Lipid Membrane Systems Research Articles

Dynamic Second Harmonic Imaging of Proton Translocation Through Water Needles in Lipid Membranes.

Proton translocation through lipid membranes is a fundamental process in the field of biology. Several theoretical models have been developed and presented over the years to explain the phenomenon, yet the exact mechanism is still not well understood. Here, we show that proton translocation is directly related to membrane potential fluctuations. Using high-throughput wide-field second harmonic (SH) microscopy, we report apparently universal transmembrane potential fluctuations in lipid membrane systems. Molecular simulations and free energy calculations suggest that H+ permeation proceeds predominantly across a thin, membrane-spanning water needle and that the transient transmembrane potential drives H+ ions across the water needle. This mechanism differs from the transport of other cations that require completely open pores for transport and follows naturally from the well-known Grotthuss mechanism for proton transport in bulk water. Furthermore, SH imaging and conductivity measurements reveal that the rate of proton transport depends on the structure of the hydrophobic core of bilayer membranes.

Influence of cholesterol on hydrogen-bond dynamics of water molecules in lipid-bilayer systems at varying temperatures.

Cholesterol (Chol) plays a crucial role in shaping the intricate physicochemical attributes of biomembranes, exerting a considerable influence on water molecules proximal to the membrane interface. In this study, we conducted molecular dynamics simulations on the bilayers of two lipid species, dipalmitoylphosphatidylcholine (DPPC) and palmitoyl sphingomyelin; they are distinct with respect to the structures of the hydrogen-bond (H-bond) acceptors. Our investigation focuses on the dynamic properties and H-bonds of water molecules in the lipid-membrane systems, with a particular emphasis on the influence of Chol at varying temperatures. Notably, in the gel phase at 303K, the presence of Chol extends the lifetimes of H-bonds of the oxygen atoms acting as H-bond acceptors within DPPC with water molecules by a factor of 1.5-2.5. In the liquid-crystalline phase at 323K, on the other hand, H-bonding dynamics with lipid membranes remain largely unaffected by Chol. This observed shift in H-bonding states serves as a crucial key to unraveling the subtle control mechanisms governing water dynamics in lipid-membrane systems.

Modulation of Phospholipase A2 Membrane Activity by Anti-inflammatory Drugs.

The phospholipase A2 (PLA2) superfamily consists of lipolytic enzymes that hydrolyze specific cell membrane phospholipids and have long been considered a central hub of biosynthetic pathways, where their lipid metabolites exert a variety of physiological roles. A misregulated PLA2 activity is associated with mainly inflammatory-derived pathologies and thus has shown relevant therapeutic potential. Many natural and synthetic anti-inflammatory drugs (AIDs) have been proposed as direct modulators of PLA2 activity. However, despite the specific chemical properties that these drugs share in common, little is known about the indirect modulation able to finely tune membrane structural changes at the precise lipid-binding site. Here, we use a novel experimental strategy based on differential scanning calorimetry to systematically study the structural properties of lipid membrane systems during PLA2 cleavage and under the influence of several AIDs. For a better understanding of the AIDs-membrane interaction, we present a comprehensive and comparative set of molecular dynamics (MD) simulations. Our thermodynamic results clearly demonstrate that PLA2 cleavage is hindered by those AIDs that significantly reduce the lipid membrane cooperativity, while the rest of the AIDs oppositely tend to catalyze PLA2 activity to different extents. On the other hand, our MD simulations support experimental results by providing atomistic details on the binding, insertion, and dynamics of each AID on a pure lipid system; the drug efficacy to impact membrane cooperativity is related to the lipid order perturbation. This work suggests a membrane-based mechanism of action for diverse AIDs against PLA2 activity and provides relevant clues that must be considered in its modulation.

Unraveling How Antimicrobial Lipid Mixtures Disrupt Virus-Mimicking Lipid Vesicles: A QCM-D Study.

