Strongly Correlated Rafts in Both Leaves of an Asymmetric Bilayer

Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics

Liquid-liquid phase separation inside the cell often results in biological condensates that can critically affect cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the "lipid raft" hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For these reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation-essentially measuring the sign (but not the amplitude) of the free-energy change upon separation-rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from MD simulations.

A Survey of Models of Cell Membranes: Toward a New Understanding of Membrane Organization

The cell membrane, the boundary that separates living cells from their environment, has been the subject of study for over a century. The fluid-mosaic model of Singer and Nicolson in 1972 proposed the plasma membrane as a two-dimensional fluid composed of lipids and proteins. Fifty years hence, advances in biophysical and biochemical tools, particularly optical imaging techniques, have allowed for a better understanding of the physical nature, organization, and composition of cell membranes. This has been made possible by visualizing membrane heterogeneities and their dynamics and appreciating the asymmetrical arrangement of lipids in living cell membranes. Despite these advances, mechanisms underlying the local spatiotemporal organization of membrane components remain unclear. This review surveys various models of membrane organization, culminating in a new model that incorporates nonequilibrium processes and forces exerted by interactions with extramembrane elements such as the actin cytoskeleton. The proposed model provides a comprehensive understanding of membrane organization, taking into account the dynamic nature of the cell membrane and its interactions with its immediate environment.

Extent of raft composition in a model plasma membrane

"Rafts" are nanometer-size inhomogeneities in the plasma membrane that, in the outer leaflet, are enriched in sphingomyelin and cholesterol. They are thought to provide a platform for proteins to carry out biological processes (1-4). Here we employ a model asymmetric plasma membrane to address the question of the range of sphingomyelin and cholesterol compositions in which one would expect the formation of rafts. We define a weight for the likelihood of raft formation, and evaluate it as a function of the sphingomyelin mole fraction in the outer leaflet for three bilayers with total cholesterol mole fractions of 0.30, 0.40, and 0.50. Not surprisingly, the weight decreases when there is little sphingomyelin. Less expected, we find that the weight also decreases when there is a large mole fraction of sphingomyelin. The weight is largest in the bilayer with a total cholesterol mole fraction of 0.30, and decreases rapidly with increasing total cholesterol. We explicate the reasons for these behaviors. In the 0.30 cholesterol bilayer, the largest weight occurrs at a sphingomyelin mole fraction in the outer leaflet of approximately 0.23. The weight falls to one half its maximum value at sphingomylin mole fractions of 0.15 and 0.33. In terms of the sphingomyelin mole fraction of the asymmetric bilayer, the maximum weight occurs at 0.12 and falls to half maximum at 0.08 and 0.17.

Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling

The spatiotemporal organization of proteins and lipids on the cell surface has direct functional consequences for signaling, sorting, and endocytosis. Earlier studies have shown that multiple types of membrane proteins, including transmembrane proteins that have cytoplasmic actin binding capacity and lipid-tethered glycosylphosphatidylinositol-anchored proteins (GPI-APs), form nanoscale clusters driven by active contractile flows generated by the actin cortex. To gain insight into the role of lipids in organizing membrane domains in living cells, we study the molecular interactions that promote the actively generated nanoclusters of GPI-APs and transmembrane proteins. This motivates a theoretical description, wherein a combination of active contractile stresses and transbilayer coupling drives the creation of active emulsions, mesoscale liquid order (lo) domains of the GPI-APs and lipids, at temperatures greater than equilibrium lipid phase segregation. To test these ideas, we use spatial imaging of molecular clustering combined with local membrane order, and we demonstrate that mesoscopic domains enriched in nanoclusters of GPI-APs are maintained by cortical actin activity and transbilayer interactions and exhibit significant lipid order, consistent with predictions of the active composite model.

Enthalpic and entropic contributions to interleaflet coupling drive domain registration and antiregistration in biological membrane

