed stretching (>15m/s), but the lower gate is still closed. The corresponding activation threshold also depends on both the tensile speed and the area strain. This means that the direct mechanical gating of TRP channels in one step is unlikely to occur.

Cations Do Not Alter the Membrane Structure of POPC—A Lipid With an Intermediate Area

Combining small-angle neutron scattering (SANS), small-angle X-ray scattering (SAXS), and densitometric measurements, we have studied the interactions of the divalent cations Ca²⁺ and Mg²⁺ with the lipid vesicles prepared of a mixed-chain palmitoyl-oleoyl-phosphatidylcholine (POPC) at 25°C. The structural parameters of the POPC bilayer, such as the bilayer thickness, lateral area, and volume per lipid, displayed no changes upon the ion addition at concentrations up to 30 mM and minor changes at > 30 mM Ca²⁺ and Mg²⁺, while some decrease in the vesicle radius was observed over the entire concentration range studied. This examination allows us to validate the concept of lipid–ion interactions governed by the area per lipid suggested previously and to propose the mixed mode of those interactions that emerge in the POPC vesicles. We speculate that the average area per POPC lipid that corresponds to the cutoff length of lipid–ion interactions generates an equal but opposite impact on ion bridges and separate lipid–ion pairs. As a result of the dynamic equilibrium, the overall structural properties of bilayers are not affected. As the molecular mechanism proposed is affected by the structural properties of a particular lipid, it might help us to understand the fundamentals of processes occurring in complex multicomponent membrane systems.

Energetic and Structural Insights into Phospholipid Transfer from Membranes with Different Curvatures by Time-Resolved Neutron Scattering

Understanding how lipid dynamics change with membrane curvature is important given that biological membranes constantly change their curvature and morphology through membrane fusion and endo-/exocytosis. Here, we used time-resolved small-angle neutron scattering and time-resolved fluorescence to characterize the properties and dynamics of phospholipids in vesicles with different curvatures. Dissociation of phospholipids from vesicles required traversing an energy barrier comprising positive enthalpy and negative entropy. However, lipids in membranes with high positive curvature have dense acyl chain packing and loose headgroup packing, leading to hydrophobic hydration due to water penetration into the membrane. These properties were found to lower the hydrophobic hydration enhancement associated with phospholipid dissociation and mitigate the acyl chain packing of lipids adjacent to the space created by the lipid dissociation, resulting in an increase in activation entropy. The results of this study provide important insights into the functions of biomembranes in relation to their dynamic structural changes.

Clustering of tetrameric influenza M2 peptides in lipid bilayers investigated by 19F solid-state NMR

The influenza M2 protein forms a drug-targeted tetrameric proton channel to mediate virus uncoating, and carries out membrane scission to enable virus release. While the proton channel function of M2 has been extensively studied, the mechanism by which M2 catalyzes membrane scission is still not well understood. Previous fluorescence and electron microscopy studies indicated that M2 tetramers concentrate at the neck of the budding virus in the host plasma membrane. However, molecular evidence for this clustering is scarce. Here, we use ¹⁹F solid-state NMR to investigate M2 clustering in phospholipid bilayers. By mixing equimolar amounts of 4F-Phe47 labeled M2 peptide and CF₃-Phe47 labeled M2 peptide and measuring F-CF₃ cross peaks in 2D ¹⁹F¹⁹F correlation spectra, we show that M2 tetramers form nanometer-scale clusters in lipid bilayers. This clustering is stronger in cholesterol-containing membranes and phosphatidylethanolamine (PE) membranes than in cholesterol-free phosphatidylcholine and phosphatidylglycerol membranes. The observed correlation peaks indicate that Phe47 sidechains from different tetramers are less than ~2 nm apart. ¹H¹⁹F correlation peaks between lipid chain protons and fluorinated Phe47 indicate that Phe47 is more deeply inserted into the lipid bilayer in the presence of cholesterol than in its absence, suggesting that Phe47 preferentially interacts with cholesterol. Static ³¹P NMR spectra indicate that M2 induces negative Gaussian curvature in the PE membrane. These results suggest that M2 tetramers cluster at cholesterol- and PE-rich regions of cell membranes to cause membrane curvature, which in turn can facilitate membrane scission in the last step of virus budding and release.

The interaction and orientation of Peptide KL4 in model membranes

We report on the orientation and location of synthetic pulmonary surfactant peptide KL₄, (KLLLL)₄K, in model lipid membranes. The partitioning depths of selectively deuterated leucine residues within KL₄ were determined in DPPC:POPG (4:1) and POPC:POPG (4:1) bilayers by oriented neutron diffraction. These measurements were combined with an NMR-generated model of the peptide structure to determine the orientation and partitioning of the peptide at the lipid-water interface. The results demonstrate KL₄ adopting an orientation that interacts with a single membrane leaflet. These observations are consistent with past ²H NMR and EPR studies (Antharam et al., 2009; Turner et al., 2014).