Single-chain lipid amphiphiles such as fatty acids and monoglycerides are promising antimicrobial alternatives to replace industrial surfactants for membrane-enveloped pathogen inhibition. Biomimetic lipid membrane platforms in combination with label-free biosensing techniques offer a promising route to compare the membrane-disruptive properties of different fatty acids and monoglycerides individually and within mixtures. Until recently, most related studies have utilized planar model membrane platforms, and there is an outstanding need to investigate how antimicrobial lipid mixtures disrupt curved model membrane platforms such as intact vesicle adlayers that are within the size range of membrane-enveloped virus particles. This need is especially evident because certain surfactants that completely disrupt planar/low-curvature membranes are appreciably less active against high-curvature membranes. Herein, we conducted quartz crystal microbalance-dissipation (QCM-D) measurements to investigate the membrane-disruptive properties of glycerol monolaurate (GML) monoglyceride and lauric acid (LA) fatty acid mixtures to rupture high-curvature, ~75 nm diameter lipid vesicle adlayers. We identified that the vesicle rupture activity of GML/LA mixtures mainly occurred above the respective critical micelle concentration (CMC) of each mixture, and that 25/75 mol% GML/LA micelles exhibited the greatest degree of vesicle rupture activity with ~100% efficiency that exceeded the rupture activity of other tested mixtures, individual compounds, and past reported values with industrial surfactants. Importantly, 25/75 GML/LA micelles outperformed 50/50 GML/LA micelles, which were previously reported to have the greatest membrane-disruptive activity towards planar model membranes. We discuss the mechanistic principles behind how antimicrobial lipid engineering can influence membrane-disruptive activity in terms of optimizing the balance between competitive membrane remodeling processes and inducing anisotropic vs. isotropic spontaneous curvature in lipid membrane systems.

Lipid Bicelles in the Study of Biomembrane Characteristics.

Simulations of lipid membranes typically make use of periodic boundary conditions to mimic macroscopically sized membranes and allow for comparison to experiments performed e.g. on planar lipid membranes or on unilamellar lipid vesicles. However, the lateral periodicity partly suppresses membrane fluctuations or membrane remodeling, processes that are of particular importance in the study of asymmetric membranes-i.e. membranes with integral or associated proteins and/or asymmetric lipid compositions. Here, we devised a simple albeit powerful lipid bicelle model system that (i) displays similar structural, dynamical, and mechanical properties compared to infinite periodic lipid membrane systems and allows (ii) for the study of asymmetric lipid bilayer systems and (iii) the unperturbed formation of local spontaneous curvature induced by lipids or proteins in molecular dynamics simulations. In addition, the system is characterized by largely unbiased thermal fluctuations as opposed to standard bilayer systems. Application of the bicelle system for an asymmetric lipid composition resembling the plasma membrane reveals that the cholesterol density for a tension-free plasma membrane with a vanishing spontaneous curvature is larger by 28% within the extracellular leaflet compared to the cytosolic leaflet.

Polymers of the candidalysin peptide become membrane pores.

C. albicans infection requires the action of the virulence factor candidalysin (CL), which damages the plasma membrane of target human cells (Moyes Nature 2016). However, the molecular mechanism that CL uses to permeabilize membranes was unknown. We have employed complementary biophysical, modeling, microscopy, and cell biology methods to reveal that CL forms membrane pores using a unique molecular mechanism (Russell eLife 2022). Unexpectedly, we observed that CL readily assembles into linear polymers in solution. We propose that the basic structural unit in polymer formation is a CL oligomer, which is sequentially added into a string configuration that can close into a loop. Our data indicate that CL loops spontaneously insert into the membrane to become membrane pores. We identified a CL mutation (G4W) that inhibited the formation of polymers in solution and prevented formation of pores in synthetic lipid membrane systems. Studies in epithelial cells showed that G4W CL failed to activate the danger response signaling pathway, a hallmark of the pathogenic effect of CL. These results indicate that CL polymerization in solution is a necessary step for the damage of cellular membranes. Analysis of thousands of CL pores by atomic force microscopy revealed co-existence of simple depressions and complex pores decorated with protrusions. Imaging and modeling indicate that the two types of pores are formed by CL oligomers assembled into alternate orientations. We propose that this structural rearrangement represents a maturation mechanism that stabilizes pore formation . The data show that CL uses a previously unknown mechanism to damage membranes, whereby pre-assembly of CL loops in solution directly leads to formation of membrane pores. Our investigation not only unravels a new paradigm for the formation of membrane pores, but additionally identifies CL polymerization as a novel therapeutic target to treat candidiasis.

