To change conformation, a protein must deform the surrounding bilayer. In this work, a three-dimensional continuum elastic model for gramicidin A in a lipid bilayer is shown to describe the sensitivity to thickness, curvature stress, and the mechanical properties of the lipid bilayer. A method is demonstrated to extract the gramicidin-lipid boundary condition from all-atom simulations that can be used in the three-dimensional continuum model. The boundary condition affects the deformation dramatically, potentially much more than typical variations in the material stiffness do as lipid composition is changed. Moreover, it directly controls the sensitivity to curvature stress. The curvature stress and hydrophobic surfaces of the all-atom and continuum models are found to be in excellent agreement. The continuum model is applied to estimate the enrichment of hydrophobically matched lipids near the channel in a mixture, and the results agree with single-channel experiments and extended molecular dynamics simulations from the companion article by Beaven et al. in this issue of Biophysical Journal.
Bibliographical noteFunding Information:
This work was supported in part by the intramural research program of the National Heart Lung Blood Institute (NHLBI) and the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the National Institutes of Health (NIH), the National Science Foundation (MCB-1157677 and MCB-1727508 to W.I.), and the extramural research program of the National Institutes of Health (GM021342 to O.S.A.).