Dynamics of the Acinetobacter baumannii inner membrane under exogenous polyunsaturated fatty acid stress

Exogenous polyunsaturated fatty acids (PUFAs) are readily incorporated into the synthesis pathways of A. baumannii membrane phospholipids, where they contribute to reduced bacterial fitness and increased antimicrobial susceptibility. Here we examine the impact of PUFA membrane modification on membrane organisation and biophysical properties using coarse grained MARTINI simulations of chemically representative membrane models developed from mass-spectrometry datasets of an untreated, arachidonic acid (AA) treated and docosahexaenoic acid (DHA) treated A. baumannii membranes. Enzymatic integration of AA or DHA into phospholipids of the A. baumannii membrane resulted in modulation of membrane biophysical properties. Membrane thickness decreased slightly following PUFA treatment, concomitant with changes in the lateral area per lipid of each lipid headgroup class. PUFA treatment resulted in a decrease in membrane ordering and an increase in lipid lateral diffusion. Changes in lateral membrane organisation were observed in the PUFA treated membranes, with a concurrent increase in ordered cardiolipin domains and disordered PUFA-containing domains. Notably, separation between ordered and disordered domains was enhanced and was more pronounced for DHA relative to AA, providing a possible mechanism for greater antimicrobial action of DHA relative to AA observed experimentally. Furthermore, the membrane active antimicrobial, pentamidine, preferentially adsorbs to cardiolipin domains of the A. baumannii model membranes. This interaction, and membrane penetration of pentamidine, was enhanced following PUFA treatment. Cumulatively, this work explores the wide-ranging effects of PUFA incorporation on the A. baumannii membrane and provides a molecular basis for bacterial inner membrane disruption by PUFAs.

Multiscale lipid membrane dynamics as revealed by neutron spectroscopy

The plasma membrane is one of the principal structural components of the cell and, therefore, one of the key components of the cellular life. Because the membrane's dynamics links the membrane's structure and function, the complexity and the broad range of the membrane's motions are essential for the enormously diverse functionality of the cell membrane. Even for the main membrane component, the lipid bilayer, considered alone, the range and complexity of the lipid motions are remarkable. Spanning the time scale from sub-picosecond to minutes and hours, the lipid motion in a bilayer is challenging to study even when a broad array of dynamic measurement techniques is employed. Neutron scattering plays a special role among such dynamic measurement techniques, particularly, because it involves the energy transfers commensurate with the typical intra- and inter- molecular dynamics and the momentum transfers commensurate with intra- and inter-molecular distances. Thus, using neutron scattering-based techniques, the spatial and temporal information on the lipid motion can be obtained and analysed simultaneously. Protium vs. deuterium sensitivity and non-destructive character of the neutron probe add to the remarkable prowess of neutron scattering for elucidating the lipid dynamics. Herein we present an overview of the neutron scattering-based studies of lipid dynamics in model membranes, with a discussion of the direct relevance and implications to the real-life cell membranes. The latter are much more complex systems than simple model membranes, consisting of heterogeneous non-stationary domains composed of lipids, proteins, and other small molecules, such as carbohydrates. Yet many fundamental aspects of the membrane behavior and membrane interactions with other molecules can be understood from neutron scattering measurements of the model membranes. For example, such studies can provide a great deal of information on the interactions of antimicrobial compounds with the lipid matrix of a pathogen membrane, or the interactions of drug molecules with the plasma membrane. Finally, we briefly discuss the recently emerging field of neutron scattering membrane studies with a reach far beyond the model membrane systems.

Phosphatidylserine and Phosphatidylethanolamine Asymmetry Have a Negligible Effect on the Global Structure, Dynamics, and Interactions of the KRAS Lipid Anchor

The intrinsically disordered C-terminus of the prominent oncogenic protein KRAS-4B (KRAS) selectively interacts and clusters with phosphatidylserine (PS) lipids in the plasma membrane (PM). This 11-residue segment, called tK, contains a polybasic domain (PBD) of six contiguous lysine residues and a farnesylated cysteine. Previous molecular dynamics (MD) simulation studies of tK in phosphatidylcholine (PC)/PS bilayers have suggested that backbone conformational dynamics modulate tK-PS interactions. These simulations have been conducted in symmetric membranes whereas the PM is compositionally asymmetric, with the inner leaflet, where KRAS is localized, being enriched with PS and phosphatidylethanolamine (PE) lipids. To examine if bilayer asymmetry affects tK conformational dynamics and interaction with lipids, we conducted two 10 μs long MD simulations of tK bound to a PC/PS and a PC/PS/PE bilayer in which the PS and PE lipids are distributed in one leaflet. We found that, first, these compositional asymmetries caused differences in acyl chain dynamics between leaflets, but the equilibrium structural and dynamic properties of the two asymmetric bilayers are similar; second, in both systems tK is highly dynamic and samples at least two distinct conformational states; third, PS-tK hydrogen-bonding interactions vary with peptide backbone conformations, and lysine side chains in the PBD predominantly interact with the serine oxygens of PS. These results are in good agreement with previous observations of tK in symmetric membranes. The effects of POPS asymmetry or the presence of POPE on tK are limited to modulating the relative contribution of individual side chains to interactions with lipids and redistributing conformational substates. Additional observations include the larger flexibility of tK in the current simulations, which we attribute to the longer duration of the simulations and the use of the CHARMM36m force field, which more accurately models intrinsically disordered peptides such as tK.