Biological membrane is a complex self-assembly of lipids, sterols, and proteins organized as a fluid bilayer of two closely stacked lipid leaflets. Differential molecular interactions among its diverse constituents give rise to heterogeneities in the membrane lateral organization. Under certain conditions, heterogeneities in the two leaflets can be spatially synchronized and exist as registered domains across the bilayer. Several contrasting theories behind mechanisms that induce registration of nanoscale domains have been suggested. Following a recent study showing the effect of position of lipid tail unsaturation on domain registration behavior, we decided to develop an analytical theory to elucidate the driving forces that create and maintain domain registry across leaflets. Towards this, we formulated a Hamiltonian for a stacked lattice system where site variables capture the lipid molecular properties such as the position of unsaturation and various other interactions that could drive phase separation and interleaflet coupling. We solve the Hamiltonian using Monte Carlo simulations and create a complete phase diagram that reports the presence or absence of registered domains as a function of various Hamiltonian parameters. We find that the interleaflet coupling should be described as a competing enthalpic contribution due to interaction of lipid tail termini, primarily due to saturated-saturated interactions, and an interleaflet entropic contribution from overlap of unsaturated tail termini. A higher position of unsaturation is seen to provide weaker interleaflet coupling. Thermodynamically stable nanodomains could also be observed for certain points in the parameter space in our bilayer model, which were further verified by carrying out extended Monte Carlo simulations. These persistent noncoalescing registered nanodomains close to the lower end of the accepted nanodomain size range also point towards a possible "nanoscale" emulsion description of lateral heterogeneities in biological membrane leaflets.

Direct imaging of liquid domains in membranes by cryo-electron tomography

Images of micrometer-scale domains in lipid bilayers have provided the gold standard of model-free evidence to understand the domains' shapes, sizes, and distributions. Corresponding techniques to directly and quantitatively assess smaller (nanoscale and submicron) liquid domains have been limited. Researchers commonly seek to correlate activities of membrane proteins with attributes of the domains in which they reside; doing so hinges on identification and characterization of membrane domains. Although some features of membrane domains can be probed by indirect methods, these methods are often constrained by the limitation that data must be analyzed in the context of models that require multiple assumptions or parameters. Here, we address this challenge by developing and testing two methods of identifying submicron domains in biomimetic membranes. Both methods leverage cryo-electron tomograms of ternary membranes under vitrified, hydrated conditions. The first method is optimized for probe-free applications: Domains are directly distinguished from the surrounding membrane by their thickness. This technique quantitatively and accurately measures area fractions of domains, in excellent agreement with known phase diagrams. The second method is optimized for applications in which a single label is deployed for imaging membranes by both high-resolution cryo-electron tomography and diffraction-limited optical microscopy. For this method, we test a panel of probes, find that a trimeric mCherry label performs best, and specify criteria for developing future high-performance, dual-use probes. These developments have led to direct and quantitative imaging of submicron membrane domains in vitrified, hydrated vesicles.

Recent Experiments Support a Microemulsion Origin of Plasma Membrane Domains: Dependence of Domain Size on Physical Parameters

It is widely, but not universally, believed that the lipids of the plasma membrane are not uniformly distributed, but that “rafts” of sphingolipids and cholesterol float in a “sea” of unsaturated lipids. The physical origin of such heterogeneities is often attributed to a phase coexistence between the two different domains. We argue that this explanation is untenable for several reasons. Further, we note that the results of recent experiments are inconsistent with this picture. However, they are quite consistent with an alternate explanation, namely, that the plasma membrane is a microemulsion of the two kinds of regions. To show this, we briefly review a simplified version of this theory and its phase diagram. We also explicate the dependence of the predicted domain size on four physical parameters. They are the energy cost of gradients in the composition, the spontaneous curvature of the membrane, its bending modulus and its surface tension. Taking values of the latter two from experiment, we obtain domain sizes for several different cell types that vary from 58 to 88 nm.

Nanodomains can persist at physiologic temperature in plasma membrane vesicles and be modulated by altering cell lipids

The formation and properties of liquid-ordered (Lo) lipid domains (rafts) in the plasma membrane are still poorly understood. This limits our ability to manipulate ordered lipid domain-dependent biological functions. Giant plasma membrane vesicles (GPMVs) undergo large-scale phase separations into coexisting Lo and liquid-disordered lipid domains. However, large-scale phase separation in GPMVs detected by light microscopy is observed only at low temperatures. Comparing Förster resonance energy transfer-detected versus light microscopy-detected domain formation, we found that nanodomains, domains of nanometer size, persist at temperatures up to 20°C higher than large-scale phases, up to physiologic temperature. The persistence of nanodomains at higher temperatures is consistent with previously reported theoretical calculations. To investigate the sensitivity of nanodomains to lipid composition, GPMVs were prepared from mammalian cells in which sterol, phospholipid, or sphingolipid composition in the plasma membrane outer leaflet had been altered by cyclodextrin-catalyzed lipid exchange. Lipid substitutions that stabilize or destabilize ordered domain formation in artificial lipid vesicles had a similar effect on the thermal stability of nanodomains and large-scale phase separation in GPMVs, with nanodomains persisting at higher temperatures than large-scale phases for a wide range of lipid compositions. This indicates that it is likely that plasma membrane nanodomains can form under physiologic conditions more readily than large-scale phase separation. We also conclude that membrane lipid substitutions carried out in intact cells are able to modulate the propensity of plasma membranes to form ordered domains. This implies lipid substitutions can be used to alter biological processes dependent upon ordered domains.

