MARTINI explained

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]

In 2021, a new version of the force field has been published, dubbed Martini 3.[3]

Overview

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. 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), S-size (small, 3:1 mapping) or T-size (tiny, 2:1 mapping). The S-particles are mainly used in ring structures whereas the T-particles are currently used in nucleic acids only. Bonded interactions (bonds, angles, dihedrals, and impropers) are derived from atomistic simulations of crystal structures.

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 1850 and 3400 times, respectively.[4] 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,[5] the simulations of the opening of mechanosensitive channels (MscL)[6] and the simulation of the domain partitioning of membrane peptides.[7]

Parameter sets

Lipids

The initial papers 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.[8]

Proteins

Compatible parameters for proteins were introduced by Monticelli et al..[9] 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,[10] 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 GōMartini approach introduced by Poma et al.[11] removes this limitation.

Carbohydrates

Compatible parameters were released in 2009.[12]

Nucleic acids

Compatible parameters were released for DNA in 2015[13] and RNA in 2017.[14]

Other

Parameters for different other molecules, including carbon nanoparticles,[15] ionic liquids,[16] and a number of polymers,[17] [18] [19] are available from the Martini website.[20]

See also

Notes and References

  1. Marrink. Siewert J.. de Vries. Alex H.. Mark. Alan E.. Coarse Grained Model for Semiquantitative Lipid Simulations. The Journal of Physical Chemistry B. 1 January 2004. 108. 2. 750–760. 10.1021/jp036508g. 11370/6f357aca-0e36-4e9f-880c-62a50aff9ccd. free.
  2. Marrink. Siewert J.. Risselada, H. Jelger . Yefimov, Serge . Tieleman, D. Peter . de Vries, Alex H. . The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. The Journal of Physical Chemistry B. 1 July 2007. 111. 27. 7812–7824. 10.1021/jp071097f. 17569554. 11370/5bdbbb23-2e1a-48a4-8c27-e1b8c28d74d6. free.
  3. Souza. Paulo C. T.. Alessandri, Riccardo . Barnoud, Jonathan . Thallmair, Sebastian . Faustino, Ignacio . 4 . Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature Methods. 29 March 2021. 18. 4. 382–388. 10.1038/s41592-021-01098-3. 33782607. 232421378.
  4. Google Scholar, 14 October 2019, https://scholar.google.com/citations?hl=nl&user=UalQWxIAAAAJ
  5. van den Bogaart. Geert. Membrane protein sequestering by ionic protein–lipid interactions. Nature. 24 November 2011. 7374. 552–555. 10.1038/nature10545. Meyenberg. Karsten. Risselada. H. Jelger. Amin. Hayder. Willig. Katrin I.. Hubrich. Barbara E.. Dier. Markus. Hell. Stefan W.. Grubmüller. Helmut. 479. 2011Natur.479..552V. Ulf. Reinhard . Diederichsen. Jahn. 22020284. 3409895.
  6. louhivuori. Martti. Release of content through mechano-sensitive gates in pressurized liposomes. Proc Natl Acad Sci USA. 16 November 2010. 107. 46. 19856–19860. 10.1073/pnas.1001316107. Risselada. H. J.. Van Der Giessen. E.. Marrink. S. J.. 2010PNAS..10719856L. 21041677. 2993341. free.
  7. Schäfer. Lars V.. Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes. Proc Natl Acad Sci USA. 25 January 2011. 108. 4. 1343–1348. 10.1073/pnas.1009362108. De Jong. D. H.. Holt. A.. Rzepiela. A. J.. De Vries. A. H.. Poolman. B.. Killian. J. A.. Marrink. S. J.. 2011PNAS..108.1343S. 21205902. 3029762. free.
  8. Risselada. H. J.. Marrink, S. J. . The molecular face of lipid rafts in model membranes. Proceedings of the National Academy of Sciences. 11 November 2008. 105. 45. 17367–17372. 10.1073/pnas.0807527105. 2008PNAS..10517367R. 18987307. 2579886. free.
  9. Monticelli. Luca. Kandasamy, Senthil K. . Periole, Xavier . Larson, Ronald G. . Tieleman, D. Peter . Marrink, Siewert-Jan . The MARTINI Coarse-Grained Force Field: Extension to Proteins. Journal of Chemical Theory and Computation. 1 May 2008. 4. 5. 819–834. 10.1021/ct700324x. 26621095. 10.1.1.456.7408.
  10. Periole. Xavier. Cavalli, Marco . Marrink, Siewert-Jan . Ceruso, Marco A. . Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. Journal of Chemical Theory and Computation. 8 September 2009. 5. 9. 2531–2543. 10.1021/ct9002114. 26616630. 10.1.1.537.4531.
  11. Poma. Adolfo. Cieplak, M. . Theodorakis, P. E.. 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. 24 Feb 2017. 13. 3. 1366–1374. 10.1021/acs.jctc.6b00986. 28195464. free.
  12. 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. . 5 . 12. 3195–3210 . 10.1021/ct900313w. 26602504 .
  13. 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 . 8. 3932–3945 . 10.1021/acs.jctc.5b00286. 26574472 . free .
  14. Uusitalo . Jaakko J. . Ingólfsson . Helgi I. . Marrink . Siewert J. . Faustino . Ignacio . 2017 . Martini Coarse-Grained Force Field: Extension to RNA . Biophys. J. . 113 . 2. 246–256 . 10.1016/j.bpj.2017.05.043. 28633759 . 5529176 . 2017BpJ...113..246U .
  15. Monticelli. Luca. On atomistic and coarse-grained models for C60 fullerene. J. Chem. Theory Comput.. 2012. 8. 4. 1370–1378. 10.1021/ct3000102. 26596752.
  16. Vazquez-Salazar. Luis Itza. Selle. Michele. de Vries. Alex H.. Marrink. Siewert J.. T. Souza. Paulo C.. 2020. Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction. Green Chemistry. 22. 21. 7376–7386. Royal Society of Chemistry. 10.1039/D0GC01823F. free.
  17. Lee. H.. Larson, R. G. . 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. 2008. 112. 26. 7778–7784. 10.1021/jp802606y. 18543869. 2504730.
  18. Rossi . Giulia . Monticelli . Luca . Puisto . Sakari R. . Vattulainen . Ilpo . Ala-Nissila . Tapio . Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case . Soft Matter . 2011 . 7. 2 . 698–708. 10.1039/C0SM00481B. 2011SMat....7..698R .
  19. Alessandri . Riccardo . Uusitalo . Jaakko J. . de Vries . Alex H. . Havenith . Remco W. A. . Marrink . Siewert J. . Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations . J. Am. Chem. Soc. . 2017 . 139. 10. 3697–3705 . 10.1021/jacs.6b11717. 28209056. 5355903.
  20. http://www.cgmartini.nl/ Martini website

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