Computer simulations of the diffusion of Na+ and Cl− ions across POPC lipid bilayer membranes

Salih, Rangeen; Matthai, Clarence Cherian

doi:10.1063/1.4977703

Cited by 8 publications

(6 citation statements)

References 32 publications

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“…While both methods can be applied to a simulation of only a single bilayer, the double bilayer system is easier to understand and is therefore presented first. Double bilayers have also been used to simulate ion gradients and pore formation. − …”

Section: Permeability From Membrane Simulations: Countingmentioning

confidence: 99%

“…Su et al simulated large vesicles with asymmetric salt concentration; the flux depended on the location of the salt (inside or outside of the vesicle), and the flux ratio varied significantly with salt concentration. Salih and Matthai used a double bilayer similar to that presented in section in their study of ion permeation and pore formation under electrochemical gradients.…”

Section: Recent Developmentsmentioning

confidence: 99%

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Molecular Dynamics Simulations of Membrane Permeability

2019

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This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of non-biological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Lastly, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.

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Section: Permeability From Membrane Simulations: Countingmentioning

confidence: 99%

Section: Recent Developmentsmentioning

confidence: 99%

Molecular Dynamics Simulations of Membrane Permeability

2019

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“…In addition, researchers have used double bilayer membrane systems to study ion gradients and pore formation. [29][30][31] For simulations with only a single water compartment, permeability can instead be calculated by counting crossings in both directions using the TB counting method for related permeation events. These types of approaches have been used in various studies of water, O 2 , and CO 2 permeation through membranes and channel proteins.…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers

Ghorbani

Wang

Krämer

et al. 2020

The Journal of Chemical Physics

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Permeation of small molecules through membranes is a fundamental biological process, and molecular dynamics simulations have proven to be a promising tool for studying the permeability of membranes by providing a precise characterization of the free energy and diffusivity. In this study, permeation of ethanol through three different membranes of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), POphosphatidylethanolamine (POPE), and PO-phosphatidylcholine (POPC) is studied. Permeabilities are calculated and compared with two different approaches based on Fick's first law and the inhomogeneous solubility-diffusion model. Microsecond simulation of double bilayers of these membranes provided a direct measurement of permeability by a flux-based counting method. These simulations show that a membrane of POPC has the highest permeability, followed by POPE and POPS. Due to the membrane-modulating properties of ethanol, the permeability increases as functions of concentration and saturation of the inner leaflet in a double bilayer setting, as opposed to the customary definition as a proportionality constant. This concentration dependence is confirmed by single bilayer simulations at different ethanol concentrations ranging from 1% to 18%, where permeability estimates are available from transition-based counting and the inhomogeneous solubilitydiffusion model. We show that the free energy and diffusion profiles for ethanol lack accuracy at higher permeant concentrations due to non-Markovian kinetics caused by collective behavior. In contrast, the counting method provides unbiased estimates. Finally, the permeabilities obtained from single bilayer simulations are combined to represent natural gradients felt by a cellular membrane, which accurately models the non-equilibrium effects on ethanol permeability from single bilayer simulations in equilibrium.

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“…That the CNT was stable in the membrane for the remainder of the simulation points to the stability of the system and suggests that such a system could be used for drug delivery as suggested by other researchers. It is also of interest to see what happens to the the thickness of the lipid bilayer as this provides a test of the robustness of the lipid bilayer [9] . Because the temperature of the simulation was set to be 300 K, any increase in energy resulting from the initial placement of the CNT could lead to a local melting of bilayer and could be manifest in the thickness measurement.…”

Section: Structure Of the Cnt In The Popc Bilayermentioning

confidence: 99%

Coarse Grained Molecular Dynamic Simulations of the interaction a Carbon Nanotube with a Bilayer Membrane

Salih

Matthai

2017

MRS Advances

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In coarse grained molecular dynamics (CGMD) simulations, small groups of atoms are treated as single particles (beads) and the forces between these particles are derived from the interatomic forces. The effect of this is to severely reduce the number of particles in a simulation, thereby allowing for the consideration of a larger number of atoms. It has also proven to be a valuable tool in probing time and length scales of systems beyond that used in all-atom molecular dynamics (AAMD) simulations. The down side of this is that the inter-particle interactions are less accurate. However, if these coarse grained particles are chosen carefully, such simulations can provide much useful information. There are different levels of how the coarse grains are constructed. For example, CG systems have been developed using tens or hundreds of atoms per CG bead in some studies of amino acids in biological science. By contrast, for other systems, a single CG bead is used to replace just two or three atoms.In this paper, the interaction of a carbon nanotube (CNT) with a lipid bilayer membrane is studied using both coarse grained and atomistic MD in an effort to understand the usefulness of the CGMD method for such simulations. Our preliminary studies of the interaction of a CNT with a lipid bilayer points indicates that such nano-tubes inserted into a membrane could be stable. This means that it could be used as an agent in the delivery of drugs. It would be good if these simulations could be repeated using AAMD simulations to confirm the validity of these results.

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Computer simulations of the diffusion of Na+ and Cl− ions across POPC lipid bilayer membranes

Cited by 8 publications

References 32 publications

Molecular Dynamics Simulations of Membrane Permeability

Molecular Dynamics Simulations of Membrane Permeability

Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers

Coarse Grained Molecular Dynamic Simulations of the interaction a Carbon Nanotube with a Bilayer Membrane

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