Composition Fluctuations in Lipid Bilayers

Building complex membranes with Martini 3

The Martini model is a popular force field for coarse-grained simulations. Membranes have always been at the center of its development, with the latest version, Martini 3, showing great promise in capturing more and more realistic behavior. In this chapter we provide a step-by-step tutorial on how to construct starting configurations, run initial simulations and perform dedicated analysis for membrane-based systems of increasing complexity, including leaflet asymmetry, curvature gradients and embedding of membrane proteins.

Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes

A multistep computational approach has been employed to study a multimillion all-atom dyed plasma membrane, with no less than 42 different lipid species spanning the major head groups and a variety of fatty acids, as well as cholesterol, with the objective of investigating its structure and dynamics, as well as its impact on the embedded di-8-ANEPPS dyes. The latter are commonly used as bioimaging probes and serve as local microscopes. So, they provide information on membrane morphology via their second harmonic nonlinear optical (NLO) responses, which have the advantage of being specific to interface regions and sensitive to the chromophore environment. In previous studies, this chromophore has only been studied in simpler membrane models, far from the complexity of real lipid bilayers, while, owing to the ever-increasing computational resources, multimillion lipid bilayers have been studied, giving access to the effects of its heterogeneity. First, using molecular dynamics (MD) simulations, it is found that the combination of lipids produces a more ordered and denser membrane compared to its homogeneous model counterparts, while the local environment of the embedded dyes becomes enriched in phosphatidylcholine. Subsequently, the second harmonic first hyperpolarizability of the probes was calculated at the TDDFT level on selected frames of MD, highlighting the influence of the lipid environment. Due to the complexity of the system, machine learning (ML) tools have been employed to establish relationships between the membrane structural parameters, the orientation of the probes, and their NLO responses. These ML approaches have revealed influential features, including the presence of diacylglycerol lipids close to the dye. On the whole, this work provides a first step toward understanding the cooperation, synergy, and interactions that occur in such complex guest-host environments, which have emerged as new targets for drug design and membrane lipid therapy.

Anomalous lateral diffusion of lipids during the fluid/gel phase transition of a lipid membrane

A lipid membrane undergoes a phase transition from fluid to gel phase upon changing external thermodynamic conditions, such as decreasing temperature and increasing pressure. Extremophilic organisms face the challenge of preventing this deleterious phase transition. The main focus of their adaptive strategy is to facilitate effective temperature sensing through sensor proteins, relying on the drastic changes in packing density and membrane fluidity during the phase transition. Although the changes in packing density parameters due to the fluid/gel phase transition are studied in detail, the impact on membrane fluidity is less explored in the literature. Understanding the lateral diffusive dynamics of lipids in response to temperature, particularly during the fluid/gel phase transition, is albeit crucial. Here we have simulated the phase transition of a single component lipid membrane composed of dipalmitoylphosphatidylcholine (DPPC) lipids using a coarse-grained (CG) model and studied the changes of the structural and dynamical properties. It is observed that near the phase transition point, both fluid and gel phase domains coexist together. The dynamics remains highly non-Gaussian for a long time even when the mean square displacement reaches the Fickian regime at a much earlier time. This Fickian yet non-Gaussian diffusion (FnGD) is a characteristic of a highly heterogeneous system, previously observed for the lateral diffusion of lipids in raft mimetic membranes having liquid-ordered and liquid-disordered phases co-existing together. We have analyzed the molecular trajectories and calculated the jump-diffusion of the lipids, stemming from sudden jump translations, using a translational jump-diffusion (TJD) approach. An overwhelming contribution of the jump-diffusion of the lipids is observed suggesting anomalous diffusion of lipids during fluid/gel phase transition of the membrane. These results are important in unravelling the intricate nature of lipid diffusion during the phase transition of the membrane and open up a new possibility of investigating the most significant change of membrane properties during phase transition, which can be effectively sensed by proteins.

Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling

It is known that the behavior of many complex systems is controlled by local dynamic rearrangements or fluctuations occurring within them. Complex molecular systems, composed of many molecules interacting with each other in a Brownian storm, make no exception. Despite the rise of machine learning and of sophisticated structural descriptors, detecting local fluctuations and collective transitions in complex dynamic ensembles remains often difficult. Here, we show a machine learning framework based on a descriptor which we name Local Environments and Neighbors Shuffling (LENS), that allows identifying dynamic domains and detecting local fluctuations in a variety of systems in an abstract and efficient way. By tracking how much the microscopic surrounding of each molecular unit changes over time in terms of neighbor individuals, LENS allows characterizing the global (macroscopic) dynamics of molecular systems in phase transition, phases-coexistence, as well as intrinsically characterized by local fluctuations (e.g., defects). Statistical analysis of the LENS time series data extracted from molecular dynamics trajectories of, for example, liquid-like, solid-like, or dynamically diverse complex molecular systems allows tracking in an efficient way the presence of different dynamic domains and of local fluctuations emerging within them. The approach is found robust, versatile, and applicable independently of the features of the system and simply provided that a trajectory containing information on the relative motion of the interacting units is available. We envisage that "such a LENS" will constitute a precious basis for exploring the dynamic complexity of a variety of systems and, given its abstract definition, not necessarily of molecular ones.

