Molecular dynamics simulations on the interactions between nucleic acids and a phospholipid bilayer

Recently,lipid nanoparticles(LNPs)have been extensively investigated as non-viral carriers of nucleic acid vaccines due to their high transport efficiency,safety,and straightforward production and scalability.However,the molecular mechanism underlying the interactions between nucleic acids and phospholipid bilayers within LNPs remains elusive.In this study,we employed the all-atom molecular dynamics simulation to investigate the interactions between single-stranded nucleic acids and a phospholipid bilayer.Our findings revealed that hydrophilic bases,specifically G in single-stranded RNA(ssRNA)and single-stranded DNA(ssDNA),displayed a higher propensity to form hydrogen bonds with phospholipid head groups.Notably,ssRNA exhibited stronger binding energy than ssDNA.Furthermore,divalent ions,particularly Ca2+,facilitated the binding of ssRNA to phospholipids due to their higher binding energy and lower dissociation rate from phospholipids.Overall,our study provides valuable insights into the molecular mechanisms underlying nucleic acidphospholipid interactions,with potential implications for the nucleic acids in biotherapies,particularly in the context of lipid carriers.

Molecular dynamics simulations of the effects of sodium dodecyl sulfate on lipid bilayer

Molecular dynamics simulations have been performed on the fully hydrated lipid bilayer with different concentrations of sodium dodecyl sulfate （SDS）. SDS can readily penetrate into the membrane. The insertion of SDS causes a decrease in the bilayer area and increases in the bilayer thickness and lipid tail order, when the fraction of SDS is less than 28%. Through calculating the binding energy, we confirm that the presence of SDS strengthens the interactions among the DPPC lipids, while SDS molecules act as intermedia. Both the strong hydrophilic interactions between sulfate and phosphocholine groups and the hydrophobic interactions between SDS and DPPC hydrocarbon chains contribute to the tight packing and ordered alignment of the lipids. These results are in good agreement with the experimental observations and provide atomic level information that complements the experiments.

Coarse-grained simulations on interactions between spectrins and phase-separated lipid bilayers

Spectrin, the principal protein of the cytoskeleton of erythrocyte, plays a crucial role in the stability and flexibility of the plasma membrane of erythrocyte. In this work, we investigate the interactions between spectrins and phase-separated lipid bilayers using coarse-grained molecular dynamics simulation. We focus on the preference of spectrins with different lipids, the effects of the anionic lipids and the residue mutation on the interactions between spectrins and the lipid bilayers. The results indicate that spectrins prefer to contact with phosphatidylethanolamine(PE) lipids rather than with phosphatidylcholine(PC) lipids, and tend to contact with the liquid-disordered(Ld) domains enriched in unsaturated PE.Additionally, the anionic lipids, which show specific interaction with the positively charged or polar amino acids on the surface of the spectrins, can enhance the attraction between the spectrins and lipid domains. The mutation leads to the decrease of the structural stability of spectrins and increases the curvature of the lipid bilayer. This work provides some theoretical insights into understanding the erythrocyte structure and the mechanism of some blood diseases.

Tail-structure regulated phase behaviors of a lipid bilayer

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.

Molecular dynamics study of the infiltration of lipid-wrapping C60 and polyhydroxylated single-walled nanotubes into lipid bilayers

Because of the many potential medical applications of nanoparticles, considerable research has been conducted on the interactions between nanoparticles and biomembranes. We employed coarse- grained molecular dynamics simulations to study the infiltration of lipid-wrapping C60 and polyhy- droxylated single-walled nanotubes. Diffusion coefficients and scaling factors are adopted to quantify the diffusivity of the biomembranes, and the rupture tension is used to measure the lateral strength of the lipid bilayer. According to our simulations, all wrapped nanoparticles, except those wrapped by dipalmitoyl-glycero-phosphoglycerol, can be inserted into the bilayers. Our simulations also re- veal that the bilayers remain in free diffusion after the nanoparticle insertions while their diffusion coefficient can be altered significantly. The polyhydroxylated single-walled nanotubes lead to signif- icant changes to the lateral strength of biomembranes and this effect depends on the quantity of the inserted nanoparticles. The simulations demonstrate the feasibility of using these methods to deliver nanopartieles while some suggestions are given for choosing the appropriate lipids for wrappiug. The results also suggest that the functionalized nanopartieles could be applied in strengthening or weakening the lateral strength of biomembranes for specific purposes.

Hydrophobic Effect in a Continuum Model of the Lipid Bilayer

We study a continuum paradigm of the lipid bilayer based on minimizing the free energy of a mixture of water and lipid molecules.This paper extends previous work of Blom and Peletier[European J.Appl.Math.,15(2004),pp.487-508]in the following ways.(a)It formulates a more general model of the hydrophobic effect to facilitate connections with microscale simulations and first-principles analysis.(b)It clarifies the meaning and role of the model parameters.(c)It outlines a method for determining parameter values so that physically-realistic bilayer density profiles can be obtained,for example for use in macroscale simulations.Points(a)-(c)suggest that the model has potential to robustly connect some micro-and macroscale levels of multiscale blood flow simulations.The mathematical modelling in point(a)is based upon a consideration of the underlying physics of inter-molecular forces.The governing equations thus obtained are minimized by gradient flows via a novel numerical approach;this enables point(b).The numerical results are shown to behave physically in terms of the effect of background concentration,in contrast to the earlier model which is shown here to not display the expected behaviour.A“short-tail”approximation of the lipid molecules also gives an analytical tool which yields critical values of some parameters under certain conditions.Point(c)involves the first quantitative comparison of the numerical data with physical experimental results.

