Coarse-grained molecular dynamics simulations of phase transitions in mixed lipid systems containing LPA, DOPA, and DOPE lipids

Small and Bright Water-Protected Upconversion Nanoparticles with Long-Time Stability in Complex, Aqueous Media by Phospholipid Membrane Coating

Chemical and colloidal stability in complex aqueous media are among the main challenges preventing nanoparticles from successfully entering into the biomedical field. Small core-shell upconversion nanoparticles (UCNPs) NaYF₄:Yb,Er@NaYF₄ of 12 nm in diameter with a high surface-to-volume ratio are utilized to demonstrate that self-assembling phospholipid bilayers (PLMs) have several benefits compared to common ligand-exchange and ligand-addition particle coatings such as poly(acrylic acid) and amphiphilic polymers. An efficient hydrophobic barrier against water quenching and toward particle disintegration is formed by PLM. Particles with this functionalization have a higher upconversion luminescence in aqueous media in contrast to common surface ligands. They attract with better colloidal stability in phosphate buffer, in a wide pH range, in high ionic solutions, and in complex cell media, as is required for biological applications. Moreover, kidney cells (NRK) are not affected by these stable PLM-coated UCNPs as first cell viability tests reveal.

Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides

The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp). Overall, we find PACE provides an improvement over MARTINI for modeling helical peptides, based on the membrane insertion energetics for WALP16 and more realistic melittin pore dynamics. Our studies on HAfp, which forms a helical hairpin structure, do not show the hairpin structure to be stable, which may point toward a deficiency in the model. © 2017 Wiley Periodicals, Inc.

A Multiscale Study on the Penetration Enhancement Mechanism of Menthol to Osthole

Menthol is a widely used penetration enhancer in clinical medicine due to its high efficiency and relative safety. However, details of the penetration enhancement mechanism of menthol on the molecular level is rarely involved in the discussion. In this work, the penetration enhancement (PE) mechanism of menthol is explored by a multiscale method containing molecular dynamics simulations, in vitro penetration experiments, and transmission electron microscopy. Osthole is chosen to be the tested drug due to its common use in external preparations and because it often accompanies menthol as a PE in the preparations. The results show that menthol in each testing concentration can impair the lipid packing of stratum corneum (SC) and promote osthole permeating into SC, and the penetration promoting effect has an optimal concentration. At a low concentration, menthol causes the bilayer to relax with a reduction in thickness and increment in the lipid headgroup area. At a high concentration, menthol destroys the bilayer structure of SC and causes lipids to form a reversed micelle structure. The penetration enhancement mechanism of menthol is characterized mainly by the disruption of the highly ordered SC lipid in low concentrations and an improvement in the partitioning of drugs into the SC in high concentrations. The results can provide some assistance for additional studies and applications of menthol as a penetration enhancer.

Interaction of menthol with mixed-lipid bilayer of stratum corneum: A coarse-grained simulation study

Menthol is a widely used penetration enhancer in clinical medicine due to its high efficiency and relative safety. Although there are many studies focused on the penetration-enhancing activity of menthol, the details of molecular mechanism are rarely involved in the discussion. In this study, we present a series of coarse-grained molecular dynamics simulations to investigate the interaction of menthol with a mixed-lipid bilayer model consisting of ceramides, cholesterol and free fatty acids in a 2:2:1 molar ratio. Taking both the concentration of menthol and temperature into consideration, it was found that a rise in temperature and concentration within a specific range (1-20%) could improve the penetration-enhancing property of menthol and the floppiness of the bilayer. However, at high concentrations (30% and more), menthol completely mixed with the lipids and the membrane can no longer maintain a bilayer structure. Our results elucidates some of the molecular basis for menthol's penetration enhancing effects and may provide some assistance for the development and applications of menthol as a penetration enhancer. Furthermore, we establish a method to investigate the penetration enhancement mechanism of traditional Chinese medicine using the mixed-lipid bilayer model of stratum corneum by molecular dynamics simulations.