Multiscale Dynamics of Lipid Vesicles in Polymeric Microenvironment

Understanding dynamic and complex interaction of biological membranes with extracellular matrices plays a crucial role in controlling a variety of cell behavior and functions, from cell adhesion and growth to signaling and differentiation. Tremendous interest in tissue engineering has made it possible to design polymeric scaffolds mimicking the topology and mechanical properties of the native extracellular microenvironment; however, a fundamental question remains unanswered: that is, how the viscoelastic extracellular environment modifies the hierarchical dynamics of lipid membranes. In this work, we used aqueous solutions of poly(ethylene glycol) (PEG) with different molecular weights to mimic the viscous medium of cells and nearly monodisperse unilamellar DMPC/DMPG liposomes as a membrane model. Using small-angle X-ray scattering (SAXS), dynamic light scattering, temperature-modulated differential scanning calorimetry, bulk rheology, and fluorescence lifetime spectroscopy, we investigated the structural phase map and multiscale dynamics of the liposome–polymer mixtures. The results suggest an unprecedented dynamic coupling between polymer chains and phospholipid bilayers at different length/time scales. The microviscosity of the lipid bilayers is directly influenced by the relaxation of the whole chain, resulting in accelerated dynamics of lipids within the bilayers in the case of short chains compared to the polymer-free liposome case. At the macroscopic level, the gel-to-fluid transition of the bilayers results in a remarkable thermal-stiffening behavior of polymer–liposome solutions that can be modified by the concentration of the liposomes and the polymer chain length.

Impact of Surface Polarity on Lipid Assembly under Spatial Confinement

Molecular dynamics (MD) simulations in the MARTINI model are used to study the assembly of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) molecules under spatial confinement, such as during solvent evaporation from ultrasmall (femtoliter quantity) droplets. The impact of surface polarity on molecular assembly is discussed in detail. To the best of our knowledge, this work represents the first of its kind. Our results reveal that solvent evaporation gives rise to the formation of well-defined stacks of lipid bilayers in a smectic alignment. These smectic mesophases form on both polar and nonpolar surfaces but with a notable distinction. On polar surfaces, the director of the stack is oriented perpendicular to the support surface. By contrast, the stacks orient at an angle on the nonpolar surfaces. The packing of head groups on surfaces and lipid molecular mobility exhibits significant differences as surface polarity changes. The role of glycerol in the assembly and stability is also revealed. The insights revealed from the simulation have a significant impact on additive manufacturing, biomaterials, model membranes, and engineering protocells. For example, POPC assemblies via evaporation of ultrasmall droplets were produced and characterized. The trends compare well with the bilayer stack models. The surface polarity influences the local morphology and structures at the interfaces, which could be rationalized via the molecule-surface interactions observed from simulations.

Studying KcsA Channel Clustering Using Single Channel Voltage-Clamp Fluorescence Imaging*

Oligomerization and complex formation play a key role for many membrane proteins and has been described to influence ion channel function in both neurons and the heart. In this study, we observed clustering of single KcsA channels in planar lipid bilayer using single molecule fluorescence, while simultaneously measuring single channel currents. Clustering coincided with cooperative opening of KcsA. We demonstrate that clustering was not caused by direct protein-protein interactions or hydrophobic mismatch with the lipid environment, as suggested earlier, but was mediated via microdomains induced by the channel in the lipid matrix. We found that single channel activity of KcsA requires conically-shaped lipids in the lamellar liquid-crystalline (L_α) phase, and the need for a negative spontaneous curvature seem to lead to the deformations in the membrane that cause the clustering. The method introduced here will be applicable to follow oligomerization of a wide range of membrane proteins.

Non-ionic detergent assists formation of supercharged nanodiscs and insertion of membrane proteins

Nanodiscs are used to stabilize membrane proteins in a lipid environment and enable investigations of the function and structure of these. Membrane proteins are often only available in small amounts, and thus the stability and ease of use of the nanodiscs are essential. We have recently explored circularizing and supercharging membrane scaffolding proteins (MSPs) for nanodisc formation and found increased temporal stability at elevated temperatures. In the present study, we investigate six different supercharged MSPs and their ability to form nanodiscs: three covalently circularized and the three non-circularized, linear versions. Using standard reconstitution protocols using cholate as the reconstitution detergent, we found that two of the linear constructs formed multiple lipid-protein species, whereas adding n-Dodecyl-B-D-maltoside (DDM) with the cholate in the reconstitution gave rise to single-species nanodisc formation for these MSPs. For all MSPs, the formed nanodiscs were analyzed by small-angle X-ray scattering (SAXS), which showed similar structures for each MSP, respectively, suggesting that the structures of the formed nanodiscs are independent of the initial DDM content, as long as cholate is present. Lastly, we incorporated the membrane protein proteorhodopsin into the supercharged nanodiscs and observed a considerable increase in incorporation yield with the addition of DDM. For the three circularized MSPs, a single major species appeared in the size exclusion chromatography (SEC) chromatogram, suggesting monodisperse nanodiscs with proteorhodopsin incorporated, which is in strong contrast to the samples without DDM showing almost no incorporation and high polydispersity.