Biphasic Nano-Domains of Planar Lipid Bilayer Complexed with Fluorogenic Polymer Reporter Tailored for Antimicrobial Detection

We have fabricated an unexpected type of supported planar bilayer composed of receptor phospholipids and single-chained diacetylenes as fluorogenic reporters using protruded anchor moieties with a positive terminal charge.Nanoscale topographical and surface thermodynamic analyses,as well as molecular dynamics simulations,revealed the coexistence of well-dispersed liquid-condensed(L_(c))domains forming nano-islands and liquid-expanded(L_(e))region in the planar bilayer,enhancing sensitivity against a prototype of ubiquitous membrane-associated antimicrobial peptides,melittin.The L_(e)regions,acting as target receptors,enabled sensitive detection as the melittin adsorbed and inserted into these regions due to strong hydrophobic interactions between phospholipids and melittin.The L_(c)domains,serving as signal reporters,enabled diacetylenes to assemble,polymerize,and fluoresce in response to the insertion of melittin into the L_(e)regions.Thus,biphasic nanodomains of the planar lipid bilayer finally endowed this sensor system with a detection range of 100μMto 50 nM and a limit of detection(LOD)of∼37 nM for melittin.This exceeded the operational performance of the colorimetric polydiacetylene vesicle solution 45 times,which reportedly ranged from 100 to 4μM with an LOD of∼1.7μM.

Study of Oligonucleotide Fixation on Bilayer Lipid Membranes by Patch-clamp Pipette Support

One kind of novel BLMs was fabricated by patch-clamp pipette technology characterized in considerably sensitive to changes of electrochemical parameters.Detectiye currents and voltage presented linear relationship when BLMs was formed and it could be confirmed by Gramicidin method.Ion current was increased by dihexyl (C_ (12)) modified ssDNA fixed on the BLMs and also indicated linear relationship to ssDNA's concentration due to the interaction of (C_ 12)-ssDNA and BLMs.Further more,the regression equations were different from BLMs fixed with ssDNA probe and a blank control BLM in the same experimental conditions.The ssDNA probe was successfully fixed on patch-clamp pipette supported-BLMs.Based on our studies,a biosensor with reactive element of patch-clamp pipette-supported BLMs has been established.

Cholesterol-induced deformation of the gramicidin A channel inhibiting potassium ion binding and transport

Gramicidin A(gA)is a kind of antibiotic peptide produced by bacillus brevis and it can dimerize across lipid bilayers to form a monovalent cation channel.In this work,we investigate the impact of cholesterol in the lipid bilayer on the binding of potassium ions with the gA channel and the transport of the ions across the channel.The results indicate that cholesterol can significantly influence the conformational stability of the gA channel and cause the channel deformation which inhibits the potassium ion binding with the channel and transport across the channel.The work provides some molecular insights into understanding of influence of lipids on the activity of gA channel in both model membranes and plasma membranes of intact cells.

Mechanical responses of the bio-nano interface: A molecular dynamics study of graphene-coated lipid membrane

Bio-nano interfaces between biological materials and functional nanodevices are of vital importance in relevant energy and information exchange processes, which thus demand an in-depth understanding. One of the critical issues from the application viewpoint is the stability of the bio-nano hybrid under mechanical perturbations. In this work we explore mechanical responses of the interface between lipid bilayer and graphene under hydrostatic coating provides remarkable resistance to the pressure or indentation loads, We find that graphene loads, and the intercalated water layer offers additional protection. These findings are discussed based on molecular dynamics simulation results that elucidate the molecular level mechanisms, which provide a basis for the rational design of bionanotechnology- enabled aoolications such as biomedical devices and nanotheraoeutics.

Modeling biomembranes and red blood cells by coarse-grained particle methods

In this work, the previously developed coarse-grained （CG） particle models for biomembranes and red blood cells （RBCs） are reviewed, and the advantages of the CG particle methods over the continuum and atomistic simulations for modeling biological phenomena are discussed. CG particle models can largely increase the length scale and time scale of atomistic simulations by eliminating the fast degrees of freedom while preserving the mesoscopic structures and properties of the simulated system. Moreover, CG particle models can be used to capture the microstructural alternations in diseased RBCs and simulate the topological changes of biomembranes and RBCs, which are the major challenges to the typical continuum representations of membranes and RBCs. The power and versatility of CG particle methods are demonstrated：through simulating the dynamical processes mvolving significant topological .changes e.g. lipid self-assembly vesicle fusion and membrane budding.

