Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations

The association of hemagglutinin (HA) with lipid rafts in the plasma membrane is an important feature of the assembly process of influenza virus A. Lipid rafts are thought to be small, fluctuating patches of membrane enriched in saturated phospholipids, sphingolipids, cholesterol and certain types of protein. However, raft-associating transmembrane (TM) proteins generally partition into Ld domains in model membranes, which are enriched in unsaturated lipids and depleted in saturated lipids and cholesterol. The reason for this apparent disparity in behavior is unclear, but model membranes differ from the plasma membrane in a number of ways. In particular, the higher protein concentration in the plasma membrane may influence the partitioning of membrane proteins for rafts. To investigate the effect of high local protein concentration, we have conducted coarse-grained molecular dynamics (CG MD) simulations of HA clusters in domain-forming bilayers. During the simulations, we observed a continuous increase in the proportion of raft-type lipids (saturated phospholipids and cholesterol) within the area of membrane spanned by the protein cluster. Lateral diffusion of unsaturated lipids was significantly attenuated within the cluster, while saturated lipids were relatively unaffected. On this basis, we suggest a possible explanation for the change in lipid distribution, namely that steric crowding by the slow-diffusing proteins increases the chemical potential for unsaturated lipids within the cluster region. We therefore suggest that a local aggregation of HA can be sufficient to drive association of the protein with raft-type lipids. This may also represent a general mechanism for the targeting of TM proteins to rafts in the plasma membrane, which is of functional importance in a wide range of cellular processes.     

Extracting Curvature Preferences of Lipids Assembled in Flat Bilayers Shows Possible Kinetic Windows for Genesis of Bilayer Asymmetry and Domain Formation in Biological Membranes

Studies on the assembly of pure lipid components allow mechanistic insights toward understanding the structural and functional aspects of biological membranes. Molecular dynamic (MD) simulations on membrane systems provide molecular details on membrane dynamics that are difficult to obtain experimentally. A large number of MD studies have remained somewhat disconnected from a key concept of amphipathic assembly resulting in membrane structures—shape parameters of lipid molecules in those structures in aqueous environments. This is because most of the MD studies have been done on flat lipid membranes. With the above in view, we analyzed MD simulations of 26 pure lipid patches as a function of (1) lipid type(s) and (2) time of MD simulations along with 35–40 ns trajectories of five pure lipids. We report, for the first time, extraction of curvature preferences of lipids from MD simulations done on flat bilayers. Our results may lead to mechanistic insights into the possible origins of bilayer asymmetries and domain formation in biological membranes.     

A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry

The resemblance of lipid membrane models to physiological membranes determines how well molecular dynamics (MD) simulations imitate the dynamic behavior of cell membranes and membrane proteins. Physiological lipid membranes are composed of multiple types of phospholipids, and the leaflet compositions are generally asymmetric. Here we describe an approach for self-assembly of a Coarse-Grained (CG) membrane model with physiological composition and leaflet asymmetry using the MARTINI force field. An initial set-up of two boxes with different types of lipids according to the leaflet asymmetry of mammalian cell membranes stacked with 0.5 nm overlap, reliably resulted in the self-assembly of bilayer membranes with leaflet asymmetry resembling that of physiological mammalian cell membranes. Self-assembly in the presence of a fragment of the plasma membrane protein syntaxin 1A led to spontaneous specific positioning of phosphatidylionositol(4,5)bisphosphate at a positively charged stretch of syntaxin consistent with experimental data. An analogous approach choosing an initial set-up with two concentric shells filled with different lipid types results in successful assembly of a spherical vesicle with asymmetric leaflet composition. Self-assembly of the vesicle in the presence of the synaptic vesicle protein synaptobrevin 2 revealed the correct position of the synaptobrevin transmembrane domain. This is the first CG MD method to form a membrane with physiological lipid composition as well as leaflet asymmetry by self-assembly and will enable unbiased studies of the incorporation and dynamics of membrane proteins in more realistic CG membrane models.     

