Coarse-grained modeling

Coarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained (simplified) representation. Coarse-grained models are widely used for molecular modeling of biomolecules[1][2] at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins,[1][2] nucleic acids,[3][4] lipid membranes,[2][5] carbohydrates[6] or water.[7] In these models, molecules are represented by individual atoms and pseudo-atoms (that replace the group of atoms), or pseudo-atoms only. By decreasing the degrees of freedom much longer simulation times can be studied than using classical atomistic models. Coarse-grained models have found practical applications in: protein structure prediction, prediction of protein interactions and molecular dynamics simulations of protein folding.[1]

In 2013, the Nobel Prize in Chemistry has been awarded “for the development of multiscale models for complex chemical systems” to Michael Levitt, Ariel Warshel, and Martin Karplus. Their early works on coarse-grained protein modeling[8][9] have been recognized by the Nobel Prize Committee as an important step in studies of large macromolecular systems.[10] Coarse-grained models are presently often used as components of multiscale modeling protocols in combination with atomistic resolution models.[1] Atomistic resolution models alone are presently not efficient enough to handle large system sizes and simulation timescales.[1][2]

References

  1. 1 2 3 4 5 Kmiecik, Sebastian; Gront, Dominik; Kolinski, Michal; Wieteska, Lukasz; Dawid, Aleksandra Elzbieta; Kolinski, Andrzej (2016-06-22). "Coarse-Grained Protein Models and Their Applications". Chemical Reviews. doi:10.1021/acs.chemrev.6b00163. ISSN 0009-2665.
  2. 1 2 3 4 Ingólfsson, Helgi I.; Lopez, Cesar A.; Uusitalo, Jaakko J.; de Jong, Djurre H.; Gopal, Srinivasa M.; Periole, Xavier; Marrink, Siewert J. (2014-05-01). "The power of coarse graining in biomolecular simulations". Wiley Interdisciplinary Reviews: Computational Molecular Science. 4 (3): 225–248. doi:10.1002/wcms.1169. ISSN 1759-0884. PMC 4171755Freely accessible. PMID 25309628.
  3. ↑ Boniecki, Michal J.; Lach, Grzegorz; Dawson, Wayne K.; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M.; Bujnicki, Janusz M. (2016-04-20). "SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction". Nucleic Acids Research. 44 (7): e63–e63. doi:10.1093/nar/gkv1479. ISSN 0305-1048. PMC 4838351Freely accessible. PMID 26687716.
  4. ↑ Potoyan, Davit A.; Savelyev, Alexey; Papoian, Garegin A. (2013-01-01). "Recent successes in coarse-grained modeling of DNA". Wiley Interdisciplinary Reviews: Computational Molecular Science. 3 (1): 69–83. doi:10.1002/wcms.1114. ISSN 1759-0884.
  5. ↑ Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H.; Elsener, Andreas; Marrink, Siewert J.; van Gunsteren, Wilfred F. (2007-02-19). "Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models". ChemPhysChem. 8 (3): 452–461. doi:10.1002/cphc.200600658. ISSN 1439-7641.
  6. ↑ López, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Hünenberger, Philippe H.; Marrink, Siewert J. (2009-12-08). "Martini Coarse-Grained Force Field: Extension to Carbohydrates". Journal of Chemical Theory and Computation. 5 (12): 3195–3210. doi:10.1021/ct900313w. ISSN 1549-9618.
  7. ↑ Hadley, Kevin R.; McCabe, Clare (2012-07-01). "Coarse-grained molecular models of water: a review". Molecular Simulation. 38 (8-9): 671–681. doi:10.1080/08927022.2012.671942. ISSN 0892-7022. PMC 3420348Freely accessible. PMID 22904601.
  8. ↑ Levitt, Michael; Warshel, Arieh (1975-02-27). "Computer simulation of protein folding". Nature. 253 (5494): 694–698. doi:10.1038/253694a0.
  9. ↑ Warshel, A.; Levitt, M. (1976-05-15). "Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme". Journal of Molecular Biology. 103 (2): 227–249. doi:10.1016/0022-2836(76)90311-9. ISSN 0022-2836. PMID 985660.
  10. ↑ Levitt, Michael (2014-09-15). "Birth and Future of Multiscale Modeling for Macromolecular Systems (Nobel Lecture)". Angewandte Chemie International Edition. 53 (38): 10006–10018. doi:10.1002/anie.201403691. ISSN 1521-3773.
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