We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.

Cell membranes contain a large number of different lipid species. Such a multicomponent mixture exhibits a complex phase behavior with regions of structural and compositional heterogeneity. Especially domains formed in ternary mixtures, composed of saturated and unsaturated lipids together with cholesterol, have received a lot of attention as they may resemble raft formation in real cells. Here we apply a simulation model to assess the molecular nature of these domains at the nanoscale, information that has thus far eluded experimental determination. We are able to show the spontaneous separation of a saturated phosphatidylcholine (PC)/ unsaturated PC/cholesterol mixture into a liquid-ordered and a liquid-disordered phase with structural and dynamic properties closely matching experimental data. The near-atomic resolution of the simulations reveals remarkable features of both domains and the boundary domain interface. Furthermore, we predict the existence of a small surface tension between the monolayer leaflets that drives registration of the domains. At the level of molecular detail, raft-like lipid mixtures show a surprising face with possible implications for many cell membrane processes.A ccording to a recent definition, rafts are small (Ͻ200 nm) heterogeneous, highly dynamic, sterol-and sphingolipidenriched domains that compartmentalize cellular processes (1) and are believed to play an important role in cellular function (2). Although direct observation of rafts in vivo remains complicated, raft-like mixtures in model membranes can form domains that have been visualized directly for an increasing number of experimental systems and conditions (3-7). At cholesterol levels representative of biological membranes (10-30%), mixtures of saturated and unsaturated lipids separate into macroscopic domains of a liquid-ordered (L o ) phase and a liquiddisordered (L d ) phase. The first, raft-like phase is enriched in both cholesterol and the saturated lipid; the second, non-raft phase consists mainly of the unsaturated lipid and is depleted of cholesterol. In order to not confuse the reader concerning the meaning and implication of the term raft, here and throughout the remainder of this article we use the term ''raft-like'' phase or domain to denote the L o phase observed in model membranes. Interestingly, isolated plasma membranes have recently been shown to be capable of forming such domains as well (8, 9). Yet it should be stressed that in real cell membranes raft formation may not resemble macroscopic phase separation. For instance, other recent experiments on plasma membranes demonstrate micrometer-scale composition fluctuations arising from critical demixing behavior (10). The focus of the current work is on phase segregation in model membranes.To interpret the experimental measurements performed on model membranes, knowledge of the structure and dynamics of the domains at the molecular level is essential. Here we report molecular dynamics simulations of the spontaneous formation of raft-like domains in ternar...

Neuronal exocytosis is catalyzed by the SNARE protein syntaxin-1A1. Syntaxin-1A is clustered in the plasma membrane at sites where synaptic vesicles undergo exocytosis2,3. However, how syntaxin-1A is sequestered is unknown. Here, we show that syntaxin clustering is mediated by electrostatic interactions with the strongly anionic lipid phosphatidylinositol-4,5-bisphosphate (PIP2). We found with super-resolution STED microscopy on the plasma membrane of PC12 cells that PIP2 is the dominant inner-leaflet lipid in ~73 nm-sized microdomains. This high accumulation of PIP2 was required for syntaxin-1A sequestering, as destruction of PIP2 by the phosphatase synaptojanin-1 reduced syntaxin-1A clustering. Furthermore, co-reconstitution of PIP2 and the C-terminal part of syntaxin-1A in artificial giant unilamellar vesicles resulted in segregation of PIP2 and syntaxin-1A into distinct domains even when cholesterol was absent. Our results demonstrate that electrostatic protein-lipid interactions can result in the formation of microdomains independent of cholesterol or lipid phases.

Synaptic vesicle exocytosis is mediated by the vesicular Ca2+-sensor synaptotagmin-1. Synaptotagmin-1 interacts with the SNARE protein syntaxin-1A and with acidic phospholipids such as phosphatidylinositol 4,5-bisphosphate (PIP2). However, it is unclear how these interactions contribute to triggering membrane fusion. Using both PC12 cells from Rattus norvegicus and artificial supported bilayers we now show that synaptotagmin-1 interacts with the polybasic linker region of syntaxin-1A independent of Ca2+ via PIP2. This interaction allows both Ca2+-binding sites of synaptotagmin-1 to bind to phosphatidylserine (PS) in the vesicle membrane upon Ca2+-triggering. We determined the crystal structure of the C2B-domain of synaptotagmin-1 bound to phosphoserine, allowing for developing a high-resolution model of synaptotagmin bridging two different membranes. Our results suggest that PIP2 clusters organized by syntaxin-1 act as molecular beacons for vesicle docking, with the subsequent Ca2+-influx bringing the vesicle membrane close enough for membrane fusion.

