Paper Citing NAMD - Abstract
Park, Soohyung; Beayen, Andrew H.; Klauda, Jeffery B.; Im, Wonpil
How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets?
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3466-3477, JUL 2015
Difficulties in estimating the correct number of lipids in each leaflet of complex bilayer membrane simulation systems make it inevitable to introduce a mismatch in lipid packing (i.e., area per lipid) and thus alter the lateral pressure of each leaflet. To investigate potential impacts of such mismatch on simulation results, we performed molecular dynamics simulations of saturated and mono-unsaturated lipid bilayers with and without gramicidin A or WALP23 at various mismatches by adjusting the number of lipids in the lower leaflet from no mismatch to a 25% reduction compared to that in the upper leaflet. All simulations were stable under the constant pressure barostat, but the mismatch induces asymmetric lipid packing between the leaflets, so that the upper leaflet becomes more ordered, and the lower leaflet becomes less ordered. The mismatch impacts on various bilayer properties are mild up to 5-10% mismatch, and bilayers with fully saturated chains appear to be more prone to these impacts than those with unsaturated tails. The nonvanishing leaflet surface tensions and the free energy derivatives with respect to the bilayer curvature indicate that the bilayer would be energetically unstable in the presence of mismatch. We propose a quantitative criterion for allowable mismatch based on the energetics derived from a continuum elastic model, which grows as a square root of the number of the lipids in the system. On the basis of this criterion, we infer that the area per lipid mismatch up to 5% would be tolerable in various membrane simulations of reasonable all-atom system sizes (40-160 lipids per leaflet).