Interaction of Docetaxel with Phosphatidylcholine Membranes: A Combined Experimental and Computational Study

The antineoplastic drug Docetaxel is a second generation taxane which is used against a great variety of cancers. The drug is highly lipophilic and produces a great array of severe toxic effects that limit its therapeutic effectiveness. The study of the interaction between Docetaxel and membranes is very scarce, however, it is required in order to get clues in relation with its function, mechanism of toxicity and possibilities of new formulations. Using phosphatidylcholine biomimetic membranes, we examine the interaction of Docetaxel with the phospholipid bilayer combining an experimental study, employing a series of biophysical techniques like Differential Scanning Calorimetry, X-Ray Diffraction and Infrared Spectroscopy, and a Molecular Dynamics simulation. Our experimental results indicated that Docetaxel incorporated into DPPC bilayer perturbing the gel to liquid crystalline phase transition and giving rise to immiscibility when the amount of the drug is increased. The drug promotes the gel ripple phase, increasing the bilayer thickness in the fluid phase, and is also able to alter the hydrogen-bonding interactions in the interfacial region of the bilayer producing a dehydration effect. The results from computational simulation agree with the experimental ones and located the Docetaxel molecule forming small clusters in the region of the carbon 8 of the acyl chain palisade overlapping with the carbonyl region of the phospholipid. Our results support the idea that the anticancer drug is embedded into the phospholipid bilayer to a limited amount and produces structural perturbations which might affect the function of the membrane.

Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis

Cleavage of membrane proteins in the lipid bilayer by intramembrane proteases is crucial for health and disease. Although different lipid environments can potently modulate their activity, how this is linked to their structural dynamics is unclear. Here, we show that the carboxy-peptidase-like activity of the archaeal intramembrane protease PSH, a homolog of the Alzheimer’s disease-associated presenilin/γ-secretase is impaired in micelles and promoted in a lipid bilayer. Comparative molecular dynamics simulations revealed that important elements for substrate binding such as transmembrane domain 6a of PSH are more labile in micelles and stabilized in the lipid bilayer. Moreover, consistent with an enhanced interaction of PSH with a transition-state analog inhibitor, the bilayer promoted the formation of the enzyme’s catalytic active site geometry. Our data indicate that the lipid environment of an intramembrane protease plays a critical role in structural stabilization and active site arrangement of the enzyme-substrate complex thereby promoting intramembrane proteolysis.

Cutting proteins into pieces is a crucial process in the cell, allowing several important processes to take place, including cell differentiation (which allows cells to develop into specific types), cell death, protein quality control, or even where in the cell a protein will end up. However, the specialized proteins that carry out this task, known as proteases, can also be involved in the development of disease. For example, in the brain, a protease called γ-secretase cuts up the amyloid-β protein precursor, producing toxic forms of amyloid-β peptides that are widely believed to cause Alzheimer’s disease.

Proteases like γ-secretase carry out their role in the membrane, the layer of fats (also known as lipids) that forms the outer boundary of the cell. The environment in this area of the cell can influence the activity of proteases, but it is poorly understood how this happens.

One way to address this question would be to compare the activity of γ-secretase in the lipid environment of the membrane to its activity when it is entirely surrounded by different molecules, such as detergent molecules. Unfortunately, γ-secretase is not active when it is removed from its lipid environment by a detergent, making it difficult to perform this comparison. To overcome this issue, Feilen et al. chose to study PSH, a protease similar to γ-secretase that produces the same amyloid-β peptides but remains active in detergent.

When Feilen et al. mixed PSH with lipid molecules like those found in the membrane and amyloid-β precursor protein, PSH produced amyloid-β peptides including those that are thought to cause Alzheimer’s. However, when a detergent was substituted for the lipid molecules this led to longer amyloid-β peptides than usual, indicating that PSH was not able to cut proteins as effectively. The change in environment appeared to reduce PSH’s ability to progressively trim small segments from the peptides.

Computer modelling of the protease’s structure in lipids versus detergent supported the experimental findings: the model predicted that the areas of PSH important for recognizing and cutting other proteins would be more stable in the membrane compared to the detergent.

These results indicate that the cell membrane plays a vital role in the stability of the active regions of proteases that are cleaving in this environment. In the future, this could help to better understand how changes to the lipid molecules in the membrane may contribute to the activity of γ-secretase and its role in Alzheimer’s disease.

Absorption of the [bmim][Cl] Ionic Liquid in DMPC Lipid Bilayers across Their Gel, Ripple, and Fluid Phases

Lipid bilayers are a key component of cell membranes and play a crucial role in life and in bio-nanotechnology. As a result, controlling their physicochemical properties holds the promise of effective therapeutic strategies. Ionic liquids (ILs)─a vast class of complex organic electrolytes─have shown a high degree of affinity with lipid bilayers and can be exploited in this context. However, the chemical physics of IL absorption and partitioning into lipid bilayers is yet to be fully understood. This work focuses on the absorption of the model IL [bmim][Cl] into 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayers across their gel, ripple, and fluid phases. Here, by small-angle neutron scattering, we show that (i) the IL cations are absorbed in the lipid bilayer in all its thermodynamic phases and (ii) the amount of IL inserted into the lipid phase increased with increasing temperature, changing from three to four IL cations per 10 lipids with increasing temperature from 10 °C in the gel phase to 40 °C in the liquid phase, respectively. An explicative hypothesis, based on the entropy gain coming from the IL hydration water, is presented to explain the observed temperature trend. The ability to control IL absorption with temperature can be used as a handle to tune the effect of ILs on biomembranes and can be exploited in bio-nanotechnological applications.