How Do Cyclopropane Fatty Acids Protect the Cell Membrane of Escherichia coli in Cold Shock?

The cyclopropanation of unsaturated lipid acyl chains of some bacterial cell membranes is an important survival strategy to protect the same against drastic cooling. To elucidate the role of cyclopropane ring-containing lipids, we have simulated the lipid membrane of Escherichia coli (E. coli) and two modified membranes by replacing the cyclopropane rings with either single or double bonds at widely different temperatures. It has been observed that the cyclopropane rings provide more rigid kinks in the lipid acyl chain compared to the double bonds and therefore further reduce the packing density of the membrane and subsequently enhance the membrane fluidity at low temperatures. They also inhibit the close packing of other lipids and deleterious phase separation by strongly interacting with them. Therefore, this study has explained why E. coli bacterial strain, susceptible to freezing environments, relies on the cyclopropanation of an unsaturated chain.

A brief history of visualizing membrane systems in molecular dynamics simulations

Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.

In Vitro Membrane Platform for the Visualization of Water Impermeability across the Liquid-Ordered Phase under Hypertonic Conditions

Passive water penetration across the cell membrane by osmotic diffusion is essential for the homeostasis of cell volume, in addition to the protein-assisted active transportation of water. Since membrane components can regulate water permeability, controlling compositional variation during the volume regulatory process is a prerequisite for investigating the underlying mechanisms of water permeation and related membrane dynamics. However, the lack of a viable in vitro membrane platform in hypertonic solutions impedes advanced knowledge of cell volume regulation processes, especially cholesterol-enriched lipid domains called lipid rafts. By reconstituting the liquid-ordered (L_o) domain as a likeness of lipid rafts, we verified suppressed water permeation across the L_o domains, which had yet to be confirmed with experimental demonstrations despite a simulation approach. With the help of direct transfer of the L_o domains from vesicles to supported lipid membranes, the biological roles of lipid composition in suppressed water translocation were experimentally confirmed. Additionally, the improvement in membrane stability under hypertonic conditions was demonstrated based on molecular dynamics simulations.

Homeoviscous Adaptation of the Lipid Membrane of a Soil Bacterium Surviving under Diurnal Temperature Variation: A Molecular Simulation Perspective

A recent experiment has reported the lipidome remodeling of a soil-based plant-associated bacterium Methylobacterium extorquens due to diurnal temperature variations. The key adaptation strategy is the headgroup-specific remodeling of the acyl chain. To understand the idiosyncratic adaptation at the molecular level, we simulate the model membrane of the same bacterium using the reported lipidome compositions at four different experimental temperatures. We investigate the temperature-dependent packing density and fluidity of the membrane, the constancy of which is key to the homeoviscous adaptation. The results show that complex lipidome remodeling approximately preserves membrane properties under heat and cold stress. The headgroup-specific remodeling of the acyl chain serves to fine-tune the packing density and fluidity of the membrane at different temperatures. While lipids with strongly interacting headgroups are more abundant at higher temperatures, the lipidome is more dominated by lipids with weaker interacting headgroups at lower temperatures. This adaptation alleviates lipid membrane disruption caused by heat and cold stress. This study provides a molecular picture of the homeoviscous adaptation of the realistic lipid membrane of a soil-based bacterium.

