Lipid Bilayers


Many properties of lipid membranes have been characterized over the past decades by all-atom models. Such properties include the area per lipid, order parameters, and density profiles for instance. Currently 100s of nanoseconds can be probed for membranes containing a few thousands of lipids.

However, for many membrane related processes more extensive sampling is required, either in the time domain or in terms of an increased system size to study collective events. In those cases the Martini model is a good alternative. Examples include the nucleation of gel domains in either pure [1] or mixed [2] lipid membranes (see figure), transition toward non-lamellar phases [3], partitioning of other compounds such as alcohols [9], voltage sensitive dyes [4], flip-flop of cholesterol [5,6] and tethered membranes [11,12].

greenpurple_slice_zoom

Furthermore the Martini model can be efficiently used for systematic studies in which a large number of simulations need to be performed. For instance, the membrane area and thickness as a function of location of double bonds [7], or the self-diffusion of transmembrane peptides as a function of peptide sequence [8] have been systematically explored with Martini. Another application of Martini is in the in-silico design of membranes with controlled properties using e.g. bolalipids [10].

  • [1] S.J. Marrink, J. Risselada, A.E. Mark. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chem. Phys. Lip., 135:223-244, 2005.
  • [2] R. Faller, S.J. Marrink. Simulation of domain formation in DLPC-DSPC mixed bilayers. Langmuir, 20:7686-7693, 2004.
  • [3] S.J. Marrink, A.E. Mark. Molecular view of hexagonal phase formation in phospholipid membranes. Biophys. J., 87:3894-3900, 2004.
  • [4] M.J. Hinner, S.J. Marrink, A.H. de Vries. Location, tilt, and binding: a molecular dynamics study of voltage sensitve dyes in biomembranes. J. Phys. Chem. B, 113:15807-15819, 2009.
  • [5] S.J. Marrink, A.H. de Vries, T.A. Harroun, J. Katsaras, S.R. Wassall. Cholesterol shows preference for the interior of polyunsaturated lipid membranes. JACS, 130:10-11, 2008.
  • [6] W.F.D. Bennett, J.L. MacCallum, M.J. Hinner, S.J. Marrink, D.P. Tieleman. A molecular view of cholesterol flip-flop and chemical potential in different membrane environments. JACS, 131:12714-12720, 2009.
  • [7] N. Kucerka, J. Gallova, D. Uhrikova, P. Balgavy, M. Bulacu, S.J. Marrink, J. Katsaras. Areas of monounsaturated diacylphosphatidylcholines. Biophys. J., 97:1926-1932, 2009.
  • [8] S. Ramadurai, A. Holt, L.V. Schäfer, V.V. Krasnikov, D.T.S. Rijkers, S.J. Marrink, J.A. Killian, B. Poolman. Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides. Biophys. J., 99:1447-1454, 2010.
  • [9] M. Klacsová,  M. Bulacu, N. Kučerka, D. Uhríková, J. Teixeirad, S.J. Marrink, P. Balgavý. The effect of aliphatic alcohols on fluid bilayers in unilamellar DOPC vesicles – a small-angle neutron scattering and molecular dynamics study. BBA Biomembr., 808:2136-2146, 2011. abstract
  • [10] M. Bulacu, X. Periole, S.J. Marrink. In-silico design of robust bolalipid membranes, Biomacromol., in press, 2011. DOI:10.1021/bm201454j. abstract
  • [11]  S. Wang, R.G. Larson. Coarse-grained molecular dynamics simulation of tethered lipid assemblies. Soft Matter, 2013, Advance Article. DOI: 10.1039/C2SM26850G
  • [12] C. Liu, R. Faller. Dynamical and Tensional Study of Tethered Bilayer Lipid Membranes in Coarse-Grained Molecular Simulations. Langmuir, Just Accepted Manuscript, 2012. DOI:10.1021/la303511p