Molecular dynamics simulation of cation–phospholipid clustering in phospholipid bilayers: Possible role in stalk formation during membrane fusion

Abstract

In this study, we performed all-atom long-timescale molecular dynamics simulations of phospholipid bilayers incorporating three different proportions of negatively charged lipids in the presence of K(+), Mg(2+), and Ca(2+) ions to systemically determine how membrane properties are affected by cations and lipid compositions. Our simulations revealed that the binding affinity of Ca(2+) ions with lipids is significantly stronger than that of K(+) and Mg(2+) ions, regardless of the composition of the lipid bilayer. The binding of Ca(2+) ions to the lipids resulted in bilayers having smaller lateral areas, greater thicknesses, greater order, and slower rotation of their lipid head groups, relative to those of corresponding K(+)- and Mg(2+)-containing systems. The Ca(2+) ions bind preferentially to the phosphate groups of the lipids. The complexes formed between the cations and the lipids further assembled to form various multiple-cation-centered clusters in the presence of anionic lipids and at higher ionic strength-most notably for Ca(2+). The formation of cation-lipid complexes and clusters dehydrated and neutralized the anionic lipids, creating a more-hydrophobic environment suitable for membrane aggregation. We propose that the formation of Ca(2+)-phospholipid clusters across apposed lipid bilayers can work as a "cation glue" to adhere apposed membranes together, providing an adequate configuration for stalk formation during membrane fusion.

The complex nature of calcium cation interactions with phospholipid bilayers

“…Under equilibrium conditions, there was 1 calcium ion adsorbed per 2 lipids in POPC/POPS and 1 ion per 3 lipids in the POPC bilayer. This is within the range of 1–4 lipids per cation as reported in earlier MD studies18263349, and 1–2 lipids per cation resulting from NMR measurements50. Cation exchange between membrane and water observed under these conditions demonstrates system equilibration.…”

“…This resulted in effectively 0 mM calcium concentration in the bulk solution, with no subsequent calcium ion desorption during 200 ns. Note that the same issue occurred in previous MD studies18263133. Here, to maintain a finite calcium concentration in the water phase, the nominal CaCl 2 concentration was raised stepwise to 400, 600 and 700 mM.…”

“…It was suggested that calcium can also bind to the carbonyl oxygen2533, which is in line with the binding of Na + and K + to PC and PC/PS carbonyls34. Regarding the local consequences of calcium binding, simulations indicate that Ca 2+ is able to cluster phospholipid molecules via ion-bridges182632.…”

“…Many studies demonstrated that calcium binds primarily to phosphate groups of all phospholipids, independent of their charge28, even in pure PC membranes172930. Molecular dynamics simulations have provided more details and generally confirmed binding to phosphate groups in PC and several anionic lipids, including PS18263132, but concurrent binding to the carboxyl group of PS has also been reported1831. It was suggested that calcium can also bind to the carbonyl oxygen2533, which is in line with the binding of Na + and K + to PC and PC/PS carbonyls34.…”

“…It is generally accepted that the presence of Ca 2+ rigidifies and orders lipid bilayers131516171819. Conformational changes of the lipid headgroup region2021, ordering of acyl chains202122, and lipid dehydration1723242526 were reported.…”