Small ionic radii limit time step in Martini 3 molecular dynamics simulations

Among other improvements, the Martini~3 coarse-grained force field provides a more accurate description of the solvation of protein pockets and channels through the consistent use of various bead types and sizes. Here, we show that the representation of Na+ and Cl- ions as ``tiny' (TQ5) beads limits the accessible time step to 25~fs. By contrast, with Martini~2, time steps of 30-40~fs were possible for lipid bilayer systems without proteins. This limitation is relevant for systems that require long equilibration times. We derive a quantitative kinetic model of time-integration instabilities in molecular dynamics as a function of time step, ion concentration and mass, system size, and simulation time. We demonstrate that ion-water interactions are the main source of instability at physiological conditions, followed closely by ion-ion interactions. We show that increasing the ionic masses makes it possible to use time steps up to 40~fs with minimal impact on static equilibrium properties and on dynamical quantities such as lipid and ion diffusion coefficients. Increasing the size of the bead representing the ions (and thus changing their hydration) also permits longer time steps. For a soluble protein, we find that increasing the mass of tiny beads also on the protein permits simulations with 30-fs time step. The use of larger time steps in Martini~3 results in a more efficient exploration of configuration space. The kinetic model of MD simulation crashes can be used to determine the maximum allowed time step upfront for an efficient use of resources and whenever sampling efficiency is critical.

Biochemical and Metabolomic Responses of Antarctic Bacterium Planococcus sp. O5 Induced by Copper Ion

Heavy metal pollution in the Antarctic has gone beyond our imagination. Copper toxicity is a selective pressure on Planococcus sp. O5. We observed relatively broad tolerance in the polar bacterium. The heavy metal resistance pattern is Pb2+ > Cu2+ > Cd2+ > Hg2+ > Zn2+. In the study, we combined biochemical and metabolomics approaches to investigate the Cu2+ adaptation mechanisms of the Antarctic bacterium. Biochemical analysis revealed that copper treatment elevated the activity of antioxidants and enzymes, maintaining the bacterial redox state balance and normal cell division and growth. Metabolomics analysis demonstrated that fatty acids, amino acids, and carbohydrates played dominant roles in copper stress adaptation. The findings suggested that the adaptive mechanisms of strain O5 to copper stress included protein synthesis and repair, accumulation of organic permeable substances, up-regulation of energy metabolism, and the formation of fatty acids.

Can Urea and Trimethylamine-N-oxide Prevent the Pressure-Induced Phase Transition of Lipid Membrane?

Organisms dwelling in ocean trenches are exposed to the high hydrostatic pressure of ocean water. Increasing pressure can alter the membrane packing density and fluidity and trigger the fluid-to-gel phase transition. To combat environmental stress, the organisms synthesize small polar solutes, which are known as osmolytes. Urea and trimethylamine-N-oxide (TMAO) are two such solutes found in deep-sea creatures. While TMAO stabilizes protein, urea induces protein denaturation. These solutes strongly influence the packing density and membrane fluidity of the lipid bilayer at different conditions. But can these solutes affect the pressure-induced phase transition of the lipid membrane? In the present work, we have studied the effect of these two solutes on pressure-induced fluid-to-gel phase transition based on the all-atom molecular dynamics (MD) simulation approach. A high-pressure-stimulated fluid-to-gel phase transition of the membrane is seen at 800 bar, which is consistent with previous experiments. We have also observed that in the low-pressure region (1-400 bar), urea slightly increases the membrane fluidity where TMAO decreases the same. However, the phase transition pressure remains almost unchanged on the addition of urea while TMAO shifts the phase transition toward a lower pressure. We have found that the hydrogen (H)-bond interaction between lipid and urea plays an important role in preserving the fluidity of the membrane in the low-pressure zone. However, at a higher pressure, both water and urea are excluded from the membrane surface. TMAO is also excluded from the interfacial region of the membrane at all pressures. Exclusion from the membrane surface further triggers the phase transition of the lipid membrane from the fluid to gel phase at a high pressure.

Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations

Molecular dynamics (MD) simulations have become an indispensable tool to investigate phase separation in model membrane systems. In particular, simulations based on coarse-grained (CG) models have found widespread use due to their increased computational efficiency, allowing for simulations of multicomponent lipid bilayers undergoing phase separation into liquid-ordered and liquid-disordered domains. Here, we show that a significant temperature difference between molecule types can artificially arise in CG MD membrane simulations with the standard Martini simulation parameters in GROMACS. In particular, the linear constraint solver (LINCS) algorithm does not converge with its default settings, resulting in serious temperature differences between molecules in a time step-dependent manner. We demonstrate that the underlying reason for this behavior is the presence of highly constrained moieties, such as cholesterol. Their presence can critically impact numerous structural and dynamic membrane properties obtained from such simulations. Furthermore, any preference of these molecules toward a certain membrane phase can lead to spatial temperature gradients, which can amplify the degree of phase separation or even induce it in compositions that would otherwise mix well. We systematically investigated the effect of the integration time step and LINCS settings on membrane properties. Our data show that for cholesterol-containing membranes, a time step of 20 fs should be combined with at least lincs_iter = 2 and lincs_order = 12, while using a time step of 30 fs requires at least lincs_iter = 3 and lincs_order = 12 to bring the temperature differences to a level where they do not perturb central membrane properties. Moreover, we show that in cases where stricter LINCS settings are computationally too demanding, coupling the lipids in multiple groups to the temperature bath offers a practical workaround to the problem, although the validity of this approach should be further verified. Finally, we show that similar temperature gradients can also emerge in atomistic simulations using the CHARMM force field in combination with settings that allow for a 5 fs integration step.