Structural elucidation of ETHR-A and ETHR-B from Plutella xylostella and insight into non-conservative mutations in transmembrane helix-6

The development of Diamondback moth (DBM) depends on the ecdysis triggering hormone receptor (ETHR); a neuronal membrane G-protein coupled receptor (GPCR) connected to the metamorphosis cascade. Lepidopteran insect DBM is an infamous pest of cruciferous plants. This study examined the full-length coding sequences (CDS) of PxETHR-A and PxETHR-B from the DBM genome. The three-dimensional (3 D) models of both receptors were generated in an inactive state. The behaviour and stability of receptors were examined using molecular dynamics simulations in a lipid membrane system for 300 ns and established a GPCR family-based view. Secondary interactions within receptors were studied to know more about factors contributing to their stability. Multiple sequence alignment revealed conserved features of insect ETHRs those compared to the GPCR family proteins. These features were helpful during the evaluation of the molecular models of both receptors. Side-chain orientation of conserved residues, non-conserved and conserved hydrogen-bond networks (HBN) and hydrophobic clusters were examined in the structures of both receptors. The non-conserved residues L6.35, T6.39, C/S6.43, and L6.48, are present in a conserved position on the transmembrane helix-6 (TM6) of ETHRs. In TM6, PxETHR-A and PxETHR-B differ at positions C/S6.43 and Y/F6.51, both being part of the HBN. Communicated by Ramaswamy H. Sarma

Usnic Acid-Mediated Exchange of Protons for Divalent Metal Cations across Lipid Membranes: Relevance to Mitochondrial Uncoupling.

Usnic acid (UA), a unique lichen metabolite, is a protonophoric uncoupler of oxidative phosphorylation, widely known as a weight-loss dietary supplement. In contrast to conventional proton-shuttling mitochondrial uncouplers, UA was found to carry protons across lipid membranes via the induction of an electrogenic proton exchange for calcium or magnesium cations. Here, we evaluated the ability of various divalent metal cations to stimulate a proton transport through both planar and vesicular bilayer lipid membranes by measuring the transmembrane electrical current and fluorescence-detected pH gradient dissipation in pyranine-loaded liposomes, respectively. Thus, we obtained the following selectivity series of calcium, magnesium, zinc, manganese and copper cations: Zn2+ > Mn2+ > Mg2+ > Ca2+ >> Cu2+. Remarkably, Cu2+ appeared to suppress the UA-mediated proton transport in both lipid membrane systems. The data on the divalent metal cation/proton exchange were supported by circular dichroism spectroscopy of UA in the presence of the corresponding cations.

A Versatile Suspended Lipid Membrane System for Probing Membrane Remodeling and Disruption.

Artificial membrane systems can serve as models to investigate molecular mechanisms of different cellular processes, including transport, pore formation, and viral fusion. However, the current, such as SUVs, GUVs, and the supported lipid bilayers suffer from issues, namely high curvature, heterogeneity, and surface artefacts, respectively. Freestanding membranes provide a facile solution to these issues, but current systems developed by various groups use silicon or aluminum oxide wafers for fabrication that involves access to a dedicated nanolithography facility and high cost while conferring poor membrane stability. Here, we report the development, characterization and applications of an easy-to-fabricate suspended lipid bilayer (SULB) membrane platform leveraging commercial track-etched porous filters (PCTE) with defined microwell size. Our SULB system offers a platform to study the lipid composition-dependent structural and functional properties of membranes with exceptional stability. With dye entrapped in PCTE microwells by SULB, we show that sphingomyelin significantly augments the activity of pore-forming toxin, Cytolysin A (ClyA) and the pore formation induces lipid exchange between the bilayer leaflets. Further, we demonstrate high efficiency and rapid kinetics of membrane fusion by dengue virus in our SULB platform. Our suspended bilayer membrane mimetic offers a novel platform to investigate a large class of biomembrane interactions and processes.

