Coarse-grained molecular simulations of the melting kinetics of small unilamellar vesicles

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.

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.

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.

Cholesterol Distribution in Small Unilamellar Vesicles

The plasma membrane has heterogeneity, where the constituents are not only asymmetrically distributed between the inner leaflet and the outer leaflet but also laterally organized within each leaflet. There is still an ongoing controversy over the cholesterol distribution between the two leaflets, and it is also significant to explore the lateral flow and localization of cholesterol. The unilamellar vesicle is extensively employed as a simplified model of the plasma membrane in research studies. In this work, we study the spontaneous spatial distribution of cholesterol in the small unilamellar vesicles with a single type of phospholipid as the bilayer backbone through coarse-grained molecular dynamics simulations. The results show that in a spherical vesicle under ambient pressure, cholesterol is more abundant in the inner leaflet than in the outer leaflet. As the vesicle is deformed under pressurization, the net lateral flow of cholesterol in the two leaflets is in the exactly opposite directions, finally leading to a distribution strongly associated with the monolayer curvature. One of the possible explanations for our results is from the point of view of curvature elastic energy. Another possibility is from the point of view of stress: according to the correlation between the cholesterol distribution and the tail angles of lipids, it is suggested that the possible governing mechanism for the distribution of cholesterol in a membrane is to alleviate the mismatch of stress between the two leaflets. Additionally, we obtain the effect of cholesterol infiltration on the bending modulus and the spontaneous curvature of the vesicles.

Short oligoalanine helical peptides for supramolecular nanopore assembly and protein cytosolic delivery

In this work we report a rational design strategy for the identification of new peptide prototypes for the non-disruptive supramolecular permeation of membranes and the transport of different macromolecular giant cargos. The approach targets a maximal enhancement of helicity in the presence of membranes with sequences bearing the minimal number of cationic and hydrophobic moieties. The here reported folding enhancement in membranes allowed the selective non-lytic translocation of different macromolecular cargos including giant proteins. The transport of different high molecular weight polymers and functional proteins was demonstrated in vesicles and in cells with excellent efficiency and optimal viability. As a proof of concept, functional monoclonal antibodies were transported for the first time into different cell lines and cornea tissues by exploiting the helical control of a short peptide sequence. This work introduces a rational design strategy that can be employed to minimize the number of charges and hydrophobic residues of short peptide carriers to achieve non-destructive transient membrane permeation and transport of different macromolecules.

The helical enhancement of a short oligoalanine peptide scaffold in anionic membranes triggered the supramolecular assembly of a nanopore, which allowed the transport and release of proteins in the cytosol of cells and tissues.

Size-dependent interaction of hydrophilic/hydrophobic ligand functionalized cationic and anionic nanoparticles with lipid bilayers

We study the nature of nanoparticle (NPs)-membrane interaction as a function of nanoparticle size for different functionalization using molecular dynamics simulation. Zinc sulphide quantum dots of size, 2 nm and 4 nm are used as model NPs, and DLPC and DPPC lipid bilayers are used as model membranes. We use coarse-grained polarizable MARTINI model (MPW) to simulate the NPs and lipid bilayers. Our simulation results show that uncharged bare NPs penetrate the lipid bilayers and embed themselves within the hydrophobic core of the bilayer both in the gel and fluid phases. NPs of size 4 nm are shown to disrupt the bilayer. The bilayer recovers from the damages caused by smaller NPs of size 2 nm. In case of either purely hydrophilic or hybrid (with hydrophilic/hydrophobic ratio of 2:1) ligand-functionalized NPs of smaller size (shell size 2 nm), only cationic NPs bind to the bilayer. However, for larger NPs with a shell size of 4 nm, both anionic and cationic hybrid functionalized NPs bind to the bilayer. The performance of standard Martini (SM) force field for the charged NP/bilayer systems has also been tested and compared with the results obtained using MPW model. Although the overall trend that the cationic NPs interact strongly with the bilayers than their anionic counterparts has been captured correctly using SM, the adsorption behaviour of the functionalized NPs differ significantly in the SM force field. The interaction of anionic NPs with both fluid and gel bilayers has been observed to be least accurately represented in the SM force field.