Modulated and spiral surface patterns on deformable lipid vesicles

We investigate the behavior of two-dimensional systems that exhibit a transition between homogeneous and spatially inhomogeneous phases, which have spherical topology, and whose mechanical properties depend on the local value of the order parameter. One example of such a system is multicomponent lipid bilayer vesicles, which serve as a model to study cellular membranes. Under certain conditions, such bilayers separate into coexisting liquid-ordered and liquid-disordered regions. When arranged into the shape of small vesicles, this phase coexistence can result in spatial patterns that are more complex than the basic two-domain configuration encountered in typical bulk systems. The difference in bending rigidity between the liquid-ordered and liquid-disordered regions couples the shape of the vesicle to the local composition. We show that this interplay gives rise to a rich phase diagram that includes homogeneous, separated, and axisymmetric modulated phases that are divided by regions of spiral patterns in the surface morphology.

Cryostabilization of the Cell Membrane of a Psychrotolerant Bacteria via Homeoviscous Adaptation

Homeoviscous adaptation (maintenance of a critical balance between the saturated and unsaturated lipids) of the cell membrane of psychrotolerant bacteria is essential to protect them against freeze-thaw cycle. But how does the homeoviscous adaptation protect the cell membrane during cold stress? In this Letter, we answer this question using a coarse-grained molecular dynamics simulation technique. On the basis of the reported fatty acid profiles of psychrotolerant bacteria at different temperatures, multiple lipid membranes are simulated at a wide range of temperatures between 250 and 300 K. We explicate how the homeoviscous adaptation minimizes the effect of cold stress on the structure and fluidity of the membrane. Partial freezing of the saturated lipid domain occurs with the self-aggregation of saturated and unsaturated lipids near the melting temperature of the unadapted lipid membrane. The gel-like phase provides necessary local packing density that can be sensed by sensor proteins responsible for the homeoviscous adaptation.

Microscopic Picture of Calcium-Assisted Lipid Demixing and Membrane Remodeling Using Multiscale Simulations

The specificity of anionic phospholipids-calcium ion interaction and lipid demixing has been established as a key regulatory mechanism in several cellular signaling processes. The mechanism and implications of this calcium-assisted demixing have not been elucidated from a microscopic point of view. Here, we present an overview of atomic interactions between calcium and phospholipids that can drive nonideal mixing of lipid molecules in a model lipid bilayer composed of zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS)) lipids with computer simulations at multiple resolutions. Lipid nanodomain formation and growth were driven by calcium-enabled lipid bridging of the charged phosphatidylserine (PS) headgroups, which were favored against inter-POPS dipole interactions. Consistent with several experimental studies of calcium-associated membrane sculpting, our analyses also suggest modifications in local membrane curvature and cross-leaflet couplings as a response to such induced lateral heterogeneity. In addition, reverse mapping to a complementary atomistic description revealed structural insights in the presence of anionic nanodomains, at timescales not accessed by previous computational studies. This work bridges information across multiple scales to reveal a mechanistic picture of calcium ion's impact on membrane biophysics.

Laterally Resolved Small-Angle Scattering Intensity from Lipid Bilayer Simulations: An Exact and a Limited-Range Treatment

When combined, molecular simulations and small-angle scattering experiments are able to provide molecular-scale resolution of structure. Separately, scattering experiments provide only intermingled pair correlations between atoms, while molecular simulations are limited by model quality and the relatively short time scales that they can access. Their combined strength relies on agreement between the experimental spectra and those computed by simulation. To date, computing the neutron spectra from a molecular simulation of a lipid bilayer is straightforward only if the structure is approximated by laterally averaging the in-plane bilayer structure. However, this neglects all information about lateral heterogeneity, e.g., clustering of components in a lipid mixture. This paper presents two methods for computing the scattering intensity of simulated bilayers with in-plane heterogeneity, enabling a full treatment of both the transverse and lateral bilayer structure for the first time. The first method, termed the Dirac Brush, computes the exact spectra including spurious artifacts resulting from using information from neighboring periodic cells to account for the long-range structure of the bilayer. The second method, termed PFFT, applies a mean-field treatment in the field far from a scattering element, resulting in a correlation range that can be tuned (eliminating correlations with neighboring periodic images), but with computational cost that prohibits obtaining the exact (Dirac Brush) spectra. Following their derivation, the two methods are applied to a coarse-grained molecular simulation of a bilayer inhomogeneity, demonstrating the contributions of lateral correlations to the resulting spectra.