Investigation of the structural and dynamical properties of human uncoupling protein 2 through molecular dynamics simulations

Uncoupling protein 2 (UCP2) is an integral membrane protein that belongs to the family of mitochondrial anion carrier proteins. The absence of human UCP2 structure, lack of understanding of Cl− ion transport mechanism in the UCP2 and the associated biological functions motivated us to model the protein and investigate its structural and dynamical properties in a realistic mitochondrial lipid membrane system. The lipid-protein and protein-protein interactions were probed since they were found to be responsible for the conformational changes of the transmembrane (TM) helices which are involved in facilitating Cl− ion transport. Here, we employed multiscale molecular dynamics simulations including unbiased and biased MD for the investigation of the transport pathway in hUCP2 and interactions of the ion with TM helices within a membrane environment. We initially validated the hUCP2 model in the lipid membrane and then explored the transport pathway of Cl− ion and its interaction with positive residues of TM2 helix that have been reported to play a major role in the Cl− ion transport along with other TM helices of the protein. The simulation results suggest that the TM2 helix plays an important role in the formation of a stable ion channel due to the presence of arginine residues, in particular Arg88 which was found to be a key residue to maintain the channel pore through which the movement of Cl− ions occurs. Based on the results, it can be said that the study provides an atomic-level description of the Cl− ion transport mechanism in hUCP2 embedded in the mitochondrial lipid membrane.

Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers.

Absolute binding free-energy (ABFE) calculations are playing an increasing role in drug design, especially as they can be performed on a range of disparate compounds and direct comparisons between them can be made. It is, however, especially important to ensure that they are as accurate as possible, as unlike relative binding free-energy (RBFE) calculations, one does not benefit as much from a cancellation of errors during the calculations. In most modern implementations of ABFE calculations, a particle mesh Ewald scheme is typically used to treat the electrostatic contribution to the free energy. A central requirement of such schemes is that the box preserves neutrality throughout the calculation. There are many ways to deal with this problem that have been discussed over the years ranging from a neutralizing plasma with a post hoc correction term through to a simple co-alchemical ion within the same box. The post hoc correction approach is the most widespread. However, the vast majority of these studies have been applied to a soluble protein in a homogeneous solvent (water or salt solution). In this work, we explore which of the more common approaches would be the most suitable for a simulation box with a lipid bilayer within it. We further develop the idea of the so-called Rocklin correction for lipid-bilayer systems and show how such a correction could work. However, we also show that it will be difficult to make this generalizable in a practical way and thus we conclude that the use of a “co-alchemical ion” is the most useful approach for simulations involving lipid membrane systems.

VV-hemorphin-5 association to lipid bilayers and alterations of membrane bending rigidity

<abstract> <p>The morphinomimetic properties of hemorphins are intensively studied with regard to new peptide drug developments. In this respect, the investigation of mechanical properties and stability of lipid membranes provides a useful background for advancement in pharmacological applications of liposomes. Here we probed the effect of the endogenous heptapeptide VV-hemorphin-5 (valorphin) on the bending elasticity of biomimetic lipid membranes of 1-palmitoyl-2-oleoyl-<italic>sn</italic>-glycero-3-phosphocholine (POPC) by analysis of thermal shape fluctuations of nearly spherical giant unilamellar vesicles. In a wide concentration range covering valorphin concentrations applied in nociceptive screening <italic>in vivo</italic>, we report alterations of the bilayer bending rigidity in a concentration-dependent non-monotonic manner. We performed quantitative characterization of VV-hemorphin-5 association to POPC membranes by isothermal titration calorimetry in order to shed light on the partitioning of the amphiphilic hemorphin between the aqueous solution and membranes. The calorimetric results correlate with flicker spectroscopy findings and support the hypothesis about the strength of valorphin-membrane interaction related to the peptide bulk concentration. A higher strength of valorphin interaction with the bilayer corresponds to a more pronounced effect of the peptide on the membrane's mechanical properties. The presented study features the comprehensive analysis of membrane bending elasticity as a biomarker for physicochemical effects of peptides on lipid bilayers. The reported data on thermodynamic parameters of valorphin interactions with phosphatidylcholine bilayers and alterations of their mechanical properties is expected to be useful for applications of lipid membrane systems in pharmacology and biomedicine.</p> </abstract>