Actin protein inside DMPC GUVs and its mechanical response to AC electric fields

Cells are dynamic systems with complex mechanical properties, regulated by the presence of different species of proteins capable to assemble (and disassemble) into filamentous forms as required by different cells functions. Giant unilamellar vesicles (GUVs) of DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) are systems frequently used as a simplified model of cells because they offer the possibility of assaying separately different stimuli, which is no possible in living cells. Here we present a study of the effect of acting protein on mechanical properties of GUVs, when the protein is inside the vesicles in either monomeric G-actin or filamentous F-actin. For this, rabbit skeletal muscle G-actin is introduced inside GUVs by the electroformation method. Protein polymerization inside the GUVs is promoted by adding to the solution MgCl₂ and the ion carrier A23187 to allow the transport of Mg⁺² ions into the GUVs. To determine how the presence of actin changes the mechanical properties of GUVs, the vesicles are deformed by the application of an AC electric field in both cases with G-actin and with polymerized F-actin. The changes in shape of the vesicles are characterized by optical microscopy and from them the bending stiffness of the membrane are determined. It is found that G-actin has no appreciable effect on the bending stiffness of DMPC GUVs, but the polymerized actin makes the vesicles more rigid and therefore more resistant to deformations. This result is supported by evidence that actin filaments tend to accumulate near the membrane.

Molecular packing of lipid membranes and action mechanisms of membrane-active peptides

Biomembranes are involved in diverse cellular activities. How membranes and proteins interact in the activities might hinge on the former's physical characteristics, which in turn are influenced by packing of lipid molecules. Yet, the validity of this understanding and its mechanism are unclear. By varying chain saturation of membranes, we explored correlations between lipid packing and peptide-mediated membrane disruption for the antimicrobial peptide, melittin, and amyloidogenic peptide, β-amyloid (1-42). Remarkably, reducing molecular packing flexibility enhanced the membrane disruption, possibly due to a shift from membrane perforation to micellization. A theoretical analysis suggested the energetic basis of this shift. This mechanistically shows that a peptide's mechanism might be dictated not only by its intrinsic properties but also by physical characteristics of membranes.

Structures and Dynamics of Anionic Lipoprotein Nanodiscs

Nanolipoprotein particles known as nanodiscs (NDs) have emerged as versatile and powerful tools for the stabilization of membrane proteins permitting a plethora of structural and biophysical studies. Part of their allure is their flexibility to accommodate many types of lipids and precise control of the composition. However, little is known about how variations in lipid composition impact their structures and dynamics. Herein, we investigate how the introduction of the anionic lipid POPG into POPC NDs impacts these features. Small-angle X-ray and neutron scattering (SAXS and SANS) of variable-composition NDs are complemented with molecular dynamics simulations to interrogate how increasing the concern of POPG impacts the ND shape, structure of the lipid core, and the dynamics of the popular membrane scaffold protein, MSP1D1(-). A convenient benefit of including POPG is that it eliminates D₂O-induced aggregation observed in pure POPC NDs, permitting studies by SANS at multiple contrasts. SAXS and SANS data could be globally fit to a stacked elliptical cylinder model as well as an extension of the model that accounts for membrane curvature. Fitting to both models supports that the introduction of POPG results in strongly elliptical NDs; however, MD simulations predict the curvature of the membrane, thereby supporting the use of the latter model. Trends in the model-independent parameters suggest that increases in POPG reduce the conformational heterogeneity of the MSP1D1(-), which is in agreement with MD simulations that show that the incorporation of sufficient POPG suppresses disengagement of the N-terminal helix from the lipid core. These studies highlight novel structural changes in NDs in response to an anionic lipid and will inform the interpretation of future structural studies of membrane proteins embedded in NDs of mixed lipid composition.

Optocapacitance: physical basis and its application

The observation that membrane capacitance increases with temperature has led to the development of new methods of neuronal stimulation using light. The optocapacitive effect refers to a light-induced change in capacitance produced by the heating of the membrane through a photothermal effect. This change in capacitance manifests as a current, named optocapacitive current that depolarizes cells and therefore can be used to stimulate excitable tissues. Here, we discuss how optocapacitance arises from basic membrane properties, the characteristics of the optocapacitive current, its use for neuronal stimulation, and the challenges for its application in vivo.