Inserting Small Molecules across Membrane Mixtures: Insight from the Potential of Mean Force

Small solutes have been shown to alter the lateral organization of cell membranes and reconstituted phospholipid bilayers; however, the mechanisms by which these changes happen are still largely unknown. Traditionally, both experiment and simulation studies have been restricted to testing only a few compounds at a time, failing to identify general molecular descriptors or chemical properties that would allow extrapolating beyond the subset of considered solutes. In this work, we probe the competing energetics of inserting a solute in different membrane environments by means of the potential of mean force. We show that these calculations can be used as a computationally efficient proxy to establish whether a solute will stabilize or destabilize domain phase separation. Combined with umbrella-sampling simulations and coarse-grained molecular dynamics simulations, we are able to screen solutes across a wide range of chemistries and polarities. Our results indicate that for the system under consideration, preferential partitioning and therefore effectiveness in altering membrane phase separation are strictly linked to the location of insertion in the bilayer (i.e., midplane or interface). Our approach represents a fast and simple tool for obtaining structural and thermodynamic insight into the partitioning of small molecules between lipid domains and its relation to phase separation, ultimately providing a platform for identifying the key determinants of this process.

Permeation of nanoparticles across the intestinal lipid membrane: dependence on shape and surface chemistry studied through molecular simulations

Nanoparticles are being explored for topical and oral drug delivery applications as they can cross various biological barriers, for example, the intestinal epithelium. The ability of nanoparticles to cross barriers depends on their morphological and surface properties such as size, surface chemistry and shape, among others. The effect of nanoparticle size on their membrane permeability has been well studied both experimentally and theoretically. However, less attention has been given to understand the role of nanoparticle shape in their translocation across biological barrier membranes. Here, we report on the influence of the nanoparticle's shape, surface chemistry and concentration on their permeation across a human intestinal apical cell membrane model. A representative multicomponent lipid bilayer model of the human intestinal apical membrane was built. The free energy of permeation of nanoparticles across the model lipid bilayer was calculated using multiple umbrella sampling simulations. The interaction of these nanoparticles with the model lipid bilayer was captured using extensive microsecond unrestrained molecular dynamics simulations. We observed that: (a) irrespective of the surface chemistry, the efficacy of nanoparticle penetration across the lipid layer was in the order of rod > disc > sphere; (b) irrespective of the shape, apolar and nonpolar nanoparticles were found to locate in the interior of the lipid bilayer, whereas charged and polar nanoparticles were either adsorbed on the lipid headgroups or remained in the water layer; (c) apolar and nonpolar disc shaped nanoparticles had higher efficacy in permeation across the lipid bilayer as compared to disc and sphere shaped nanoparticles; and (d) at a higher concentration of nanoparticles, sphere and disc shaped nanoparticles exhibited more agglomeration as compared to rod shaped nanoparticles. Based on these outcomes, a few nanoparticles were designed which penetrated readily into the lipid layer and these nanoparticles were also able to co-deliver a therapeutic protein inside the lipid layer. The apical model lipid membrane and protocols used in this study can thus be utilized for the in silico design of nanoparticles for the oral delivery of therapeutics.

Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane

Protein design is a powerful tool for elucidating mechanisms of function and engineering new therapeutics and nanotechnologies. Although soluble protein design has advanced, membrane protein design remains challenging because of difficulties in modeling the lipid bilayer. In this work, we developed an implicit approach that captures the anisotropic structure, shape of water-filled pores, and nanoscale dimensions of membranes with different lipid compositions. The model improves performance in computational benchmarks against experimental targets, including prediction of protein orientations in the bilayer, ΔΔG calculations, native structure discrimination, and native sequence recovery. When applied to de novo protein design, this approach designs sequences with an amino acid distribution near the native amino acid distribution in membrane proteins, overcoming a critical flaw in previous membrane models that were prone to generating leucine-rich designs. Furthermore, the proteins designed in the new membrane model exhibit native-like features including interfacial aromatic side chains, hydrophobic lengths compatible with bilayer thickness, and polar pores. Our method advances high-resolution membrane protein structure prediction and design toward tackling key biological questions and engineering challenges.