Selectivity of mTOR-Phosphatidic Acid Interactions Is Driven by Acyl Chain Structure and Cholesterol.

The need to gain insights into the molecular details of peripheral membrane proteins’ specificity towards phosphatidic acid (PA) is undeniable. The variety of PA species classified in terms of acyl chain length and saturation translates into a complicated, enigmatic network of functional effects that exert a critical influence on cell physiology. As a consequence, numerous studies on the importance of phosphatidic acid in human diseases have been conducted in recent years. One of the key proteins in this context is mTOR, considered to be the most important cellular sensor of essential nutrients while regulating cell proliferation, and which also appears to require PA to build stable and active complexes. Here, we investigated the specific recognition of three physiologically important PA species by the mTOR FRB domain in the presence or absence of cholesterol in targeted membranes. Using a broad range of methods based on model lipid membrane systems, we elucidated how the length and saturation of PA acyl chains influence specific binding of the mTOR FRB domain to the membrane. We also discovered that cholesterol exerts a strong modulatory effect on PA-FRB recognition. Our data provide insight into the molecular details of some physiological effects reported previously and reveal novel mechanisms of fine-tuning the signaling cascades dependent on PA.

Structural and mechanistic insights into amyloid-β and α-synuclein fibril formation and polyphenol inhibitor efficacy in phospholipid bilayers.

Under certain cellular conditions, functional proteins undergo misfolding, leading to a transition into oligomers which precede the formation of amyloid fibrils. Misfolding proteins are associated with neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. While the importance of lipid membranes in misfolding and disease aetiology is broadly accepted, the influence of lipid membranes during therapeutic design has been largely overlooked. This study utilized a biophysical approach to provide mechanistic insights into the effects of two lipid membrane systems (anionic and zwitterionic) on the inhibition of amyloid-β 40 and α-synuclein amyloid formation at the monomer, oligomer and fibril level. Large unilamellar vesicles (LUVs) were shown to increase fibrillization and largely decrease the effectiveness of two well-known polyphenol fibril inhibitors, (-)-epigallocatechin gallate (EGCG) and resveratrol; however, use of immunoblotting and ion mobility mass spectrometry revealed this occurs through varying mechanisms. Oligomeric populations in particular were differentially affected by LUVs in the presence of resveratrol, an elongation phase inhibitor, compared to EGCG, a nucleation targeted inhibitor. Ion mobility mass spectrometry showed EGCG interacts with or induces more compact forms of monomeric protein typical of off-pathway structures; however, binding is reduced in the presence of LUVs, likely due to partitioning in the membrane environment. Competing effects of the lipids and inhibitor, along with reduced inhibitor binding in the presence of LUVs, provide a mechanistic understanding of decreased inhibitor efficacy in a lipid environment. Together, this study highlights that amyloid inhibitor design may be misguided if effects of lipid membrane composition and architecture are not considered during development.