Lipid monolayers at an air-water interface can be compressed laterally and reach high surface density. Beyond a certain threshold, they become unstable and collapse. Lipid monolayer collapse plays an important role in the regulation of surface tension at the air-liquid interface in the lungs. Although the structures of lipid aggregates formed upon collapse can be characterized experimentally, the mechanism leading to these structures is not fully understood. We investigate the molecular mechanism of monolayer collapse using molecular dynamics simulations. Upon lateral compression, the collapse begins with buckling of the monolayer, followed by folding of the buckle into a bilayer in the water phase. Folding leads to an increase in the monolayer surface tension, which reaches the equilibrium spreading value. Immediately after their formation, the bilayer folds have a flat semielliptical shape, in agreement with theoretical predictions. The folds undergo further transformation and form either flat circular bilayers or vesicles. The transformation pathway depends on macroscopic parameters of the system: the bending modulus, the line tension at the monolayer-bilayer connection, and the line tension at the bilayer perimeter. These parameters are determined by the system composition and temperature. Coexistence of the monolayer with lipid aggregates is favorable at lower tensions of the monolayerbilayer connection. Transformation into a vesicle reduces the energy of the fold perimeter and is facilitated for softer bilayers, e.g., those with a higher content of unsaturated lipids, or at higher temperatures.lung surfactant ͉ bilayer reservoir ͉ course grain ͉ vesicle budding ͉ molecular dynamics L ipid molecules are insoluble in both polar and apolar media because of their amphipathic nature. At polar-apolar interfaces, they form monomolecular films that reduce the surface tension. Lipid monolayers form the main structural component (Ϸ97% by weight) of lung surfactant at the gas-exchange interface in the lung alveoli (1) and constitute the outer layer of tear film in the eyes (2). The properties of lipid monolayers vary with their surface density (3). For example, the higher the density, the lower is the resulting surface tension at the interface. At a certain very high surface density, however, a further reduction of the surface tension is not possible: the monolayers become unstable at the interface and collapse (4) (see scheme in Fig. 1). Besides being of fundamental interest for surface science, lipid monolayer collapse is crucial for maintaining low surface tension at the gas-exchange interface in the lungs during breathing (5).Collapse is characterized by loss of material from the interface and can proceed through different pathways. The modes of collapse and the surface tension at which collapse occurs depend on the molecular composition of the monolayer and on temperature (6-13), which determine the morphology and material properties of the monolayer. Although lipid monolayers in the liquid state do not usually ...

We present an algorithm to reconstruct atomistic structures from their corresponding coarse-grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via restraints. A number of examples demonstrate the application of the reconstruction procedure to obtain low-energy atomistic structural ensembles from their CG counterparts. We reconstructed individual molecules in vacuo (NCQ tripeptide, dipalmitoylphosphatidylcholine, and cholesterol), bulk water, and a WALP transmembrane peptide embedded in a solvated lipid bilayer. The first examples serve to optimize the parameters for the reconstruction procedure, whereas the latter examples illustrate the applicability to condensed-phase biomolecular systems.

The molecular packing details of lipids in planar bilayers are well characterized. For curved bilayers, however, little data is available. In this paper we study the effect of temperature and membrane composition on the structural and dynamical properties of a liposomal membrane in the limit of high curvature (liposomal diameter of 15-20 nm), using coarse grained molecular dynamics simulations. Both pure dipalmitoyl phosphatidylcholine (DPPC) liposomes and binary mixtures of DPPC and either dipalmitoylphosphatidylethanolamine (DPPE) or polyunsaturated dilinoleylphosphatidylcholine (DLiPC) lipids are modeled. We take special care in the equilibration of the liposomes requiring lipid flip-flopping, which can be facilitated by the temporary insertion of artificial pores. The equilibrated liposomes show some remarkable properties. Curvature induces membrane thinning and reduces the thermal expansivity of the membrane. In the inner monolayer the lipid head groups are very closely packed and dehydrated, and the lipids tails relatively disordered. The opposite packing effects are seen in the outer monolayer. In addition, we noticed an increased tendency of the lipid tails to backfold toward the interface in the outer monolayer. The distribution of lipids over the monolayers was found to be strongly temperature dependent. Higher temperatures favor more equally populated monolayers. Relaxation times of the lipid tails were found to increase with increasing curvature, with the lipid tails in the outer monolayer showing a significant slower dynamics compared to the lipid tails in the inner monolayer. In the binary systems there is a clear tendency toward partial transversal demixing of the two components, with especially DPPE enriched in the inner monolayer. This observation is in line with a static shape concept which dictates that inverted-cone shaped lipids such as DPPE and DLiPC would prefer the concave volume of the inner monolayer. However, our results for DLiPC show that another effect comes into play that is almost equally strong and provides a counter-acting driving force toward the outer, rather than the inner monolayer. This effect is the ability of the polyunsaturated tails of DLiPC to backfold, which is advantageous in the outer monolayer. We speculate that polyunsaturated lipids in biological membranes may play an important role in stabilizing both positive and negative regions of curvature.

We calculate full 3D pressure fields for inhomogeneous nanoscale systems using molecular dynamics simulation data. The fields represent systems with increasing level of complexity, ranging from semivesicles and vesicles to membranes characterized by coexistence of two phases, including also a protein-membrane complex. We show that the 3D pressure field is distinctly different for curved and planar bilayers, the pressure field depends strongly on the phase of the membrane, and that an integral protein modulates the tension and elastic properties of the membrane.