The Fats of Life: Using Computational Chemistry to Characterise the Eukaryotic Cell Membrane

Our current knowledge of the structural dynamics and complexity of lipid bilayers is still developing. Computational techniques, especially molecular dynamics simulations, have increased our understanding significantly as they allow us to model functions that cannot currently be experimentally resolved. Here we review available computational tools and techniques, the role of the major lipid species, insights gained into lipid bilayer structure and function from molecular dynamics simulations, and recent progress towards the computational modelling of the physiological complexity of eukaryotic lipid bilayers.

Contribution of headgroup and chain length of glycerophospholipids to thermal stability and permeability of liposomes loaded with calcein

Biological membranes are complex systems that are composed of lipids, proteins and carbohydrates. They are difficult to study, so it is established practice to use lipid vesicles that consist of closed 'shells' of phospholipid bilayers as model systems to study various functional and structural aspects of lipid organisation. To define the effects of the structural properties of lipid vesicles on their phase behaviour, we investigated their headgroup and chain length, and the chemical bonds by which their acyl chains are attached to the glycerol moiety of glycerophospholipid species, in terms of phase transition temperature, enthalpy change and calcein permeability. We used differential scanning calorimetry to measure the temperature and enthalpy changes of phase transition, and fluorescence to follow calcein release through the bilayer structure. Our data show that longer acyl chains increase the stability of the lipid bilayers, whereas higher salt concentrations decrease the thermal stability and widen the phase transitions of these lipid bilayers. We discuss the possible reasons for the observed phase transition behaviour.

Mycorrhizas enhance drought tolerance of citrus by altering root fatty acid compositions and their saturation levels

Arbuscular mycorrhizas (AMs) have the ability to enhance drought tolerance of citrus, but the underlying mechanisms have not been clearly elucidated. Considering the strong association of cell membrane fatty acid (FA) unsaturation with plant drought tolerance, the present study hypothesized that AM fungi (AMF) modulated the composition and unsaturation of FAs to enhance drought tolerance of host plants. Drought-sensitive citrus rootstocks, trifoliate orange (Poncirus trifoliata) seedlings, were inoculated with AMF (Funneliformis mosseae) for 3 months and were subsequently exposed to drought stress (DS) for 8 weeks. Mycorrhizal seedlings exhibited better plant growth performance, higher leaf water potential and lower root abscisic acid concentrations under both well-watered (WW) and DS conditions. Arbuscular mycorrhiza fungus inoculation considerably increased root methyl oleate (C18:1), methyl linoleate (C18:2) and methyl linolenate (C18:3N3) concentrations under both WW and DS conditions, and root methyl palmitoleate (C16:1) concentrations under WW, while it decreased root methyl stearate (C18:0) levels under both WW and DS. These changes in the composition of FAs of mycorrhized roots resulted in higher unsaturation index of root FAs, which later aided in reducing the oxidative damage on account of lower concentration of malondialdehyde and superoxide radicals. The changes of these FAs were a result of AMF-up-regulating root FA desaturase 2 (PtFAD2), FA desaturase 6 (PtFAD6) and Δ9 FA desaturase (PtΔ9) genes under WW and PtFAD2, PtFAD6 and Δ15 FA desaturase (PtΔ15) genes under DS conditions. Our results confirmed that mycorrhization brought significant changes in root FA compositions, in addition to regulation of gene expression responsible for increasing the unsaturation level of FAs, a predisposing physiological event for better drought tolerance of citrus.

Unusual confinement properties of a water insoluble small peptide hydrogel

Unlike polymeric hydrogels, in the case of supramolecular hydrogels, the cross-linked network formation is governed by non-covalent forces. Hence, in these cases, the gelator molecules inside the network retain their characteristic physicochemical properties as no covalent modification is involved. Supramolecular hydrogels thus get dissolved easily in aqueous medium as the dissolution leads to a gain in entropy. Thus, any supramolecular hydrogel, insoluble in bulk water, is beyond the present understanding and hitherto not reported as well. Herein, we present a peptide-based (PyKC) hydrogel which remained insoluble in water for more than a year. Moreover, in the gel state, any movement of solvent or solute to and from the hydrogel is highly restricted resulting in a high degree of compartmentalization. The hydrogel could be re-dissolved in the presence of some biomolecules which makes it a prospective material for in vivo applications. Experimental studies and all atom molecular dynamics simulations revealed that a cysteine containing gelator forms dimers through disulfide linkage which self-assemble into PyKC layers with a distinct PyKC-water interface. The hydrogel is stabilized by intra-molecular hydrogen bonds within the peptide-conjugates and the π-π stacking of the pyrene rings. The unique confinement ability of the hydrogel is attributed to the slow dynamics of water which remains confined in the core region of PyKC via hydrogen bonds. The hydrogen bonds present in the confined water need activation energies to move through the water depleted hydrophobic environment of pyrene rings which significantly reduces water transport across the hydrogel. The compartmentalizing ability is effectively used to protect enzymes for a long time from denaturing agents like urea, heat or methanol. Overall, the presented system shows unique insolubility and confinement properties that could be a milestone in the research of soft-materials.

