Paper Citing NAMD - Abstract
Yang, Jing; Calero, Carles; Bonomi, Massimiliano; Marti, Jordi
Specific Ion Binding at Phospholipid Membrane Surfaces
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4495-4499, SEP 2015
Metal cations are ubiquitous components in biological environments and play an important role in regulating cellular functions and membrane properties. By applying metadynamics simulations, we have performed systematic free energy calculations of Na+, K+, Ca+, and Mg2+ bound to phospholipid membrane surfaces for the first time. The free energy landscapes unveil specific binding behaviors of metal cations on phospholipid membranes. Na+ and K+ are more likely to stay in the aqueous solution and can bind easily to a few lipid oxygens by overcoming low free energy barriers. Ca2+ is most stable when it is bound to four lipid oxygens of the membrane rather than being hydrated in the aqueous solution. Mg2+ is tightly hydrated, and it shows hardly any loss of a hydration water or binding directly to the membrane. When bound to the membrane, the cations' most favorable total coordination numbers with water and lipid oxygens are the same as their corresponding hydration numbers in aqueous solution, indicating a competition between ion binding to water and lipids. The binding specificity of metal cations on membranes is highly correlated with the hydration free energy and the size of the hydration shell.