Lipid tails modulate antimicrobial peptide membrane incorporation and activity

Membrane disrupting antimicrobial peptides (AMPs) are often amphipathic peptides that interact directly with lipid bilayers. AMPs are generally thought to interact mostly with lipid head groups, but it is less clear how the lipid alkyl chain length and saturation modulate interactions with membranes. Here, we used native mass spectrometry to measure the stoichiometry of three different AMPs-LL-37, indolicidin, and magainin-2-in lipid nanodiscs. We also measured the activity of these AMPs in unilamellar vesicle leakage assays. We found that LL-37 formed specific hexamer complexes but with different intermediates and affinities that depended on the bilayer thickness. LL-37 was also most active in lipid bilayers containing longer, unsaturated lipids. In contrast, indolicidin incorporated to a higher degree into more fluid lipid bilayers but was more active with bilayers with thinner, less fluid lipids. Finally, magainin-2 incorporated to a higher degree into bilayers with longer, unsaturated alkyl chains and showed more activity in these same conditions. Together, these data show that higher amounts of peptide incorporation generally led to higher activity and that AMPs tend to incorporate more into longer unsaturated lipid bilayers. However, the activity of AMPs was not always directly related to amount of peptide incorporated.

The interaction of styrene maleic acid copolymers with phospholipids in Langmuir monolayers, vesicles and nanodiscs; a structural study

HYPOTHESIS

Self-assembly of amphipathic styrene maleic acid copolymers with phospholipids in aqueous solution results in the formation of 'nanodiscs' containing a planar segment of phospholipid bilayer encapsulated by a polymer belt. Recently, studies have reported that lipids rapidly exchange between both nanodiscs in solution and external sources of lipids. Outstanding questions remain regarding details of polymer-lipid interactions, factors influencing lipid exchange and structural effects of such exchange processes. Here, the dynamic behaviour of nanodiscs is investigated, specifically the role of membrane charge and polymer chemistry.

EXPERIMENTS

Two model systems are investigated: fluorescently labelled phospholipid vesicles, and Langmuir monolayers of phospholipids. Using fluorescence spectroscopy and time-resolved neutron reflectometry, the membrane potential, monolayer structure and composition are monitored with respect to time upon polymer and nanodisc interactions.

FINDINGS

In the presence of external lipids, polymer chains embed throughout lipid membranes, the extent of which is governed by the net membrane charge. Nanodiscs stabilised by three different polymers will all exchange lipids and polymer with monolayers to differing extents, related to the properties of the stabilising polymer belt. These results demonstrate the dynamic nature of nanodiscs which interact with the local environment and are likely to deposit both lipids and polymer at all stages of use.

Hydrocarbon Penetration into Phospholipid Monolayers Formed at Hydrocarbon-Water Interfaces

Phospholipid monolayers formed at oil-water interfaces are used for various biological applications. However, monolayer structures are not well understood. Herein, we investigated hydrocarbon partitioning in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine monolayers formed at hydrocarbon-water interfaces using fluorescence microscopy and pendant drop tensiometry. The monolayers strongly interacted with squalene, n-hexadecane, n-tetradecane, n-dodecane, n-decane, and n-butylcyclohexane. These alkane and alkylcyclohexane molecules remained within the monolayers during area compression. In contrast, the monolayers interacted weakly with n-pentylbenzene and n-butylbenzene. These alkylbenzenes were gradually removed from the monolayers upon area compression and were completely expelled at an area per lipid of ∼70 Ų. Surface pressure analysis indicated that the ability of hydrocarbons to penetrate the monolayers was enhanced in the order of n-butylbenzene < n-pentylbenzene < n-butylcyclohexane < n-hexadecane.

A vesicle microrheometer for high-throughput viscosity measurements of lipid and polymer membranes

Viscosity is a key property of cell membranes that controls mobility of embedded proteins and membrane remodeling. Measuring it is challenging because existing approaches involve complex experimental designs and/or models, and the applicability of some methods is limited to specific systems and membrane compositions. As a result there is scarcity of systematic data, and the reported values for membrane viscosity vary by orders of magnitude for the same system. Here, we show how viscosity of membranes can be easily obtained from the transient deformation of giant unilamellar vesicles. The approach enables a noninvasive, probe-independent, and high-throughput measurement of the viscosity of membranes made of lipids or polymers with a wide range of compositions and phase state. Using this novel method, we have collected a significant amount of data that provides insights into the relation between membrane viscosity, composition, and structure.

A Water Soluble 2-Phenyl-5-(pyridin-3-yl)-1,3,4-oxadiazole Based Probe: Antimicrobial Activity and Colorimetric/Fluorescence pH Response

The growing demand of responsive tools for biological and biomedical applications pushes towards new low-cost probes easy to synthesize and versatile. Current optical probes are theranostic tools simultaneously responsive to biological parameters/analyte and therapeutically operating. Among the optical methods for pH monitoring, simple small organic molecules including multifunctional probes for simultaneous biological activity being highly desired by scientists and technicians. Here, we present a novel pH-responsive probe with a three-ring heteroaromatic pattern and a flexible cationic chain. The novel molecule shows real-time naked-eye colorimetric and fluorescence response in the slightly acidic pH range besides its excellent solubility both in the organic phase and in water. In addition, the small probe shows significant antibacterial activity, particularly against Escherichia coli. Single-crystal X-ray study and density functional theory (DFT) calculations rationalize the molecule spectroscopic response. Finally, molecular dynamics (MD) elucidate the interactions between the probe and a model cell membrane.