Cell penetrating peptide modulation of membrane biomechanics by Molecular dynamics

The efficacy of a pharmaceutical treatment is often countered by the inadequate membrane permeability, that prevents drugs from reaching their specific intracellular targets. Cell penetrating peptides (CPPs) are able to route across cells’ membrane various types of cargo, including drugs and nanoparticles. However, CPPs internalization mechanisms are not yet fully understood and depend on a wide variety of aspects. In this contest, the entry of a CPP into the lipid bilayer might induce molecular conformational changes, including marked variations on membrane’s mechanical properties. Understanding how the CPP does influence the mechanical properties of cells membrane is crucial to design, engineer and improve new and existing penetrating peptides. Here, all atom Molecular Dynamics (MD) simulations were used to investigate the interaction between different types of CPPs embedded in a lipid bilayer of dioleoyl phosphatidylcholine (DOPC). In a greater detail, we systematically highlighted how CPP properties are responsible for modulating the membrane bending modulus. Our findings highlighted the CPP hydropathy strongly correlated with penetration of water molecules in the lipid bilayer, thus supporting the hypothesis that the amount of water each CPP can route inside the membrane is modulated by the hydrophobic and hydrophilic character of the peptide. Water penetration promoted by CPPs leads to a local decrease of the lipid order, which emerges macroscopically as a reduction of the membrane bending modulus.     

Multiscale modeling of lipids and lipid bilayers

A multiscale modeling approach is applied for simulations of lipids and lipid assemblies on mesoscale. First, molecular dynamics simulation of initially disordered system of lipid molecules in water within all-atomic model was carried out. On the next stage, structural data obtained from the molecular dynamics (MD) simulation were used to build a coarse-grained (ten sites) lipid model, with effective interaction potentials computed by the inverse Monte Carlo method. Finally, several simulations of the coarse-grained model on longer length- and time-scale were performed, both within Monte Carlo and molecular dynamics simulations: a periodical sample of lipid molecules ordered in bilayer, a free sheet of such bilayer without periodic boundary conditions, formation of vesicle from a plain membrane, process of self-assembly of lipids randomly dispersed in volume. It was shown that the coarse-grained model, developed exclusively from all-atomic simulation data, reproduces well all the basic features of lipids in water solution.     

Simulations Show that Virus Assembly and Budding Are Facilitated by Membrane Microdomains

For many viruses, assembly and budding occur simultaneously during virion formation. Understanding the mechanisms underlying this process could promote biomedical efforts to block viral propagation and enable use of capsids in nanomaterials applications. To this end, we have performed molecular dynamics simulations on a coarse-grained model that describes virus assembly on a fluctuating lipid membrane. Our simulations show that the membrane can promote association of adsorbed subunits through dimensional reduction, but it also introduces thermodynamic and kinetic effects that can inhibit complete assembly. We find several mechanisms by which membrane microdomains, such as lipid rafts, reduce these effects, and thus, enhance assembly. We show how these predicted mechanisms can be experimentally tested. Furthermore, the simulations demonstrate that assembly and budding depend crucially on the system dynamics via multiple timescales related to membrane deformation, protein diffusion, association, and adsorption onto the membrane.     

In Vitro Reconstitution of the Initial Stages of the Bacterial Cell Division Machinery

Fission of many prokaryotes as well as some eukaryotic organelles depends on the self-assembly of the FtsZ protein into a membrane-associated ring structure early in the division process. Different components of the machinery are then sequentially recruited. Although the assembly order has been established, the molecular interactions and the understanding of the force-generating mechanism of this dividing machinery have remained elusive. It is desirable to develop simple reconstituted systems that attempt to reproduce, at least partially, some of the stages of the process. High-resolution studies of Escherichia coli FtsZ filaments’ structure and dynamics on mica have allowed the identification of relevant interactions between filaments that suggest a mechanism by which the polymers could generate force on the membrane. Reconstituting the membrane-anchoring protein ZipA on E. coli lipid membrane on surfaces is now providing information on how the membrane attachment regulates FtsZ polymer dynamics and indicates the important role played by the lipid composition of the membrane.     