Model cell membranes: discerning lipid and protein contributions in shaping the cell

The high complexity of biological membranes has motivated the development and application of a wide range of model membrane systems to study biochemical and biophysical aspects of membranes in situ under well defined conditions. The aim is to provide fundamental understanding of processes controlled by membrane structure, permeability and curvature as well as membrane proteins by using a wide range of biochemical, biophysical and microscopic techniques. This review gives an overview of some currently used model biomembrane systems. We will also discuss some key membrane protein properties that are relevant for protein-membrane interactions in terms of protein structure and how it is affected by membrane composition, phase behavior and curvature.

Molecular dynamics simulations of membranes composed of glycolipids and phospholipids

Lipid membranes composed of 1,2-di-(9Z,12Z,15Z)-octadecatrienoyl-3-O-β-D-galactosyl-sn-glycerol or monogalactosyldiacylglycerol (MGDG) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) were studied by means of molecular dynamics (MD) computer simulations. Three lipid compositions were considered: 0%, 20%, and 45% MGDG (by mole) denoted as MG-0, MG-20, and MG-45, respectively. The article is focused on the calculation of NMR dipolar interactions, which were confronted with previously reported experimental couplings. Dynamical processes and orientational distributions relevant for the averaging of dipolar interactions were evaluated. Furthermore, several parameters important for characterization of the bilayer structure, molecular organization, and dynamics were investigated. In general, only a minor change in DMPC properties was observed upon the increased MGDG/DMPC ratio, whereas properties related to MGDG undergo a more pronounced change. This effect was ascribed to the fact that DMPC is a bilayer (L(α)) forming lipid, whereas MGDG prefers a reverse hexagonal (H(II)) arrangement.

Elastic deformations in hexagonal phases studied by small-angle X-ray diffraction and simulations

In this study we present experimental and theoretical results which concern the deviations from circularity of the pivotal plane in the inverse hexagonal phases (H(II)) of phospholipid self-assemblies. Due to packing constraints, the cross-section of the polar/apolar interface deviates from a circle, which we studied in minute detail by analysing small-angle X-ray diffraction data of dioleoyl-phosphatidylethanolamine (DOPE) and stearoyl-oleoyl-phosphatidylethanolamine (SOPE), respectively. On this structural basis, Monte Carlo (MC) simulated annealing variations of the free energy were carried out, both on the formation of the H(II)-phase and on the particular shape of the cross-section in the H(II)-phase. The equilibrium of the H(II)-phase pivotal plane contour and the corresponding values of the mean intrinsic curvature, H(m), and the hydrocarbon chain stiffness, τ, were determined from MC calculations. The results of these calculations were tested by solving the corresponding system of non-linear differential equations derived using variational calculus. Here our main aim is to predict the range of possible values of H(m) and τ. Comparing the measured structural data with predictions from MC calculations including lipid anisotropy, and accounting for the elastic deformations of the pivotal plane allowed us to determine a relationship between the bending deformation and stretching of hydrocarbon chains.

Molecular dynamics simulations of polyglutamine aggregation using solvent-free multiscale coarse-grained models

The multiscale coarse-graining (MS-CG) method is used to construct solvent-free CG models for polyglutamine peptides having various repeat lengths. Because the resulting CG models have fewer degrees of freedom than a corresponding all-atom simulations, they make it possible to study the self-assembly of polyglutamines at high concentrations for the first time by allowing for better equilibration and statistical sampling that is well beyond the range achievable by all-atom models. Molecular dynamics (MD) simulations performed with these models show that polyglutamine monomers with repeat lengths < or = 28 fluctuate between their folded and unfolded states. Monomers with 32 or more residues are stable and form alpha-helix solid structures. The degree of monomer compactness increases with chain length in both cases. CG MD simulations of equilibrium polyglutamine aggregates show that even at high concentrations, the system statistically fluctuates between heterogeneous and homogeneous configurations, rather than simply aggregates. The degree of aggregation and fluctuation increases with concentration and chain length. All of these phenomena are consistent with the experimental observations and may be explained by a mechanism that the collective nonbonded interactions between polyglutamine molecules in water solution are only weakly attractive. Finally, this work demonstrates that computer simulation of polypeptides self-assembly and aggregation, which is presently beyond the reach of all-atom MD simulations, is attainable using solvent-free MS-CG models.