MLKL forms cation channels

OBJECTIVE To investigate how MLKL functions on the membrane and explore its electrophysiological characters and structure.METHODS The full-length human MLKL were expressed in SF21 cells and purified using glutathione-sepharose affinity chromatography.The currents of purified MLKL proteins were recorded in avoltage-clamp mode using a Warner BC-535 bilayer clamp amplifier.The currents were digitized using p CLAMP 10.2 software.HEK293 cells were cultured and transfected with MLKL plasmid.Cell viability was examined using the Cell Titer-Glo Luminescent Cell Viability Assay kit.RESULT MLKL forms cation channels that are permeable preferentially to Mg2+rather than Ca2+in the presence of Na+and K+.Moreover,each MLKL monomer contains five transmembrane helices:H1,H2,H3,H5 and H6 of the N-terminal domain which is sufficient to form channels.Finally,MLKL-induced membrane depolarization and cell death exhibit a positive correlation to its channel activity.

Study of the Ion Channel Behavior of Didodecyldimethylammonium Bromide Formed Bilayer Lipid Membrane Stimulated by PF_6^-

Bilayer lipid membranes (BLM) formed from didodecyldimethylammonium bromide were made on the freshly exposed surface of a glassy carbon (GC) and were demonstrated by the ac impedance spectroscopy. The ion channels of membrane properties induced by PF -_6 were studied by the cyclic voltammetric methods. Experimental results indicated that the ion channel of BLM was open in the presence of the PF -_6 due to the interaction of PF -_6 with the BLM, while it was switched off in the absence of PF -_6. Because the ion channel behavior was affected by the concentration of PF -_6, a sensor for PF -_6 can be developed.

Ion Channel Behavior of a Supported Bilayer Lipid Membrane Composed of 5,5-Ditetradecyl-2-(2-trimethyl-ammonioethyl)-1,3-dioxane Bromide Modified Glassy Carbon Electrode

A synthetic cationic surfactant, 5,5-ditetradecyl-2-(2-trimethyl-ammonioethyl)-1,3-dioxane bromide (DTDB), was used to construct a supported bilayer lipid membrane (s-BLM) coated on an underlying glassy carbon electrode (GCE). Electrochemical impedance spectroscopy (EIS), small-angle X-ray diffraction (SAXD) and cyclic voltammetry were used to characterize the s-BLM. Both EIS and SAXD data indicated that the synthetic lipid exists as a well-oriented bilayer in the membrane. The voltammetric study showed that the lipid membrane can open ion channels in the presence of C1O4- stimulant with Ru(bpy)32+ as marker ions and give distinct channel currents. The channels can be closed and open up again many times by removing or introducing ClO4- anions.

Vesicle fusion induced by zwitterionic amphiphilic channels

A new strategy to induce vesicle fusion has been developed by employing pillar[5]arene derivatives that were channel-like and were prepared by appending side chains onto pillar[5]arenes backbones.The channels feature with hydrophilic negatively and positively charged groups at both ends and hydrophobic Trp residues at the outer surface,which endows the channels with amphiphilicity.The zwitterionic amphiphilic channels could spontaneously incorporate into the bilayer membranes of lipid vesicles to induce vesicle fusion driven by the electrostatic interactions between negatively charged and positively charged groups.

Fast Simulation of Lipid Vesicle Deformation Using Spherical Harmonic Approximation

Lipid vesicles appear ubiquitously in biological systems.Understanding how the mechanical and intermolecular interactions deform vesicle membranes is a fundamental question in biophysics.In this article we develop a fast algorithm to compute the surface configurations of lipid vesicles by introducing surface harmonic functions to approximate themembrane surface.This parameterization allows an analytical computation of themembrane curvature energy and its gradient for the efficient minimization of the curvature energy using a nonlinear conjugate gradient method.Our approach drastically reduces the degrees of freedom for approximating the membrane surfaces compared to the previously developed finite element and finite difference methods.Vesicle deformations with a reduced volume larger than 0.65 can be well approximated by using as small as 49 surface harmonic functions.The method thus has a great potential to reduce the computational expense of tracking multiple vesicles which deform for their interaction with external fields.

Novel Experimental Strategy for High Resolution AFM Imaging of Membrane-Associated Bacterial Toxins

Bacterial pore-forming toxins(PFTs) are essential virulence factors of many human pathogens. Knowledge of their structure within the membrane is critical for an understanding of their function in pathogenesis and for the development of useful therapy. Atomic force microscopy(AFM) has often been employed to structurally interrogate many membrane proteins, including PFTs, owing to its ability to produce sub-nanometer resolution images of samples under aqueous solution. However, an absolute prerequisite for AFM studies is that the samples are single-layered and closely-packed, which is frequently challenging with PFTs. Here, using the prototypical member of the cholesterol-dependent cytolysin family of PFTs, perfringolysin O(PFO), as a test sample, we have developed a simple, highly robust method that routinely produces clean, closely-packed samples across the entire specimen surface. In this approach, we first use a small Teflon well to prepare the supported lipid bilayer, remove the sample from the well, and then directly apply the proteins to the bilayer. For reasons that are not clear,bilayer preparation in the Teflon well is essential. We anticipate that this simple method will prove widely useful for the preparation of similar samples, and thereby enable AFM imaging of the greatest range of bacterial PFTs to the highest possible resolution.