title: Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions.
abstract: The periodic Saffman-Delbrück (PSD) model, an extension of the Saffman-Delbrück model developed to describe the effects of periodic boundary conditions on the diffusion constants of lipids and proteins obtained from simulation, is tested using the coarse-grained Martini and all-atom CHARMM36 (C36) force fields. Simulations of pure Martini dipalmitoylphosphatidylcholine (DPPC) bilayers and those with one embedded gramicidin A (gA) dimer or one gA monomer with sizes ranging from 512 to 2048 lipids support the PSD model. Underestimates of D∞(the value of the diffusion constant for an infinite system) from the 512-lipid system are 35% for DPPC, 45% for the gA monomer, and 70% for the gA dimer. Simulations of all-atom DPPC and dioleoylphosphatidylcholine (DOPC) bilayers yield diffusion constants not far from experiment. However, the PSD model predicts that diffusion constants at the sizes of the simulation should underestimate experiment by approximately a factor of 3 for DPPC and 2 for DOPC. This likely implies a deficiency in the C36 force field. A Bayesian method for extrapolating diffusion constants of lipids and proteins in membranes obtained from simulation to infinite system size is provided.
authors.affiliation: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Venable
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Helgi I
authors.initials: HI
authors.lastname: Ingólfsson
authors.affiliation: Department of Chemistry & Biochemistry and Department of Physics and Astronomy, Earlham College , Richmond, Indiana 47374, United States.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Lerner
authors.affiliation: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: B Scott
authors.initials: BS
authors.lastname: Perrin
authors.affiliation: Department of Physics, University of California , San Diego, California 92093, United States.
authors.forename: Brian A
authors.initials: BA
authors.lastname: Camley
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Siewert J
authors.initials: SJ
authors.lastname: Marrink
authors.affiliation: Department of Chemistry & Biochemistry and Department of Physics, University of California , Santa Barbara, California 93106, United States.
authors.forename: Frank L H
authors.initials: FLH
authors.lastname: Brown
authors.affiliation: Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Richard W
authors.identifier: 0000-0002-2454-5131
authors.initials: RW
authors.lastname: Pastor
mesh_terms: D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry*; D004058:Diffusion; D006096:Gramicidin / Q000737:chemistry*; D008051:Lipid Bilayers / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010316:Particle Size; D013499:Surface Properties
chemical_list: D008051:Lipid Bilayers; D006096:Gramicidin; D015060:1,2-Dipalmitoylphosphatidylcholine