MARTINI

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. However, the use of the elastic network restricts the use of the MARTINI force field for the study of large conformational changes (e.g. folding). The GoMARTINI approach introduced by Poma et al..[10] removes this limitation.

Carbohydrates

Compatible parameters were released in 2009.[11]

DNA

Compatible parameters were released in 2015.[12]

Other

Parameters for different other molecules, including a number of polymers[13][14][15], are available from the Martini website.[16]

See also

References

  1. 1 2 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. 1 2 3 4 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 (7374): 552–555. Bibcode:2011Natur.479..552V. doi:10.1038/nature10545. PMC 3409895. PMID 22020284.
  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. PMC 2993341. PMID 21041677.
  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. PMC 3029762. PMID 21205902.
  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. PMC 2579886. PMID 18987307.
  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. ↑ Poma, Adolfo; Cieplak, M.; Theodorakis, P. E. (24 Feb 2017). "Combining the MARTINI and structure-based coarse-grained approaches for the molecular dynamics studies of conformational transitions in proteins". Journal of Chemical Theory and Computation. 13 (3): 1366–1374. doi:10.1021/acs.jctc.6b00986.
  11. ↑ López, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Hünenberger, Philippe H.; Marrink, Siewert J. (2009). "Martini Coarse-Grained Force Field: Extension to Carbohydrates". J. Chem. Theory Comput. 12: 3195–3210. doi:10.1021/ct900313w.
  12. ↑ Uusitalo, Jaakko J.; Ingólfsson, Helgi I.; Akhshi, Parisa; Tieleman, D. Peter; Marrink, Siewert J. (2015). "Martini Coarse-Grained Force Field: Extension to DNA". J. Chem. Theory Comput. 11: 3932–3945. doi:10.1021/acs.jctc.5b00286.
  13. ↑ Lee, H.; Larson, R. G. (2008). "Coarse-Grained Molecular Dynamics Studies of the Concentration and Size Dependence of Fifth- and Seventh-Generation PAMAM Dendrimers on Pore Formation in DMPC Bilayer". The Journal of Physical Chemistry B. 112 (26): 7778–7784. doi:10.1021/jp802606y. PMC 2504730.
  14. ↑ Rossi, Giulia; Monticelli, Luca; Puisto, Sakari R.; Vattulainen, Ilpo; Ala-Nissila, Tapio (2011). "Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case". Soft Matter. 7: 698–708. Bibcode:2011SMat....7..698R. doi:10.1039/C0SM00481B.
  15. ↑ Alessandri, Riccardo; Uusitalo, Jaakko J.; de Vries, Alex H.; Havenith, Remco W. A.; Marrink, Siewert J. (2017). "Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations". J. Am. Chem. Soc. 139 (10): 3697–3705. doi:10.1021/jacs.6b11717.
  16. ↑ Martini website
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