Computational Modeling of Realistic Cell Membranes

Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin

The composition of the plasma membrane of malignant cells is thought to influence the cellular uptake of cisplatin and to take part in developing resistance to this widespread anti-cancer drug. In this work we study the permeation of cisplatin through the model membranes of normal and cancer cells using molecular dynamics simulations. A special attention is paid to lipid asymmetry and cholesterol content of the membranes. The loss of lipid asymmetry, which is common for cancer cells, leads to a decrease in their permeability to cisplatin by one order of magnitude in comparison to the membranes of normal cells. The change in the cholesterol molar ratio from 0% to 33% also decreases the permeability of the membrane by approximately one order of magnitude. The permeability of pure DOPC membrane is 5-6 orders of magnitude higher than one of the membranes with realistic lipid composition, which makes it as an inadequate model for the studies of drug permeability.

Structure of lateral heterogeneities in a coarse-grained model for multicomponent membranes

We study the lateral domain structure in a coarse-grained molecular model for multicomponent lipid bilayers by semi-grandcanonical Monte Carlo simulations. The membranes are filled with liquid ordered (lo) domains surrounded by a liquid disordered (ld) matrix. Depending on the membrane composition and temperature, we identify different morphological regimes: one regime (I) where the lo domains are small and relatively compact, and two regimes (II, II') where they are larger and often interconnected. In the latter two regimes, the ld matrix forms a network of disordered trenches separating the lo domains, with a relatively high content of interdigitated line defects. Since such defects are also a structural element of the modulated ripple phase in one component membranes, we argue that the regimes II, II' may be amorphous equivalents of the ripple phase in multicomponent membranes. We also analyze the local structure and provide evidence that the domains in regime I are stabilized by a monolayer curvature mechanism postulated in earlier work [S. Meinhardt et al., PNAS, 2013, 110, 4476].

Cholesterol Flip-Flop in Heterogeneous Membranes

Cholesterol is the most abundant molecule in the plasma membrane of mammals. Its distribution across the two membrane leaflets is critical for understanding how cells work. Cholesterol trans-bilayer motion (flip-flop) is a key process influencing its distribution in membranes. Despite extensive investigations, the rate of cholesterol flip-flop and its dependence on the lateral heterogeneity of membranes remain uncertain. In this work, we used atomistic molecular dynamics simulations to sample spontaneous cholesterol flip-flop events in a DPPC:DOPC:cholesterol mixture with heterogeneous lateral distribution of lipids. In addition to an overall flip-flop rate at the time scale of sub-milliseconds, we identified a significant impact of local environment on flip-flop rate. We discuss the atomistic details of the flip-flop events observed in our simulations.

How to Determine Lipid Interactions in Membranes from Experiment Through the Ising Model

The determination and the meaning of interactions in lipid bilayers are discussed and interpreted through the Ising model. Originally developed to understand phase transitions in ferromagnetic systems, the Ising model applies equally well to lipid bilayers. In the case of a membrane, the essence of the Ising model is that each lipid is represented by a site on a lattice and that the interaction of each site with its nearest neighbors is represented by an energy parameter ω. To calculate the thermodynamic properties of the system, such as the enthalpy, the Gibbs energy, and the heat capacity, the partition function is derived. The calculation of the configurational entropy factor in the partition function, however, requires approximations or the use of Monte Carlo (MC) simulations. Those approximations are described. Ultimately, MC simulations are used in combination with experiment to determine the interaction parameters ω in lipid bilayers. Several experimental approaches are described, which can be used to obtain interaction parameters. They include nearest-neighbor recognition, differential scanning calorimetry, and Förster resonance energy transfer. Those approaches are most powerful when used in combination of MC simulations of Ising models. Lipid membranes of different compositions are discussed, which have been studied with these approaches. They include mixtures of cholesterol, saturated (ordered) phospholipids, and unsaturated (disordered) phospholipids. The interactions between those lipid species are examined as a function of molecular properties such as the degree of unsaturation and the acyl chain length. The general rule that emerges is that interactions between different lipids are usually unfavorable. The exception is that cholesterol interacts favorably with saturated (ordered) phospholipids. However, the interaction of cholesterol with unsaturated phospholipids becomes extremely unfavorable as the degree of unsaturation increases.