Atomistic simulations of bicelle mixtures

Mixtures of long- and short-tail phosphatidylcholine lipids are known to self-assemble into a variety of aggregates combining flat bilayerlike and curved micellelike features, commonly called bicelles. Atomistic simulations of bilayer ribbons and perforated bilayers containing dimyristoylphosphatidylcholine (DMPC, di-C(14) tails) and dihexanoylphosphatidylcholine (DHPC, di-C(6) tails) have been carried out to investigate the partitioning of these components between flat and curved microenvironments and the stabilization of the bilayer edge by DHPC. To approach equilibrium partitioning of lipids on an achievable simulation timescale, configuration-bias Monte Carlo mutation moves were used to allow individual lipids to change tail length within a semigrand-canonical ensemble. Since acceptance probabilities for direct transitions between DMPC and DHPC were negligible, a third component with intermediate tail length (didecanoylphosphatidylcholine, di-C(10) tails) was included at a low concentration to serve as an intermediate for transitions between DMPC and DHPC. Strong enrichment of DHPC is seen at ribbon and pore edges, with an excess linear density of approximately 3 nm(-1). The simulation model yields estimates for the onset of edge stability with increasing bilayer DHPC content between 5% and 15% DHPC at 300 K and between 7% and 17% DHPC at 323 K, higher than experimental estimates. Local structure and composition at points of close contact between pores suggest a possible mechanism for effective attractions between pores, providing a rationalization for the tendency of bicelle mixtures to aggregate into perforated vesicles and perforated sheets.

Peptide nanopores and lipid bilayers: interactions by coarse-grained molecular-dynamics simulations

A set of 49 protein nanopore-lipid bilayer systems was explored by means of coarse-grained molecular-dynamics simulations to study the interactions between nanopores and the lipid bilayers in which they are embedded. The seven nanopore species investigated represent the two main structural classes of membrane proteins (alpha-helical and beta-barrel), and the seven different bilayer systems range in thickness from approximately 28 to approximately 43 A. The study focuses on the local effects of hydrophobic mismatch between the nanopore and the lipid bilayer. The effects of nanopore insertion on lipid bilayer thickness, the dependence between hydrophobic thickness and the observed nanopore tilt angle, and the local distribution of lipid types around a nanopore in mixed-lipid bilayers are all analyzed. Different behavior for nanopores of similar hydrophobic length but different geometry is observed. The local lipid bilayer perturbation caused by the inserted nanopores suggests possible mechanisms for both lipid bilayer-induced protein sorting and protein-induced lipid sorting. A correlation between smaller lipid bilayer thickness (larger hydrophobic mismatch) and larger nanopore tilt angle is observed and, in the case of larger hydrophobic mismatches, the simulated tilt angle distribution seems to broaden. Furthermore, both nanopore size and key residue types (e.g., tryptophan) seem to influence the level of protein tilt, emphasizing the reciprocal nature of nanopore-lipid bilayer interactions.

Lipid gymnastics: evidence of complete acyl chain reversal in oxidized phospholipids from molecular simulations

In oxidative environments, biomembranes contain oxidized lipids with short, polar acyl chains. Two stable lipid oxidation products are PoxnoPC and PazePC. PoxnoPC has a carbonyl group, and PazePC has an anionic carboxyl group pendant at the end of the short, oxidized acyl chain. We have used MD simulations to explore the possibility of complete chain reversal in OXPLs in POPC-OXPL mixtures. The polar AZ chain of PazePC undergoes chain reversal without compromising the lipid bilayer integrity at concentrations up to 25% OXPL, and the carboxyl group points into the aqueous phase. Counterintuitively, the perturbation of overall membrane structural and dynamic properties is stronger for PoxnoPC than for PazePC. This is because of the overall condensing and ordering effect of sodium ions bound strongly to the lipids in the PazePC simulations. The reorientation of AZ chain is similar for two different lipid force fields. This work provides the first molecular evidence of the "extended lipid conformation" in phospholipid membranes. The chain reversal of PazePC lipids decorates the membrane interface with reactive, negatively charged functional groups. Such chain reversal is likely to exert a profound influence on the structure and dynamics of biological membranes, and on membrane-associated biological processes.

