arXiv subjects

Naofumi Shimokawa

Publications and source records attributed to Naofumi Shimokawa.

8 recordsLinked to original sources

arXiv2023

Lateral transport of domains in anionic lipid bilayer membranes under DC electric fields: A coarse-grained molecular dynamics study

Dynamic lateral transport of lipids, proteins, and self-assembled structures in biomembranes plays crucial roles in diverse cellular processes. In this study, we perform a coarse-grained molecular dynamics simulation on a vesicle composed of a binary mixture of neutral and anionic lipids to investigate the lateral transport of individual lipid molecules and the self-assembled lipid domains upon an applied direct current (DC) electric field. Under the potential force of the electric field, a phase-separated domain rich in the anionic lipids is trapped in the opposite direction of the electric field. The subsequent reversal of the electric field induces the unidirectional domain motion. During the domain motion, the domain size remains constant, but a considerable amount of the anionic lipids is exchanged between the anionic-lipid-rich domain and the surrounding bulk. While the speed of the domain motion (collective lipid motion) shows a significant positive correlation with the electric field strength, the exchange of anionic lipids between the domain and bulk (individual lipid motion) exhibits no clear correlation with the field strength. The mean velocity field of the lipids surrounding the domain displays a two-dimensional (2D) source dipole. We revealed that the balance between the potential force of the applied electric field and the quasi-2D hydrodynamic frictional force well explains the dependence of the domain motions on the electric-field strengths. The present results provide insight into the hierarchical dynamic responses of self-assembled lipid domains to the applied electric field and contribute to controlling the lateral transportation of lipids and membrane inclusions.

cond-mat.soft↗

arXiv2021

Three-phase coexistence in binary charged lipid membranes in hypotonic solution

We investigated the phase separation of dioleoylphosphatidylserine (DOPS) and dipalmitoylphosphatidylcholine (DPPC) in giant unilamellar vesicles in hypotonic solution using fluorescence and confocal laser scanning microscopy. Although phase separation in charged lipid membranes is generally suppressed by the electrostatic repulsion between the charged headgroups, osmotic stress can promote the formation of charged lipid domains. Interestingly, we observed three-phase coexistence even in DOPS/DPPC binary lipid mixtures. The three phases were DPPC-rich, dissociated DOPS-rich, and nondissociated DOPS-rich phases. The two forms of DOPS were found to coexist owing to the ionization of the DOPS headgroup, such that the system could be regarded as quasi-ternary. The three formed phases with differently ionized DOPS domains were successfully identified experimentally by monitoring the adsorption of positively charged particles. In addition, coarse-grained molecular dynamics simulations confirmed the stability of the three-phase coexistence. Attraction mediated by hydrogen bonding between protonated DOPS molecules and reduction of the electrostatic interactions at the domain boundaries stabilized the three-phase coexistence.

cond-mat.soft↗

arXiv2019

Coarse-grained molecular dynamics simulation for uptake of nanoparticles into a charged lipid vesicle dominated by electrostatic interactions

We use a coarse-grained molecular dynamics simulation to investigate the interaction between neutral or charged nanoparticles (NPs) and a vesicle consisting of neutral and negatively charged lipids. We focus on the interaction strengths of hydrophilic and hydrophobic attraction and electrostatic interactions between a lipid molecule and an NP. A neutral NP passes through the lipid membrane when the hydrophobic interaction is sufficiently strong. As the valence of the positively charged NP increases, the membrane permeation speed of the NP is increased compared with the neutral NP and charged lipids are accumulated around the charged NP. A charged NP with a high valence passes through the lipid membrane via a transient channel formed by charged lipids or transport-like endocytosis. These permeation processes can be classified based on analyses of the density correlation function. When the non-electrostatic interaction parameters are large enough, a negatively charged NP can be adsorbed on the membrane and a neutral lipid-rich region is formed directly below the NP. The NP is spontaneously incorporated into the vesicle under various conditions and the incorporation is mediated by the membrane curvature. We reveal how the NP's behavior depends on the NP valence, size, and the non-electrostatic interaction parameters.

cond-mat.soft↗

arXiv2016

Coarse-grained molecular dynamics simulation of binary charged lipid membranes: Phase separation and morphological dynamics

Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and morphological dynamics in charged lipid bilayer vesicles. The screened long-range electrostatic repulsion among charged head groups delays or inhibits the lateral phase separation in charged vesicles compared with neutral vesicles, suggesting the transition of the phase-separation mechanism from spinodal decomposition to nucleation or homogeneous dispersion. Moreover, the electrostatic repulsion causes morphological changes, such as pore formation, and further transformations into disk, string, and bicelle structures, which are spatiotemporally coupled to the lateral segregation of charged lipids. Based on our coarse-grained MD simulation, we propose a plausible mechanism of pore formation at the molecular level. The pore formation in a charged-lipid-rich domain is initiated by the prior disturbance of the local molecular orientation in the domain.

cond-mat.soft↗

arXiv2016

Phase diagrams and ordering in charged membranes: Binary mixtures of charged and neutral lipids