Visualizing Lipid Dynamics Role in Infrared Neural Stimulation using Stimulated Raman Scattering

Infrared neural stimulation, or INS, uses pulsed infrared light to yield label-free neural stimulation with broad experimental and translational utility. Despite its robust demonstration, INS's mechanistic and biophysical underpinnings have been the subject of debate for more than a decade. The role of lipid membrane thermodynamics appears to play an important role in how fast IR-mediated heating nonspecifically drives action potential generation. Direct observation of lipid membrane dynamics during INS remains to be shown in a live neural model system. We used hyperspectral stimulated Raman scattering (hsSRS) microscopy to study biochemical signatures of high-speed vibrational dynamics underlying INS in a live neural cell culture model. Findings suggest that lipid bilayer structural changes are occurring during INS in vitro in NG108-15 neuroglioma cells. Lipid-specific signatures of cell SRS spectra varied with stimulation energy and radiant exposure. Spectroscopic observations agree with high-speed ratiometric fluorescence imaging of a conventional lipophilic membrane structure reporter, di-4-ANNEPS. Overall, the presented findings support the hypothesis that INS causes changes in the lipid membrane of neural cells by changing lipid membrane packing order. Furthermore, this work highlights the potential of hsSRS as a method to study biophysical and biochemical dynamics safely in live cells.

Structure and dynamics of the somatostatin receptor 3-ligand binding in the presence of lipids examined using computational structural biology methods

In the past two decades, the structural biology studies on G-protein coupled receptors (GPCRs) are on the rise. Understanding the relation between the structure and function of GPCRs is important as they play a huge role in various signaling mechanisms in a eukaryotic cell. Somatostatin receptor 3 (SSTR3), one of the GPCRs, is one such important receptor which oversees different cellular processes including cell-to-cell signaling. However, the information available regarding the structural features of SSTR3 responsible for their bioactivity is scarce. In this study, we report a structural understanding of SSTR3-ligand binding that could be helpful in demystifying the structural complexities related to functioning of the receptor. An integrated protocol consisting of different computational structural biology tools including protein structure prediction via comparative modeling, binding site characterization, three-dimensional quantitative structure-activity relationship based on comparative molecular field analysis and comparative molecular similarity indices analysis, density functional theory, and molecular dynamics simulations were performed. Different understandings from the simulation of SSTR3-ligand complexes, mainly the conditions that are favorable for the formation of lowest bioactive state of SSTR3 ligands are reported. In addition to that, we report the important physicochemical descriptors of SSTR3 ligands that could significantly influence their bioactivity. The results of the study could be helpful in developing novel SSTR3 ligands (both agonists and antagonists) with high potency and receptor selectivity.

Probing lipid membrane bending mechanics using gold nanorod tracking

Lipid bilayer membranes undergo rapid bending undulations with wavelengths from tens of nanometers to tens of microns due to thermal fluctuations. Here, we probe such undulations and the membranes' mechanics by measuring the time-varying orientation of single gold nanorods (GNRs) adhered to the membrane, using high-speed dark field microscopy. In a lipid vesicle, such measurements allow the determination of the membrane's viscosity, bending rigidity, and tension as well as the friction coefficient for sliding of the monolayers over one another. The in-plane rotation of the GNR is hindered by undulations in a tension dependent manner, consistent with simulations. The motion of single GNRs adhered to the plasma membrane of living cultured cells similarly reveals the membrane's complex physics and coupling to the cell's actomyosin cortex.

Lipid-mediated antimicrobial resistance: a phantom menace or a new hope?

The proposition of a post-antimicrobial era is all the more realistic with the continued rise of antimicrobial resistance. The development of new antimicrobials is failing to counter the ever-increasing rates of bacterial antimicrobial resistance. This necessitates novel antimicrobials and drug targets. The bacterial cell membrane is an essential and highly conserved cellular component in bacteria and acts as the primary barrier for entry of antimicrobials into the cell. Although previously under-exploited as an antimicrobial target, the bacterial cell membrane is attractive for the development of novel antimicrobials due to its importance in pathogen viability. Bacterial cell membranes are diverse assemblies of macromolecules built around a central lipid bilayer core. This lipid bilayer governs the overall membrane biophysical properties and function of its membrane-embedded proteins. This mini-review will outline the mechanisms by which the bacterial membrane causes and controls resistance, with a focus on alterations in the membrane lipid composition, chemical modification of constituent lipids, and the efflux of antimicrobials by membrane-embedded efflux systems. Thorough insight into the interplay between membrane-active antimicrobials and lipid-mediated resistance is needed to enable the rational development of new antimicrobials. In particular, the union of computational approaches and experimental techniques for the development of innovative and efficacious membrane-active antimicrobials is explored.

The Role of Lipids in Allosteric Modulation of Dopamine D2 Receptor-In Silico Study

The dopamine D₂ receptor, belonging to the class A G protein-coupled receptors (GPCRs), is an important drug target for several diseases, including schizophrenia and Parkinson’s disease. The D₂ receptor can be activated by the natural neurotransmitter dopamine or by synthetic ligands, which in both cases leads to the receptor coupling with a G protein. In addition to receptor modulation by orthosteric or allosteric ligands, it has been shown that lipids may affect the behaviour of membrane proteins. We constructed a model of a D₂ receptor with a long intracellular loop (ICL3) coupled with G_iα1 or G_iα2 proteins, embedded in a complex asymmetric membrane, and simulated it in complex with positive, negative or neutral allosteric ligands. In this study, we focused on the influence of ligand binding and G protein coupling on the membrane–receptor interactions. We show that there is a noticeable interplay between the cell membrane, G proteins, D₂ receptor and its modulators.

