Systematic Implicit Solvent Coarse Graining of Dimyristoylphosphatidylcholine Lipids
2014 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 16, 1208-1218 p.Article in journal (Refereed) Published
We have used systematic structure-based coarse graining to derive effective site-site potentials for a 10-site coarse-grained dimyristoylphosphatidylcholine (DMPC) lipid model and investigated their state point dependence. The potentials provide for the coarse-grained model the same site-site radial distribution functions, bond and angle distributions as those computed in atomistic simulations carried out at four different lipid-water molar ratios. It was shown that there is a non-negligible dependence of the effective potentials on the concentration at which they were generated, which is also manifested in the properties of the lipid bilayers simulated using these potentials. Thus, effective potentials computed at low lipid concentration favor to more condensed and ordered structure of the bilayer with lower average area per lipid, while potentials obtained at higher lipid concentrations provide more fluid-like structure. The best agreement with the reference data and experiment was achieved using the set of potentials derived from atomistic simulations at 1:30 lipid:water molar ratio providing fully saturated hydration of DMPC lipids. Despite theoretical limitations of pairwise coarse-grained potentials expressed in their state point dependence, all the resulting potentials provide a stable bilayer structure with correct partitioning of different lipid groups across the bilayer as well as acceptable values of the average lipid area, compressibility and orientational ordering. In addition to bilayer simulations, the model has proven its robustness in modeling of self-aggregation of lipids from randomly dispersed solution to ordered bilayer structures, bicelles, and vesicles.
Place, publisher, year, edition, pages
2014. Vol. 35, no 16, 1208-1218 p.
bottom-up coarse graining, inverse Monte Carlo, lipid bilayers, dimyristoylphosphatidylcholine lipids, implicit solvent potentials
IdentifiersURN: urn:nbn:se:su:diva-104379DOI: 10.1002/jcc.23610ISI: 000335507300003OAI: oai:DiVA.org:su-104379DiVA: diva2:723606