A computer simulation study of the hierarchical assembly behaviour of triblock patchy particles

We study the hierarchical self-assembly behaviour of ACB triblock patchy particles via Brownian dynamics (BD) simulations, where the product of the first stage is set as the initial structure for the second stage. We offer a promising design rule to investigate the assembly mechanism of ACB triblock patchy particles in selective solvent conditions by two-stage optimisation. At the first stage, the attractive hydrophobic interactions only exist between patches A at low concentration in order to generate subunits. At the second stage, the attractions also exist between patches B for studying the assembly process from subunits to target structures by heating/cooling method. By regulating the interactions between patches B as well as the concentrations of patchy particles, the ordered structures that determined by various influence factors are studied. Via properly designing the assembly models and routes, we can observe the formation process of simple cubic lattice and kagome lattice structures, respectively. The results reveal that the concentration and attractive strength play the critical roles in the whole process of hierarchical self-assembly.     

Influence of hydrophobic mismatching on membrane protein diffusion

The observation of membrane domains in vivo and in vitro has triggered a renewed interest in the size-dependent diffusion of membrane inclusions (e.g., clusters of transmembrane proteins and lipid rafts). Here, we have used coarse-grained membrane simulations to quantify the influence of a hydrophobic mismatch between the inclusion's transmembrane portion and the surrounding lipid bilayer on the diffusive mobility of the inclusion. Our data indicate only slight changes in the mobility (<30%) when altering the hydrophobic mismatch, and the scaling of the diffusion coefficient D is most consistent with previous hydrodynamic predictions, i.e., with the Saffman-Delbruck relation and the edgewise motion of a thin disk in the limit of small and large radii, respectively.     

Algorithm to catalogue topologies of dynamic lipid hydrogen-bond networks

Lipid membrane interfaces host reactions essential for the functioning of cells. The hydrogen-bonding environment at the membrane interface is particularly important for binding of proteins, drug molecules, and ions. We present here the implementation and applications of a depth-first search algorithm that analyzes dynamic lipid interaction networks. Lipid hydrogen-bond networks sampled transiently during simulations of lipid bilayers are clustered according to main types of topologies that characterize three-dimensional arrangements of lipids connected to each other via short water bridges. We characterize the dynamics of hydrogen-bonded lipid clusters in simulations of model POPE and POPE:POPG membranes that are often used for bacterial membrane proteins, in a model of the Escherichia coli membrane with six different lipid types, and in POPS membranes. We find that all lipids sample dynamic hydrogen-bonded networks with linear, star, or circular arrangements of the lipid headgroups, and larger networks with combinations of these three types of topologies. Overall, linear lipid-water bridges tend to be short. Water-mediated lipid clusters in all membranes with PE lipids tend to be somewhat small, with about four lipids in all membranes studied here. POPS membranes allow circular arrangements of three POPS lipids to be sampled frequently, and complex arrangements of linear, star, and circular paths may also be sampled. These findings suggest a molecular picture of the membrane interface whereby lipid molecules transiently connect in clusters with somewhat small spatial extension.     

Computer simulation studies of self-assembling macromolecules

Coarse-grained (CG) molecular models are now widely used to understand the structure and functionality of macromolecular self-assembling systems. In the last few years, significant efforts have been devoted to construct quantitative CG models based on data from molecular dynamics (MD) simulations with more detailed all-atom (AA) intermolecular force fields as well as experimental thermodynamic data. We review some of the recent progress pertaining to the MD simulation of self-assembling macromolecular systems, using as illustrations the application of CG models to probe surfactant and lipid self-assembly including liposome and dendrimersome formation as well as the interaction of biomembranes with nanoparticles.     

Coating of magnetic nanoparticles affects their interactions with model cell membranes

