title: Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model.
abstract: 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.
authors.affiliation: Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland. Electronic address: alexander.sodt@nih.gov.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Sodt
authors.affiliation: Department of Chemistry, The University of Kansas, Lawrence, Kansas.
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Beaven
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
authors.forename: Olaf S
authors.initials: OS
authors.lastname: Andersen
authors.affiliation: Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania.
authors.forename: Wonpil
authors.initials: W
authors.lastname: Im
authors.affiliation: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
authors.forename: Richard W
authors.initials: RW
authors.lastname: Pastor
mesh_terms: D001696:Biomechanical Phenomena; D019245:Compressive Strength; D004058:Diffusion; D004548:Elasticity; D006096:Gramicidin / Q000737:chemistry* / Q000378:metabolism*; D057927:Hydrophobic and Hydrophilic Interactions; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D013816:Thermodynamics
chemical_list: D008051:Lipid Bilayers; D006096:Gramicidin