Intramitochondrial crystalline inclusions in nonalcoholic steatohepatitis

Mitochondrial dysfunction is an important element in the pathogenesis of nonalcoholic steatohepatitis (NASH). Intramitochondrial crystals (IMCs) are a well-documented morphological abnormality seen on transmission electron microscopy in this disease. It has been suggested that IMCs consist of phospholipids, but their exact composition remain uncertain many years after their discovery. Micellar phase transitions of phospholipid bilayers is a well-known but little-studied phenomenon in living systems. Its presence in the mitochondria of NASH would offer significant insight into the disease with possible therapeutic implications. We postulated that intramitochondrial disturbances in NASH are sufficient to produce such transitions and that their detection in fresh biopsies would therefore be a dynamic process. To test this, we performed a blinded, prospective analysis of fresh liver biopsy samples immediately fixed under different conditions. Quantitative transmission electron microscopy morphometry, performed by systematically counting total mitochondria and IMCs within areas of uniform dimension, showed a stepwise decline in IMCs with cooler fixation temperature in each subject studied. Randomization testing (Monte Carlo resampling) confirmed that the detection of IMCs was strongly dependent on fixation temperature (P < 0.0001).

CONCLUSION

These results indicate that the intramitochondrial crystals characteristic of NASH are highly dynamic and unstable structures. The findings offer the strongest support yet for their origin in micellar phase transitions. We speculate that such transitions result from microenvironmental changes within the mitochondria and carry therapeutic implications, especially in regard to dietary manipulations of mitochondrial lipid composition.

Coarse-grained modeling of lipids

Molecular modeling of phospholipids on many scales has progressed significantly over the last years. Here we review several membrane models on intermediate to large length scales restricting ourselves to particle based coarse-grained models with implicit and explicit solvent. We explain similarities and differences as well as their connection to experiments and fine-grained models. We neglect any field descriptions on larger scales. We discuss then a few examples where we focus on studies of lipid phase behavior as well as supported lipid bilayers as these examples can only be meaningfully studied using large-scale models to date.

Multiscale modeling of emergent materials: biological and soft matter

In this review, we focus on four current related issues in multiscale modeling of soft and biological matter. First, we discuss how to use structural information from detailed models (or experiments) to construct coarse-grained ones in a hierarchical and systematic way. This is discussed in the context of the so-called Henderson theorem and the inverse Monte Carlo method of Lyubartsev and Laaksonen. In the second part, we take a different look at coarse graining by analyzing conformations of molecules. This is done by the application of self-organizing maps, i.e., a neural network type approach. Such an approach can be used to guide the selection of the relevant degrees of freedom. Then, we discuss technical issues related to the popular dissipative particle dynamics (DPD) method. Importantly, the potentials derived using the inverse Monte Carlo method can be used together with the DPD thermostat. In the final part we focus on solvent-free modeling which offers a different route to coarse graining by integrating out the degrees of freedom associated with solvent.

Visualization of complex processes in lipid systems using computer simulations and molecular graphics

Computer simulation has become an increasingly popular tool in the study of lipid membranes, complementing experimental techniques by providing information on structure and dynamics at high spatial and temporal resolution. Molecular visualization is the most powerful way to represent the results of molecular simulations, and can be used to illustrate complex transformations of lipid aggregates more easily and more effectively than written text. In this chapter, we review some basic aspects of simulation methodologies commonly employed in the study of lipid membranes and we describe a few examples of complex phenomena that have been recently investigated using molecular simulations. We then explain how molecular visualization provides added value to computational work in the field of biological membranes, and we conclude by listing a few molecular graphics packages widely used in scientific publications.

Lipids on the move: simulations of membrane pores, domains, stalks and curves

In this review we describe the state-of-the-art of computer simulation studies of lipid membranes. We focus on collective lipid-lipid and lipid-protein interactions that trigger deformations of the natural lamellar membrane state, showing that many important biological processes including self-aggregation of membrane components into domains, the formation of non-lamellar phases, and membrane poration and curving, are now amenable to detailed simulation studies.