BackgroundThe use of functionalized iron oxide nanoparticles of various chemical properties and architectures offers a new promising direction in theranostic applications. The increasing applications of nanoparticles in medicine require that these engineered nanomaterials will contact human cells without damaging essential tissues. Thus, efficient delivery must be achieved, while minimizing cytotoxicity during passage through cell membranes to reach intracellular target compartments.MethodsDifferential Scanning Calorimetry (DSC), molecular modeling, and atomistic Molecular Dynamics (MD) simulations were performed for two magnetite nanoparticles coated with polyvinyl alcohol (PVA) and polyarabic acid (ARA) in order to assess their interactions with model DPPC membranes.ResultsDSC experiments showed that both nanoparticles interact strongly with DPPC lipid head groups, albeit to a different degree, which was further confirmed and quantified by MD simulations. The two systems were simulated, and dynamical and structural properties were monitored. A bimodal diffusion was observed for both nanoparticles, representing the diffusion in the water phase and in the proximity of the lipid bilayer. Nanoparticles did not enter the bilayer, but caused ordering of the head groups and reduced the area per lipid compared to the pure bilayer, with MAG-PVA interacting more strongly and being closer to the lipid bilayer.ConclusionsResults of DSC experiments and MD simulations were in excellent agreement. Our findings demonstrate that the external coating is a key factor that affects nanoparticle-membrane interactions. Magnetite nanoparticles coated with PVA and ARA did not destabilize the model membrane and can be considered promising platforms for biomedical applications.General significanceUnderstanding the physico-chemical interactions of different nanoparticle coatings in contact with model cell membranes is the first step for assessing toxic response and could lead to predictive models for estimating toxicity. DSC in combination with MD simulations is an effective strategy to assess physico-chemical interactions of coated nanoparticles with lipid bilayers.     

Binding and calcium-induced aggregation of laminin onto lipid bilayers

Direct binding of laminin in the form of its complex with nidogen to planar lipid bilayers was demonstrated with total internal reflection fluorescence microscopy. Binding occurred equally well to zwitterionic (phosphatidylcholine) and negatively charged (phosphatidylglycerol) lipids and was enhanced by sulfatides but only at nonphysiological molar ratios higher than 30 mol %. Strong interactions with lipid bilayers were also observed for bovine serum albumin. This explains a strong inhibition of laminin binding by this protein. However, binding of laminin to sulfatide-rich bilayers was not completely inhibited. Observable by the microscopic technique was the formation of laminin clusters on the surface of the bilayer which occurred concomitantly with binding. Both processes were strongly enhanced by the presence of calcium. These results show that calcium-induced laminin self-assembly is enhanced at lipid surfaces.     

The computer as a laboratory for the physical chemistry of membranes

A mini-review is given of some recent advances in the use of computer-simulation approaches to the study of physico-chemical properties of lipid bilayers and biological membranes. The simulations are based on microscopic molecular interaction models as well as random-surface models of fluid membranes. Particular emphasis is put on those properties that are controlled by the many-particle character of the lamellar membrane, i.e. correlations and fluctuations in density, composition and large-scale conformational structure. It is discussed how dynamic membrane heterogeneity arises and how it is affected by various molecular species interacting with membranes, such as cholesterol, drugs, insecticides, as well as polypeptides and integral membrane proteins. The influence of bending rigidity and osmotic-pressure gradients on large-scale membrane conformation and topology is described.     

Amyloids of Alpha-Synuclein Affect the Structure and Dynamics of Supported Lipid Bilayers

Interactions of monomeric alpha-synuclein (αS) with lipid membranes have been suggested to play an important role in initiating aggregation of αS. We have systematically analyzed the distribution and self-assembly of monomeric αS on supported lipid bilayers. We observe that at protein/lipid ratios higher than 1:10, αS forms micrometer-sized clusters, leading to observable membrane defects and decrease in lateral diffusion of both lipids and proteins. An αS deletion mutant lacking amino-acid residues 71–82 binds to membranes, but does not observably affect membrane integrity. Although this deletion mutant cannot form amyloid, significant amyloid formation is observed in the wild-type αS clusters. These results suggest that the process of amyloid formation, rather than binding of αS on membranes, is crucial in compromising membrane integrity.     

Coexistence of Lipid Phases Stabilizes Interstitial Water in the Outer Layer of Mammalian Skin

The lipid matrix in the outer layer of mammalian skin, the stratum corneum, has been previously investigated by multiple biophysical techniques aimed at identifying hydrophilic and lipophilic pathways of permeation. Although consensus is developing over the microscopic structure of the lipid matrix, no molecular-resolution model describes the permeability of all chemical species simultaneously. Using molecular dynamics simulations of a model mixture of skin lipids, the self-assembly of the lipid matrix lamellae has been studied. At higher humidity, the resulting lamellar phase is maintained by partitioning excess water into isolated droplets of controlled size and spatial distribution. The droplets may fuse together to form intralamellar water channels, thereby providing a pathway for the permeation of hydrophilic species. These results reconcile competing data on the outer skin’s structure and broaden the scope of molecular-based methods to improve the safety of topical products and to advance transdermal drug delivery.     