Simulation of fluid/gel phase equilibrium in lipid vesicles

Simulation of single component dipalmitoylphosphatidylcholine (DPPC) coarse-grained DRY-MARTINI lipid vesicles of diameter 10 nm (1350 lipids), 20 nm (5100 lipids) and 40 nm (17 600 lipids) is performed using statistical temperature molecular dynamics (STMD), to study finite size effects upon the order-disorder gel/fluid transition. STMD obtains enhanced sampling using a generalized ensemble, obtaining a flat energy distribution between upper and lower cutoffs, with little computational cost over canonical molecular dynamics. A single STMD trajectory of moderate length is sufficient to sample 20+ transition events, without trapping in the gel phase, and obtain well averaged properties. Phase transitions are analyzed via the energy-dependence of the statistical temperature, T_S(U). The transition temperature decreases with decreasing diameter, in agreement with experiment, and the transition changes from first order to borderline first-second order. The size- and layer-dependence of the structure of both stable phases, and of the pathway of the phase transition, are determined. It is argued that the finite size effects are primarily caused by the disruption of the gel packing by curvature. Inhomogeneous states with faceted gel patches connected by unusual fluid seams are observed at high curvature, with visually different structure in the inner and outer layers due to the different curvatures. Thus a simple physical picture describes phase transitions in nanoscale finite systems far from the thermodynamic limit.

Lipid Packing in Lipid-Wrapped Nanoparticles

Equilibrium simulations of lipid-wrapped nanoparticles (LNP) were performed using a hybrid molecular dynamics/Monte Carlo (MD/MC) approach. The radius, R, of a spherical nanoparticle (NP) core was adjusted with MC moves while a surrounding lipid bilayer was treated with MD. A wide range of LNP sizes, with the largest R ∼ 40 nm, were studied to determine the average NP radius for a given total number of lipids, N, the number of lipids in each layer, and configurational information. A three-bead lipid model was used to allow large N. A nonequilibrium Jarzynski free energy calculation of the optimal R for a given N, was also demonstrated validating the MD/MC method. An order/disorder transition was described, unique to LNP and distinct from lamellar bilayers, that is weak and continuous with small N, but sharpens to a first order transition with N > 10000 at T ≈ 1.1, shifting to higher T with increasing N. The radius and the overlap of the inner and outer layers were used as order parameters charactering the whole system, and the density vs distance from the origin served to describe the transition in individual layers. The ordering effect of the core on the inner layer, and the disordering effect of curvature, are evident. Excellent fits for the number of lipids in the inner and outer layers vs R are presented, based on the idea that the inner layer is described as usual by an area and area/lipid but that the outer layer is slaved to the inner. The most ordered states exhibit interdigitation of the inner head groups with themselves.

Binding, folding and insertion of a β-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing

Antimicrobial peptides (AMPs) act as host defenses against microbial pathogens. Here we investigate the interactions of SVS-1 (KVKVKVKV^dP^lPTKVKVKVK), an engineered AMP and anti-cancer β-hairpin peptide, with lipid bilayers using spectroscopic studies and atomistic molecular dynamics simulations. In agreement with literature reports, simulation and experiment show preferential binding of SVS-1 peptides to anionic over neutral bilayers. Fluorescence and circular dichroism studies of a Trp-substituted SVS-1 analogue indicate, however, that it will bind to a zwitterionic DPPC bilayer under high-curvature conditions and folds into a hairpin. In bilayers formed from a 1:1 mixture of DPPC and anionic DPPG lipids, curvature and lipid fluidity are also observed to promote deeper insertion of the fluorescent peptide. Simulations using the CHARMM C36m force field offer complementary insight into timescales and mechanisms of folding and insertion. SVS-1 simulated at an anionic mixed POPC/POPG bilayer folded into a hairpin over a microsecond, the final stage in folding coinciding with the establishment of contact between the peptide's valine sidechains and the lipid tails through a "flip and dip" mechanism. Partial, transient folding and superficial bilayer contact are seen in simulation of the peptide at a zwitterionic POPC bilayer. Only when external surface tension is applied does the peptide establish lasting contact with the POPC bilayer. Our findings reveal the influence of disruption to lipid headgroup packing (via curvature or surface tension) on the pathway of binding and insertion, highlighting the collaborative effort of electrostatic and hydrophobic interactions on interaction of SVS-1 with lipid bilayers.