Lipid21: Complex Lipid Membrane Simulations with AMBER

We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell membrane lipid compositions, including raft-like domains. Head group torsion parameters are revised, resulting in improved agreement with NMR order parameters, and hydrocarbon chain parameters are updated, providing a better match with phase transition temperature. Extensive validation runs (0.9 μs per lipid type) show good agreement with experimental measurements. Furthermore, the simulation of raft-like bilayers demonstrates the perturbing effect of increasing PUFA concentrations on cholesterol molecules. The force field derivation is consistent with the AMBER philosophy, meaning it can be easily mixed with protein, small molecule, nucleic acid, and carbohydrate force fields.

Cell-Free Expression to Probe Co-Translational Insertion of an Alpha Helical Membrane Protein

The majority of alpha helical membrane proteins fold co-translationally during their synthesis on the ribosome. In contrast, most mechanistic folding studies address refolding of full-length proteins from artificially induced denatured states that are far removed from the natural co-translational process. Cell-free translation of membrane proteins is emerging as a useful tool to address folding during translation by a ribosome. We summarise the benefits of this approach and show how it can be successfully extended to a membrane protein with a complex topology. The bacterial leucine transporter, LeuT can be synthesised and inserted into lipid membranes using a variety of in vitro transcription translation systems. Unlike major facilitator superfamily transporters, where changes in lipids can optimise the amount of correctly inserted protein, LeuT insertion yields are much less dependent on the lipid composition. The presence of a bacterial translocon either in native membrane extracts or in reconstituted membranes also has little influence on the yield of LeuT incorporated into the lipid membrane, except at high reconstitution concentrations. LeuT is considered a paradigm for neurotransmitter transporters and possesses a knotted structure that is characteristic of this transporter family. This work provides a method in which to probe the formation of a protein as the polypeptide chain is being synthesised on a ribosome and inserting into lipids. We show that in comparison with the simpler major facilitator transporter structures, LeuT inserts less efficiently into membranes when synthesised cell-free, suggesting that more of the protein aggregates, likely as a result of the challenging formation of the knotted topology in the membrane.

A general computational framework for the dynamics of single- and multi-phase vesicles and membranes

The dynamics of thin, membrane-like structures are ubiquitous in nature. They play especially important roles in cell biology. Cell membranes separate the inside of a cell from the outside, and vesicles compartmentalize proteins into functional microregions, such as the lysosome. Proteins and/or lipid molecules also aggregate and deform membranes to carry out cellular functions. For example, some viral particles can induce the membrane to invaginate and form an endocytic vesicle that pulls the virus into the cell. While the physics of membranes has been extensively studied since the pioneering work of Helfrich in the 1970's, simulating the dynamics of large scale deformations remains challenging, especially for cases where the membrane composition is spatially heterogeneous. Here, we develop a general computational framework to simulate the overdamped dynamics of membranes and vesicles. We start by considering a membrane with an energy that is a generalized functional of the shape invariants and also includes line discontinuities that arise due to phase boundaries. Using this energy, we derive the internal restoring forces and construct a level set-based algorithm that can stably simulate the large-scale dynamics of these generalized membranes, including scenarios that lead to membrane fission. This method is applied to solve for shapes of single-phase vesicles using a range of reduced volumes, reduced area differences, and preferred curvatures. Our results match well the experimentally measured shapes of corresponding vesicles. The method is then applied to explore the dynamics of multiphase vesicles, predicting equilibrium shapes and conditions that lead to fission near phase boundaries.

Oligosaccharide Presentation Modulates the Molecular Recognition of Glycolipids by Galectins on Membrane Surfaces

Galectins are a family of glycan binding proteins that stand out for the wide range of biological phenomena in which they are involved. Most galectin functions are associated with their glycan binding capacities, which are generally well characterized at the oligosaccharide level, but not at the glycoprotein or glycolipid level. Glycolipids form the part of cell membranes where they can act as galectin cellular receptors. In this scenario, glycan presentation as well as the membrane chemical and structural features are expected to have a strong impact in these molecular association processes. Herein, liposomes were used as membrane mimicking scaffolds for the presentation of glycosphingolipids (GSLs) and to investigate their interaction with Galectin-3 and the N-domain of Galectin-8 (Gal8N). The binding towards GM3 and GM1 and their non-silaylated GSLs was compared to the binding to the free glycans, devoid of lipid. The analysis was carried out using a combination of NMR methods, membrane perturbation studies, and molecular modeling. Our results showed a different tendency of the two galectins in their binding capacities towards the glycans, depending on whether they were free oligosaccharides or as part of GSL inserted into a lipid bilayer, highlighting the significance of GSL glycan presentation on membranes in lectin binding.