Model Plasma Membrane Exhibits a Microemulsion in Both Leaves Providing a Foundation for "Rafts"

We consider a model lipid plasma membrane, one that describes the outer leaf as consisting of sphingomyelin, phosphatidylcholine, and cholesterol and the inner leaf of phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, and cholesterol. Their relative compositions are taken from experiment; the cholesterol freely interchanges between leaves. Fluctuations in local composition are coupled to fluctuations in the local membrane curvature, as in the Leibler-Andelman mechanism. Structure factors of components in both leaves display a peak at nonzero wavevector. This indicates that the disordered fluid membrane is characterized by structure of the corresponding wavelength. The scale is given by membrane properties: its bending modulus and its surface tension, which arises from the membrane's connections to the cytoskeleton. From measurements on the plasma membrane, this scale is on the order of 100 nm. We find that the membrane can be divided into two different kinds of domains that differ not only in their composition but also in their curvature. The first domain in the outer, exoplasmic leaf is rich in cholesterol and sphingomyelin, whereas the inner, cytoplasmic leaf is rich in phosphatidylserine and phosphatidylcholine. The second kind of domain is rich in phosphatidylcholine in the outer leaf and in cholesterol and phosphatidylethanolamine in the inner leaf. The theory provides a tenable basis for the origin of structure in the plasma membrane and an illuminating picture of the organization of lipids therein.

Artificial Phospholipids and Their Vesicles

Phospholipids are at the heart and origin of life on this planet. The possibilities in terms of phospholipid self-assembly and biological functions seem limitless. Nonetheless, nature exploits only a small fraction of the available chemical space of phospholipids. Using chemical synthesis, artificial phospholipid structures become accessible, and the study of their biophysics may reveal unprecedented properties. In this article, the recent advances by our work group in the field of chemical lipidology are summarized. The family of diamidophospholipids is discussed in detail from monolayer characterization to the formation of faceted vesicles, culminating in the template-free self-assembly of phospholipid cubes and the possible applications of vesicle origami in modern personalized medicine.

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.

Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation

Cholesterol is essential to the formation of phase-separated lipid domains in membranes. Lipid domains can exist in different thermodynamic phases depending on the molecular composition and play significant roles in determining structure and function of membrane proteins. We investigate the role of cholesterol in the structure and dynamics of ternary lipid mixtures displaying phase separation using molecular dynamics simulations, employing a physiologically relevant span of cholesterol concentration. We find that cholesterol can induce formation of three regimes of phase behavior: 1) miscible liquid-disordered bulk, 2) phase-separated, domain-registered coexistence of liquid-disordered and liquid-ordered domains, and 3) phase-separated, domain-antiregistered coexistence of liquid-disordered and newly identified nanoscopic gel domains composed of cholesterol threads we name "cholesterolic gel" domains. These findings are validated and discussed in the context of current experimental knowledge, models of cholesterol spatial distributions, and models of ternary lipid-mixture phase separation.

Tuning Length Scales of Small Domains in Cell-Derived Membranes and Synthetic Model Membranes

Micron-scale, coexisting liquid-ordered (L_o) and liquid-disordered (L_d) phases are straightforward to observe in giant unilamellar vesicles (GUVs) composed of ternary lipid mixtures. Experimentally, uniform membranes undergo demixing when temperature is decreased: domains subsequently nucleate, diffuse, collide, and coalesce until only one domain of each phase remains. The sizes of these two domains are limited only by the size of the system. Under different conditions, vesicles exhibit smaller-scale domains of fixed sizes, leading to the question of what sets the length scale. In membranes with excess area, small domains are expected when coarsening is hindered or when a microemulsion or modulated phase arises. Here, we test predictions of how the size, morphology, and fluorescence levels of small domains vary with the membrane's temperature, tension, and composition. Using GUVs and cell-derived giant plasma membrane vesicles, we find that 1) the characteristic size of domains decreases when temperature is increased or membrane tension is decreased, 2) stripes are favored over circular domains for lipid compositions with low energy per unit interface, 3) fluorescence levels are consistent with domain registration across both monolayer leaflets of the bilayer, and 4) small domains form in GUVs composed of lipids both with and without ester-linked lipids. Our experimental results are consistent with several elements of current theories for microemulsions and modulated phases and inconsistent with others, suggesting a motivation to modify or enhance current theories.