Nanostructure regularity in white beetle scales for stability and strong optical scattering [Invited

Cyphochilus white beetle scales exhibit exceptionally strong light scattering power that originates from their regular random fibrillar network nanostructure. The structure is believed to be formed by late-stage spinodal decomposition in a lipid membrane system. However, the structure is characterized by nonconstant mean curvatures and appreciable anisotropy, which are not expected from late-stage spinodal decomposition, so that the surface free energy is not minimized. Nevertheless, a high degree of regularity represented by the relatively uniform fibril dimensions and smooth fibril surfaces in the structure may result from a process similar to spinodal decomposition. In this study, we investigate the role of regularity in the Cyphochilus white beetle scale structure in realizing strong light scattering. Irregularity is computationally introduced into the structure in a systematic fashion such that its anisotropy is preserved and its surface area is kept constant. Calculations show that optical scattering power decreases as irregularity increases with a high sensitivity. This effect happens because, remarkably, irregularity on a scale much smaller than the wavelength destroys anisotropy in optical diffusion. Thus, the result shows that the in vivo process in Cyphochilus white beetle scales utilizes structural regularity and anisotropy to achieve strong light scattering at a tolerable surface free energy. In typical fabrication of random media, irregularity and multiple length scales typically increase surface area, so that durability of the nanostructures may be negatively affected. Our study indicates that regularity in anisotropic random nanostructures can achieve strong light scattering with a moderate surface free energy.

Tail-structure regulated phase behaviors of a lipid bilayer* *Project supported by the National Natural Science Foundation of China (Grant Nos. 21422404, 21774092, U1532108, 21728502, and U1932121), the Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions. K Yang and B Yuan acknowledge the support of the Natural Science Foundation of Jiangsu Province of China (Grant Nos. BK20171207 and BK20171210).

Lateral heterogeneity of a cell membrane, including the formation of lipid raft-like clusters and the inter-leaflet coupling of specific phase domains, is crucial for cellular functions such as membrane trafficking and transmembrane signaling. However, the wide diversity in lipid species and the consequent complexity in lipid–lipid interplays hinder our understanding of the underlying mechanism. In this work, with coarse-grained molecular dynamics simulations, the effect of lipid tail structures on the phase behavior of a model ternary lipid membrane was systematically explored. A serial of 27 lipid membrane systems consisting of saturated, unsaturated lipids, and cholesterol (Chol) molecules, at a fixed molar ratio of 4:4:2 while varying in lipid structures including tail length, unsaturation degree, and/or position of unsaturated atoms, were constructed. These structural factors were found to exert sophisticated influences on packing states of the constituent molecules, especially Chol, in a bilayer, and modulate the complicated entropy–enthalpy competition of the membrane system accordingly. Specifically, an appropriate difference in effective tail length and distinct feature of the tail ends between the saturated and unsaturated lipid compositions promised an enhanced phase separation of the membrane into the Chol-rich Lo and Chol-poor Ld phase domains, with a full inter-leaflet coupling of each domain. Our results provide insights into the lipid organizations and segregations of the cellular plasma membrane.

Temporary Membrane Permeabilization via the Pore-Forming Toxin Lysenin.

Pore-forming toxins are alluring tools for delivering biologically-active, impermeable cargoes to intracellular environments by introducing large conductance pathways into cell membranes. However, the lack of regulation often leads to the dissipation of electrical and chemical gradients, which might significantly affect the viability of cells under scrutiny. To mitigate these problems, we explored the use of lysenin channels to reversibly control the barrier function of natural and artificial lipid membrane systems by controlling the lysenin’s transport properties. We employed artificial membranes and electrophysiology measurements in order to identify the influence of labels and media on the lysenin channel’s conductance. Two cell culture models: Jurkat cells in suspension and adherent ATDC5 cells were utilized to demonstrate that lysenin channels may provide temporary cytosol access to membrane non-permeant propidium iodide and phalloidin. Permeability and cell viability were assessed by fluorescence spectroscopy and microscopy. Membrane resealing by chitosan or specific media addition proved to be an effective way of maintaining cellular viability. In addition, we loaded non-permeant dyes into liposomes via lysenin channels by controlling their conducting state with multivalent metal cations. The improved control over membrane permeability might prove fruitful for a large variety of biological or biomedical applications that require only temporary, non-destructive access to the inner environment enclosed by natural and artificial membranes.

Development of lipid membrane based assays to accurately predict the transfection efficiency of cell-penetrating peptide-based gene nanoparticles.

