Pore Formation Coupled to Ion Transport through Lipid Membranes as Induced by Transmembrane Ionic Charge Imbalance:  Atomistic Molecular Dynamics Study

Abstract

Formation of transient water pores in biological membranes lies at the heart of many important cellular processes, including fusion events, maintenance of osmotic balance, drug and antibody delivery into cells, and ion transport across the membrane. Ion transport, in particular, is of central interest since membranes strive to maintain a cationic electrochemical gradient used for ATP synthesis as well as a variety of activities, such as transport of nutrients and conveyance of electrical signals. While maintaining the electrochemical gradient is essential, ions yet leak through lipid membranes. The mechanisms of ion leakage are not well understood, however.In this Communication, we show that ion leakage can take place in protein-free membranes through transient water pores induced by a transmembrane ionic charge imbalance (see Figure 1). This mechanism can be expected in cells characterized by ionic concentration differences across the membrane. The view presented here further complements and lends support to previous studies 1-4 for pore formation induced by external fields.We have performed atomic-scale molecular dynamics (MD) simulations on dimyristoylphosphatidylcholine (DMPC) bilayers in the liquid crystalline phase (T ) 323 K) using a united-atom forcefield of Berger et al. 5 Recently, we have used that successfully in MD simulations for mixtures of charged lipids with DMPC. 6 For completeness, we have also conducted simulations at the physiological temperature (T ) 310 K). To implement a transmembrane ionic charge imbalance, we employed a double bilayer setup (i.e., two distinct bilayers in a simulation box). 7,8 All of the simulations were performed using the Gromacs suite. 9 For further simulation details, see Supporting Information (SI).The charge imbalance of six sodium ions per bilayer (i.e., the imbalance of 12 Na + ions in the whole double bilayer system), imposed at the two sides of a DMPC bilayer of 128 lipids, was found to induce, on average, a transmembrane voltage of ∼2.85 ( 0.49 V across the membrane (see Figure 2). This voltage corresponds to an electric field of ∼0.41 V/nm (averaged over the simulation box), which is close to values used in previous studies to induce pore formation by an external electric field. 1,2,4 The applied charge imbalance gives rise to a rapid formation of a water pore within ∼1 ns in one of the two bilayers, the other staying intact. The pore formation starts with the creation of a single water defect (a chain of water molecules) spanning the entire membrane in ∼0.5 ns (see Figure 1B), which then expands rapidly within the next 0.5 ns (see Figures 1C and 3 as well as SI). The latter stage involves considerable redistribution of lipid headgroups close to the defect, surrounding and stabilizing the pore 1,2,4 (see SI).Once a pore has been formed, we find transport of Na + ions through the pore along the Na + concentration gradient ( Figures 1D and 3). The permeation of Na + ions through the pore and the size of the pore are both controlled by the field: the higher t...

Ion Dynamics in Cationic Lipid Bilayer Systems in Saline Solutions

“…These asymmetries are, however, not long-lived or strong enough to cause pore formation, reported for asymmetric bilayer systems. 47 They should, however, be taken into account when evaluating if a system containg ions has reached its equilibrium, as well as when estimating the simulation times required to get meaningful averages from such systems.…”

“…[28][29][30][31][32][33][34][35][36][37][38][39][40][41] As for molecular-level computational studies, the increase in computing power in the past few years has made it possible to extend computer simulations beyond the relatively long relaxation times of tens to hundreds of nanoseconds required for equilibration of ions in lipid/water systems. Although most computational studies by far have focused on the effects of salt ions on zwitterionic (neutral) lipid bilayers, 33,[42][43][44][45][46][47][48][49][50][51][52][53] there is also an increasing number of studies on anionic [54][55][56][57][58][59] and cationic 60,61 lipid bilayers. Most simulations have addressed the effect of ions on the structural and electrostatic properties of lipid membranes.…”

“…Böckmann et al studied the effects of salt on lipid diffusion and estimated the typical times required for different ions to bind on a membrane. 33,44 As far as the dynamics of ions in lipid systems is concerned, to the best of our knowledge, the recent computational studies by Sachs et al, 45 Patra and Karttunen, 62 and Gurtovenko and Vattulainen 47,50 are the only ones. The number of experimental studies is also limited.…”

Molecular Mechanism for Lipid Flip-Flops

“…22,28 To model the transmembrane ionic charge imbalance explicitly, a double-bilayer setup (i.e., two lipid bilayers of 128 lipids each in a simulation box) was employed, 29,30 amounting to about 42 000 atoms in the system. The time step used in the integration of equations of motion was 2 fs.…”

Probing Lipid Bilayers under Ionic Imbalance

“…However, an electric-field-emulated TMP is different from an ionic-imbalance-generated TMP, and thus may lead to an erroneous prediction of membrane structure and electrostatics. A few studies that employed ionic imbalance to induce a TMP were carried out using atomistic MD simulations (31)(32)(33). However, these studies were limited by system size constraints and therefore the TMP could not be changed in a continuous fashion.…”