Salt induced asymmetry in membrane simulations by partial restriction of ionic motion.
The specific ionic composition differs considerably at both sides of biological membranes and specific lipid/electrolyte interactions may be essential for their structure, stability and function. Hence, explicit consideration of the ionic asymmetry is important to achieve an accurate description of lipid bilayers. Molecular dynamics simulations have proven to be a reliable tool to study biomembranes at atomic detail. Nevertheless, the use of periodic boundary conditions allows ions to diffuse rapidly and reach both sides of the bilayer. Therefore, ad hoc simulation schemes have to be applied to take into account ionic asymmetry. In this work we present a simple implementation to overcome this problem. A more realistic description of the biomembranes can be achieved by partially restricting the ionic motion in the direction normal to the membrane within a region of the space near to only one of the leaflets. This creates two different situations: one leaflet is highly exposed to ions while the second one can be completely or partially depleted of them. Comparison between this new method and control simulations performed using a previously proposed approach consisting of a double-membrane setup yielded an excellent agreement with a speed-up of nearly 60%. The performance of the method with different ionic species is explored and remaining limitations are examined.
Herrera
Fernando E
FE
Institut Pasteur of Montevideo, Calle Mataojo 2020. CP 11400 Montevideo, Uruguay.
Pantano
Sergio
S
D002462:Cell Membrane / Q000737:chemistry* / Q000378:metabolism; D004058:Diffusion / Q000187:drug effects; D008055:Lipids / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D009068:Movement / Q000187:drug effects*; D012965:Sodium Chloride / Q000494:pharmacology*; D055672:Static Electricity; D014867:Water / Q000737:chemistry
D008055:Lipids; D014867:Water; D012965:Sodium Chloride