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Microsecond Molecular Dynamics Simulations of Lipid Mixing

[Image: see text] Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-lo...

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Autores principales: Hong, Chunkit, Tieleman, D. Peter, Wang, Yi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2014
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196744/
https://www.ncbi.nlm.nih.gov/pubmed/25237736
http://dx.doi.org/10.1021/la502363b
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author Hong, Chunkit
Tieleman, D. Peter
Wang, Yi
author_facet Hong, Chunkit
Tieleman, D. Peter
Wang, Yi
author_sort Hong, Chunkit
collection PubMed
description [Image: see text] Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na(+) ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes.
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spelling pubmed-41967442015-09-19 Microsecond Molecular Dynamics Simulations of Lipid Mixing Hong, Chunkit Tieleman, D. Peter Wang, Yi Langmuir [Image: see text] Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na(+) ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes. American Chemical Society 2014-09-19 2014-10-14 /pmc/articles/PMC4196744/ /pubmed/25237736 http://dx.doi.org/10.1021/la502363b Text en Copyright © 2014 American Chemical Society Terms of Use (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html)
spellingShingle Hong, Chunkit
Tieleman, D. Peter
Wang, Yi
Microsecond Molecular Dynamics Simulations of Lipid Mixing
title Microsecond Molecular Dynamics Simulations of Lipid Mixing
title_full Microsecond Molecular Dynamics Simulations of Lipid Mixing
title_fullStr Microsecond Molecular Dynamics Simulations of Lipid Mixing
title_full_unstemmed Microsecond Molecular Dynamics Simulations of Lipid Mixing
title_short Microsecond Molecular Dynamics Simulations of Lipid Mixing
title_sort microsecond molecular dynamics simulations of lipid mixing
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196744/
https://www.ncbi.nlm.nih.gov/pubmed/25237736
http://dx.doi.org/10.1021/la502363b
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