Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers.
Free energy calculations are vital for our understanding of biological processes on an atomistic scale and can offer insight to various mechanisms. However, in some cases, degrees of freedom (DOFs) orthogonal to the reaction coordinate have high energy barriers and/or long equilibration times, which prohibit proper sampling. Here we identify these orthogonal DOFs when studying the transfer of a solute from water to a model membrane. Important DOFs are identified in bulk liquids of different dielectric nature with metadynamics simulations and are used as reaction coordinates for the translocation process, resulting in two- and three-dimensional space of reaction coordinates. The results are in good agreement with experiments and elucidate the pitfalls of using one-dimensional reaction coordinates. The calculations performed here offer the most detailed free energy landscape of solutes embedded in lipid bilayers to date and show that free energy calculations can be used to study complex membrane translocation phenomena.
Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden.
Joakim P M
JP
Jämbeck
Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden.
Alexander P
AP
Lyubartsev
enhanced sampling; lipid bilayers; metadynamics; molecular dynamics; potential of mean force; umbrella sampling