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MARTINI

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Martini is a coarse-grained (CG) force field developed by Marrink and coworkers at the University of Groningen, initially developed in 2004 for molecular dynamics simulation of lipids,[1] later (2007) extended to various other molecules. The force field applies a mapping of four heavy atoms to one CG interaction site and is parametrized with the aim of reproducing thermodynamic properties.[2]

Philosophy

For the Martini force field 4 bead categories have been defined: Q (charged), P (polar), N (nonpolar), and C (apolar). These bead types are in turn split in 4 or 5 different levels, giving a total of 20 beadtypes.[2] For the interactions between the beads, 10 different interaction levels are defined (O-IX). The beads can be used at normal size (4:1 mapping) or S-size (small, 3:1 mapping). The latter is mainly used in ring structures. Bonded interactions (bonds, angles, dihedrals, and impropers) are derived from atomistic simulations of crystal structures.[2]

Use

The Martini force field has become one of the most used coarse grained force fields in the field of molecular dynamics simulations for biomolecules. The original 2004 and 2007 papers have been cited 654 and 608 times, respectively.[3] The force field has been implemented in three major simulation codes: GROningen MAchine for Chemical Simulations (GROMACS), GROningen MOlecular Simulation (GROMOS), and Nanoscale Molecular Dynamics (NAMD). Notable successes are simulations of the clustering behavior of syntaxin-1A,[4] the simulations of the opening of mechanosensitive channels (MscL)[5] and the simulation of the domain partitioning of membrane peptides.[6]

Parameter sets

Lipids

The initial papers[1][2] contained parameters for water, simple alkanes, organic solvents, surfactants, a wide range of lipids and cholesterol. They semiquantitatively reproduce the phase behavior of bilayers with other bilayer properties, and more complex bilayer behavior.[7]

Proteins

Compatible parameters for proteins were introduced by Monticelli et al..[8] Secondary structure elements, like alpha helixes and beta sheets (β-sheets), are constrained. Martini proteins are often simulated in combination with an elastic network, such as Elnedyn,[9] to maintain the overall structure.

Carbohydrates

Compatible parameters were released in 2009.[10]

Other

Parameters for different other molecules are available from the Martini website.[11]

See also

References

  1. ^ a b Marrink, Siewert J.; de Vries, Alex H.; Mark, Alan E. (1 January 2004). "Coarse Grained Model for Semiquantitative Lipid Simulations". The Journal of Physical Chemistry B. 108 (2): 750–760. doi:10.1021/jp036508g.
  2. ^ a b c d Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge; Tieleman, D. Peter; de Vries, Alex H. (1 July 2007). "The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations". The Journal of Physical Chemistry B. 111 (27): 7812–7824. doi:10.1021/jp071097f. PMID 17569554.
  3. ^ Google Scholar, 9 September 2012, scholar.google.com
  4. ^ van den Bogaart, Geert; Meyenberg, Karsten; Risselada, H. Jelger; Amin, Hayder; Willig, Katrin I.; Hubrich, Barbara E.; Dier, Markus; Hell, Stefan W.; Grubmüller, Helmut; Diederichsen, Ulf; Jahn, Reinhard (24 November 2011). "Membrane protein sequestering by ionic protein–lipid interactions". Nature. 479 (479): 552–555. Bibcode:2011Natur.479..552V. doi:10.1038/nature10545.
  5. ^ louhivuori, Martti; Risselada, H. J.; Van Der Giessen, E.; Marrink, S. J. (16 November 2010). "Release of content through mechano-sensitive gates in pressurized liposomes". Proc Natl Acad Sci USA. 107 (46): 19856–19860. Bibcode:2010PNAS..10719856L. doi:10.1073/pnas.1001316107.
  6. ^ Schäfer, Lars V.; De Jong, D. H.; Holt, A.; Rzepiela, A. J.; De Vries, A. H.; Poolman, B.; Killian, J. A.; Marrink, S. J. (25 January 2011). "Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes". Proc Natl Acad Sci USA. 108 (4): 1343–1348. Bibcode:2011PNAS..108.1343S. doi:10.1073/pnas.1009362108.
  7. ^ Risselada, H. J.; Marrink, S. J. (11 November 2008). "The molecular face of lipid rafts in model membranes". Proceedings of the National Academy of Sciences. 105 (45): 17367–17372. Bibcode:2008PNAS..10517367R. doi:10.1073/pnas.0807527105.
  8. ^ Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier; Larson, Ronald G.; Tieleman, D. Peter; Marrink, Siewert-Jan (1 May 2008). "The MARTINI Coarse-Grained Force Field: Extension to Proteins". Journal of Chemical Theory and Computation. 4 (5): 819–834. doi:10.1021/ct700324x.
  9. ^ Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A. (8 September 2009). "Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition". Journal of Chemical Theory and Computation. 5 (9): 2531–2543. doi:10.1021/ct9002114.
  10. ^ Cesar A. López, Andrzej J. Rzepiela, Alex H. de Vries, Lubbert Dijkhuizen, Philippe H. Hünenberger and Siewert J. Marrink. (2009) "Martini Coarse-Grained Force Field: Extension to Carbohydrates" J. Chem. Theory Comput. 12 3195–3210
  11. ^ Martini website
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