Cotranslational assembly of membrane protein/nanoparticles in cell-free systems

Nanoparticles composed of amphiphilic scaffold proteins and small lipid bilayers are valuable tools for reconstitution and subsequent functional and structural characterization of membrane proteins. In combination with cell-free protein production systems, nanoparticles can be used to cotranslationally and translocon independently insert membrane proteins into tailored lipid environments. This strategy enables rapid generation of protein/nanoparticle complexes by avoiding detergent contact of nascent membrane proteins. Frequently in use are nanoparticles assembled with engineered derivatives of either the membrane scaffold protein (MSP) or the Saposin A (SapA) scaffold. Furthermore, several strategies for the formation of membrane protein/nanoparticle complexes in cell-free reactions exist. However, it is unknown how these strategies affect functional folding, oligomeric assembly and membrane insertion efficiency of cell-free synthesized membrane proteins.We systematically studied membrane protein insertion efficiency and sample quality of cell-free synthesized proteorhodopsin (PR) which was cotranslationally inserted in MSP and SapA based nanoparticles. Three possible PR/nanoparticle formation strategies were analyzed: (i) PR integration into supplied preassembled nanoparticles, (ii) coassembly of nanoparticles from supplied scaffold proteins and lipids upon PR expression, and (iii) coexpression of scaffold proteins together with PR in presence of supplied lipids. Yield, homogeneity as well as the formation of higher PR oligomeric complexes from samples generated by the three strategies were analyzed. Conditions found optimal for PR were applied for the synthesis of a G-protein coupled receptor. The study gives a comprehensive guideline for the rapid synthesis of membrane protein/nanoparticle samples by different processes and identifies key parameters to modulate sample yield and quality.     

Nanoparticle-induced assembly of hydrophobically modified chitosan

Hydrophobically modified chitosan (HMC) self-assembles in solution to form gels, making it suitable for applications in oil dispersion, hydrogel design and wound dressing. The self-assembly of HMC is driven by the association of hydrophobic moieties that are attached to chitosan monomers along the polymer chain. We present the results of discontinuous molecular dynamics simulations aimed at understanding how the length and density of the hydrophobic modification chains attached to HMC affect self-assembly and the structure of the resulting network. Long modification chains are required to promote the formation of a stable network in solution at a modification density of 5%; the networks form more readily at a modification density of 10%. The pore size distribution of the resulting HMC network is relatively independent of the modification chain length and density. Insertion of different sized hydrophobic nanoparticles into HMC has a significant impact on network formation, with the particles acting as junction points that promote the association of several HMC chains. The networks form faster in the presence of many small nanoparticles than in the presence of few large nanoparticles. We conclude that HMC could be a viable candidate to form hydrogels in solution.     

A structurally relevant coarse-grained model for cholesterol

Detailed atomistic computer simulations are now widely used to study biological membranes, including increasingly mixed lipid systems that involve, for example, cholesterol, which is a key membrane lipid. Typically, simulations of these systems start from a preassembled bilayer because the timescale on which self-assembly occurs in mixed lipid systems is beyond the practical abilities of fully atomistic simulations. To overcome this limitation and study bilayer self-assembly, coarse-grained models have been developed. Although there are several coarse-grained models for cholesterol reported in the literature, these generally fail to account explicitly for the unique molecular features of cholesterol that relate to its function and role as a membrane lipid. In this work, we propose a new coarse-grained model for cholesterol that retains the molecule's unique features and, as a result, can be used to study crystalline structures of cholesterol. In the development of the model, two levels of coarse-graining are explored and the importance of retaining key molecular features in the coarse-grained model that are relevant to structural properties is investigated.     

Modelling of proteins in membranes

This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly affected by the lipid environment. Theoretical predictions are pointed out, and compared to experimental findings, if available. Among others, the following phenomena are discussed: interactions of interfacially adsorbed peptides, pore-forming amphipathic peptides, adsorption of charged proteins onto oppositely charged lipid membranes, lipid-induced tilting of proteins embedded in lipid bilayers, protein-induced bilayer deformations, protein insertion and assembly, and lipid-controlled functioning of membrane proteins.