Cholesterol Effects on the Physical Properties of Lipid Membranes Viewed by Solid-state NMR Spectroscopy

In this chapter, we review the physical properties of lipid/cholesterol mixtures involving studies of model membranes using solid-state NMR spectroscopy. The approach allows one to quantify the average membrane structure, fluctuations, and elastic deformation upon cholesterol interaction. Emphasis is placed on understanding the membrane structural deformation and emergent fluctuations at an atomistic level. Lineshape measurements using solid-state NMR spectroscopy give equilibrium structural properties, while relaxation time measurements study the molecular dynamics over a wide timescale range. The equilibrium properties of glycerophospholipids, sphingolipids, and their binary and tertiary mixtures with cholesterol are accessible. Nonideal mixing of cholesterol with other lipids explains the occurrence of liquid-ordered domains. The entropic loss upon addition of cholesterol to sphingolipids is less than for glycerophospholipids, and may drive formation of lipid rafts. The functional dependence of ²H NMR spin-lattice relaxation (R _1Z) rates on segmental order parameters (S _CD) for lipid membranes is indicative of emergent viscoelastic properties. Addition of cholesterol shows stiffening of the bilayer relative to the pure lipids and this effect is diminished for lanosterol. Opposite influences of cholesterol and detergents on collective dynamics and elasticity at an atomistic scale can potentially affect lipid raft formation in cellular membranes.

Membrane Lipid Nanodomains

Lipid membranes can spontaneously organize their components into domains of different sizes and properties. The organization of membrane lipids into nanodomains might potentially play a role in vital functions of cells and organisms. Model membranes represent attractive systems to study lipid nanodomains, which cannot be directly addressed in living cells with the currently available methods. This review summarizes the knowledge on lipid nanodomains in model membranes and exposes how their specific character contrasts with large-scale phase separation. The overview on lipid nanodomains in membranes composed of diverse lipids (e.g., zwitterionic and anionic glycerophospholipids, ceramides, glycosphingolipids) and cholesterol aims to evidence the impact of chemical, electrostatic, and geometric properties of lipids on nanodomain formation. Furthermore, the effects of curvature, asymmetry, and ions on membrane nanodomains are shown to be highly relevant aspects that may also modulate lipid nanodomains in cellular membranes. Potential mechanisms responsible for the formation and dynamics of nanodomains are discussed with support from available theories and computational studies. A brief description of current fluorescence techniques and analytical tools that enabled progress in lipid nanodomain studies is also included. Further directions are proposed to successfully extend this research to cells.

A Rationale for Mesoscopic Domain Formation in Biomembranes

Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also be observed in vitro on model systems such as supported membranes or lipid vesicles. Lipid mixtures separating in liquid-ordered and liquid-disordered phases below a demixing temperature play a pivotal role in this context. Protein-protein and protein-lipid interactions also contribute to membrane shaping by promoting small domains or clusters. Such phase separations displaying characteristic length-scales falling in-between the nanoscopic, molecular scale on the one hand and the macroscopic scale on the other hand, are named mesophases in soft condensed matter physics. In this review, we propose a classification of the diverse mechanisms leading to mesophase separation in biomembranes. We distinguish between mechanisms relying upon equilibrium thermodynamics and those involving out-of-equilibrium mechanisms, notably active membrane recycling. In equilibrium, we especially focus on the many mechanisms that dwell on an up-down symmetry breaking between the upper and lower bilayer leaflets. Symmetry breaking is an ubiquitous mechanism in condensed matter physics at the heart of several important phenomena. In the present case, it can be either spontaneous (domain buckling) or explicit, i.e., due to an external cause (global or local vesicle bending properties). Whenever possible, theoretical predictions and simulation results are confronted to experiments on model systems or living cells, which enables us to identify the most realistic mechanisms from a biological perspective.

Relating the structure factors of two-dimensional materials in planar and spherical geometries

Scattering structure factors provide essential insight into material properties and are routinely obtained in experiments, computer simulations, and theoretical analyses. Different approaches favor different geometries of the material. In case of lipid bilayers, scattering experiments can be performed on spherical vesicles, while simulations and theory often consider planar membrane patches. We derive an approximate relationship between the structure functions of such a material in planar and spherical geometries. We illustrate the usefulness of this relationship in a case study of a Gaussian material that supports both homogeneous and microemulsion phases. Within its range of applicability, this relationship enables a model-free comparison of structure factors of the same material in different geometries.