We propose a model describing the phase behavior of two-component membranes consisting of binary mixtures of electrically charged and neutral lipids. We take into account the structural phase transition (main-transition) of the hydrocarbon chains, and investigate the interplay between this phase transition and the lateral phase separation. The presence of charged lipids significantly affects the phase behavior of the multi-component membrane. Due to the conservation of lipid molecular volume, the main-transition temperature of charged lipids is lower than that of neutral ones. Furthermore, as compared with binary mixtures of neutral lipids, the membrane phase separation in binary mixtures of charged lipids is suppressed, in accord with recent experiments. We distinguish between two types of charged membranes: mixtures of charged saturated lipid/neutral unsaturated lipid and a second case of mixtures of neutral saturated lipid/charged unsaturated lipid. The corresponding phase behavior is calculated and shown to be very different. Finally, we discuss the effect of added salt on the phase separation and the temperature dependence of the lipid molecular area.

cond-mat.soft↗

arXiv2016

Nano-domain formation in charged membranes: Beyond Debye-Huckel approximation

We investigate the microphase separation in a membrane composed of charged lipid, by taking into account explicitly the electrostatic potential and the ion densities in the surrounding solvent. While the overall (membrane and solvent) charge neutrality is assumed, the membrane can have a non-zero net charge. The static structure factor in the homogeneous state is analytically obtained without using the Debye-Huckel approximation and is found to have a peak at an intermediate wave number. For a binary membrane composed of anionic and neutral lipids, the characteristic wave number corresponds to a scale from several to tens of nanometers. Our numerical calculation further predicts the existence of nano-domains in charged membranes.

cond-mat.soft↗

arXiv2016

Coupling between pore formation and phase separation in charged lipid membranes

We investigated the effect of charge on the membrane morphology of giant unilamellar vesicles (GUVs) composed of various mixtures containing charged lipids. We observed the membrane morphologies by fluorescent and confocal laser microscopy in lipid mixtures consisting of a neutral unsaturated lipid [dioleoylphosphatidylcholine (DOPC)], a neutral saturated lipid [dipalmitoylphosphatidylcholine (DPPC)], a charged unsaturated lipid [dioleoylphosphatidylglycerol (DOPG$^{\scriptsize{(-)}}$)], a charged saturated lipid [dipalmitoylphosphatidylglycerol (DPPG$^{\scriptsize{(-)}}$)], and cholesterol (Chol). In binary mixtures of neutral DOPC/DPPC and charged DOPC/DPPG$^{\scriptsize{(-)}}$, spherical vesicles were formed. On the other hand, pore formation was often observed with GUVs consisting of DOPG$^{\scriptsize{(-)}}$ and DPPC. In a DPPC/DPPG$^{\scriptsize{(-)}}$/Chol ternary mixture, pore-formed vesicles were also frequently observed. The percentage of pore-formed vesicles increased with the DPPG$^{\scriptsize{(-)}}$ concentration. Moreover, when the head group charges of charged lipids were screened by the addition of salt, pore-formed vesicles were suppressed in both the binary and ternary charged lipid mixtures. We discuss the mechanisms of pore formation in charged lipid mixtures and the relationship between phase separation and the membrane morphology. Finally, we reproduce the results seen in experimental systems by using coarse-grained molecular dynamics simulations.

cond-mat.soft↗

arXiv2014

Charge-induced phase separation in lipid membranes

The phase separation in lipid bilayers that include negatively charged lipids is examined experimentally. We observed phase-separated structures and determined the membrane miscibility temperatures in several binary and ternary lipid mixtures of unsaturated neutral lipid, dioleoylphosphatidylcholine (DOPC), saturated neutral lipid, dipalmitoylphosphatidylcholine (DPPC), unsaturated charged lipid, dioleoylphosphatidylglycerol (DOPG$^{\scriptsize{(-)}}$), saturated charged lipid, dipalmitoylphosphatidylglycerol (DPPG$^{\scriptsize{(-)}}$), and cholesterol. In binary mixtures of saturated and unsaturated charged lipids, the combination of the charged head with the saturation of hydrocarbon tail is a dominant factor for the stability of membrane phase separation. DPPG$^{\scriptsize{(-)}}$ enhances phase separation, while DOPG$^{\scriptsize{(-)}}$ suppresses it. Furthermore, the addition of DPPG$^{\scriptsize{(-)}}$ to a binary mixture of DPPC/cholesterol induces phase separation between DPPG$^{\scriptsize{(-)}}$-rich and cholesterol-rich phases. This indicates that cholesterol localization depends strongly on the electric charge on the hydrophilic head group rather than on the ordering of the hydrocarbon tails. Finally, when DPPG$^{\scriptsize{(-)}}$ was added to a neutral ternary system of DOPC/DPPC/Cholesterol (a conventional model of membrane rafts), a three-phase coexistence was produced. We conclude by discussing some qualitative features of the phase behaviour in charged membranes using a free energy approach.

cond-mat.soft↗