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]

Contents

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. [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), 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. [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 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 [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. [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

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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. hdl: 11370/6f357aca-0e36-4e9f-880c-62a50aff9ccd .
  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. hdl: 11370/5bdbbb23-2e1a-48a4-8c27-e1b8c28d74d6 . PMID   17569554.
  3. ↑ Souza, Paulo C. T.; Alessandri, Riccardo; Barnoud, Jonathan; Thallmair, Sebastian; et al. (29 March 2021). "Martini 3: a general purpose force field for coarse-grained molecular dynamics". Nature Methods. 18 (4): 382–388. doi:10.1038/s41592-021-01098-3. PMID   33782607. S2CID   232421378.
  4. ↑ Google Scholar, 14 October 2019, https://scholar.google.com/citations?hl=nl&user=UalQWxIAAAAJ
  5. ↑ 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.
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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.
  9. ↑ 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. CiteSeerX   10.1.1.456.7408 . doi:10.1021/ct700324x. PMID   26621095.
  10. ↑ 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. CiteSeerX   10.1.1.537.4531 . doi:10.1021/ct9002114. PMID   26616630.
  11. ↑ 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 . PMID   28195464.
  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. doi:10.1021/ct900313w. PMID   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. doi: 10.1021/acs.jctc.5b00286 . PMID   26574472.
  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. Bibcode:2017BpJ...113..246U. doi:10.1016/j.bpj.2017.05.043. PMC   5529176 . PMID   28633759.
  15. ↑ Monticelli, Luca (2012). "On atomistic and coarse-grained models for C60 fullerene". J. Chem. Theory Comput. 8 (4): 1370–1378. doi:10.1021/ct3000102. PMID   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. Royal Society of Chemistry. 22 (21): 7376–7386. doi: 10.1039/D0GC01823F .
  17. ↑ 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 . PMID   18543869.
  18. ↑ 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 (2): 698–708. Bibcode:2011SMat....7..698R. doi:10.1039/C0SM00481B.
  19. ↑ 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. PMC   5355903 . PMID   28209056.
  20. ↑ Martini website
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