Successful gene therapy requires the development of vectors that enable efficient delivery of genetic materials (e.g., pDNA or siRNA) to targeted cells, without degradation of the genetic materials. We have shown that nanoparticles formed by combining cell-penetrating peptide and pDNA (CPP-pDNA) into complexes and condensing them with calcium chloride can provide gene nanoparticles with high transfection efficiency and low cytotoxicity. In this work, we compare in situ measurements of the membrane insertion potential of three arginine-based gene nanoparticles (RW9-NPs, R9-NPs, and RH9-NPs) using four lipid compositions and two types of model membrane (Langmuir monolayers vs. supported bilayers) with their transfection efficiency in two human cancer cell lines. Using a Langmuir trough, we measured the membrane insertion potential of our gene nanoparticles to model membrane monolayers. A Quartz Crystal Microbalance with Dissipation (QCM-D) technique was used to monitor the adsorption of these nanoparticles to lipid bilayers of various compositions. Finally, gene expression using these nanoparticles was measured in breast cancer and cervical cancer cell lines. Our cell culture studies indicate that although R9-NPs and RW9-NPs show a significant increase in transfection efficiency compared to free pDNA, RH9-NPs do not show any significant difference. Both the Langmuir monolayer and QCM-D bilayer studies show that these results are best reflected in the in situ measurement assays when lipid systems containing a mixture of phospholipids, cholesterol, and sphingolipids are used. It is important to note that the mechanism of penetration is expected to differ for RW9 vs. R9; however, gene nanoparticles containing either of these CPPs show similar transfection efficiency. Our results therefore demonstrate that the design of predictive assays for gene therapy using CPPs must involve carefully chosen model lipid membrane systems that accurately represent the varying compositions of cell membranes.

Principal component analysis highlights the influence of temperature, curvature and cholesterol on conformational dynamics of lipids

Membrane lipids are inherently highly dynamic molecules. Currently, it is difficult to probe the structures of individual lipids experimentally at the timescales corresponding to atomic motions, and consequently molecular dynamics simulations are used widely. In our previous work, we have introduced the principal component analysis (PCA) as a convenient framework for comprehensive quantitative description of lipid motions. Here, we present a newly developed open source script, PCAlipids, which automates the analysis and allows us to refine the approach and test its limitations. We use PCAlipids to determine the influence of temperature, cholesterol and curvature on individual lipids, and show that the most prominent lipid tail scissoring motion is strongly affected by these factors and allows tracking of phase transition. Addition of cholesterol affects the conformations and selectively changes the dynamics of lipid molecules, impacting the large-amplitude motions. Introduction of curvature biases the conformational ensembles towards more extended structures. We hope that the developed approach will be useful for understanding the molecular basis of different processes occurring in lipid membrane systems and will stimulate development of complementary experimental techniques probing the conformations of individual lipid molecules.

The u-series: A separable decomposition for electrostatics computation with improved accuracy.

The evaluation of electrostatic energy for a set of point charges in a periodic lattice is a computationally expensive part of molecular dynamics simulations (and other applications) because of the long-range nature of the Coulomb interaction. A standard approach is to decompose the Coulomb potential into a near part, typically evaluated by direct summation up to a cutoff radius, and a far part, typically evaluated in Fourier space. In practice, all decomposition approaches involve approximations-such as cutting off the near-part direct sum-but it may be possible to find new decompositions with improved trade-offs between accuracy and performance. Here, we present the u-series, a new decomposition of the Coulomb potential that is more accurate than the standard (Ewald) decomposition for a given amount of computational effort and achieves the same accuracy as the Ewald decomposition with approximately half the computational effort. These improvements, which we demonstrate numerically using a lipid membrane system, arise because the u-series is smooth on the entire real axis and exact up to the cutoff radius. Additional performance improvements over the Ewald decomposition may be possible in certain situations because the far part of the u-series is a sum of Gaussians and can thus be evaluated using algorithms that require a separable convolution kernel; we describe one such algorithm that reduces communication latency at the expense of communication bandwidth and computation, a trade-off that may be advantageous on modern massively parallel supercomputers.