Time-resolved measurements of an ion channel conformational change driven by a membrane phase transition

Using temperature-jump infrared spectroscopy, we are able to trigger a gel-to-fluid phase transition in lipid vesicles and monitor in real time how a membrane protein responds to structural changes in the membrane. The melting of lipid domains in 1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles is observed to occur in as fast as 50 ns, with a temperature dependence characteristic of critical slowing. Gramicidin D (gD) added to the membrane responds primarily to the change in thickness of the membrane on a timescale coincident with the membrane melting. Using structure-based spectral modeling, we assign the conformational changes to compression and rotation of a partially dissociated gD dimer. Free energy calculations indicate that the high rate is a result of near-barrierless diffusion on a protein energy landscape that is radically reshaped by membrane thinning. The structural changes associated with the phase transition are similar to the fluctuation modes of fluid phase membranes, highlighting the importance of understanding the dynamic nature of the membrane environment around proteins.

Enhanced Sampling of Phase Transitions in Coarse-Grained Lipid Bilayers

Freezing and melting of dipalmitoylphosphatidylcholine (DPPC) bilayers are simulated in both the explicit (Wet) and implicit solvent (Dry) coarse-grained MARTINI force fields with enhanced sampling, via the isobaric, molecular dynamics version of the generalized replica exchange method (gREM). Phase transitions are described with the entropic viewpoint, based upon the statistical temperature as a function of enthalpy, T_S(H) = 1/(dS(H)/dH), where S is the configurational entropy. Bilayer thickness, area per lipid, and the second-rank order parameter (P2) are calculated vs temperature in the transition range. In a 32-lipid Wet MARTINI system, transitions in the lipid and water subsystems are strongly coupled, giving rise to considerable structure in T_S(H) and the need to specify the state of the water when reporting a lipid transition temperature. For gel lipid + liquid water → fluid lipid + liquid water, we find 292.4 K. The small system is influenced by finite-size effects, but it is argued that the entropic approach is well suited to revealing them, which will be particularly relevant for studies of finite nanosystems where there is no thermodynamic limit. In a 390-lipid Dry MARTINI system, two-dimensional analogues of the topographies of coexisting states ("subphases") seen in pure fluids are found. They are not seen in the 32-lipid Wet or Dry system, but the Dry lipids show a new type of state with gel in one leaflet and tilted gel in the other. Dry bilayer transition temperatures are 333.3 K (390 lipids) and 338 K (32 lipids), indicating that the 32-lipid system is not too small for a qualitative study of the transition. Physical arguments are given for Dry lipid system size dependence and for the difference between Wet and Dry systems.

Line Tension Assists Membrane Permeation at the Transition Temperature in Mixed-Phase Lipid Bilayers

The umbrella sampling method has been used to evaluate the free energy profile for a large permeant moving through a lipid bilayer, represented using a coarse-grained simulation model, at and below its gel-fluid transition temperature. At the lipid transition temperature, determined to be 302 K for the MARTINI 2.0 model of DPPC, the permeation barrier for passage through an enclosed fluid domain embedded in a patch of gel was significantly lower than that for passage through a fluid stripe domain. In contrast, permeation through a fluid domain in a stripe geometry produced a free energy profile nearly identical to that of a gel-free fluid bilayer. In both cases, insertion of the permeant into a fluid domain coexisting with the gel phase led to a shift in phase composition, as lipids transitioned from fluid to gel to accommodate the area occupied by the permeant. In the case of the enclosed fluid domain, this transition produced a decrease in the length of the fluid-gel interface as the approximately circular fluid domain shrank. The observed decrease in the apparent permeation barrier, combined with an approximation for the change in interfacial length, enabled estimation of the interfacial line tension to be between 10 and 13 pN for this model. The permeation barrier was shown to drop even further in simulations performed at temperatures below the transition temperature. The results suggest a mechanism to explain the experimentally observed anomalous peak in the temperature-dependent permeability of lipid bilayers near their transition temperatures. The contribution of this mechanism toward the permeability of a gel phase containing a thermal distribution of fluid-phase domains is estimated using a simple statistical thermodynamic model.

The self-assembly mechanism of tetra-peptides from the motif of β-amyloid peptides: a combined coarse-grained and all-atom molecular dynamics simulation

Understanding the self-assembly mechanisms of tetra-peptides from Aβ-peptides into different nanostructures.