database; force fields; lipid; model membrane; molecular dynamics
Abstract :
[en] Cellular membranes are composed of a wide diversity of lipid species in varying proportions and these compositions are representative of the organism, cellular type and organelle to which they belong. Because models of these molecular systems simulated by MD steadily gain in size and complexity, they are increasingly representative of specific compositions and behaviors of biological membranes. Due to the number of lipid species involved, of force fields and topologies and because of the complexity of membrane objects that have been simulated, LIMONADA has been developed as an open database allowing to handle the various aspects of lipid membrane simulation. LIMONADA presents published membrane patches with their simulation files and the cellular membrane it models. Their compositions are then detailed based on the lipid identification from LIPID MAPS database plus the lipid topologies and the force field used. LIMONADA is freely accessible on the web at https://limonada.univ-reims.fr/.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Crowet, Jean-Marc
Buchoux, Sébastien
Belloy, Nicolas
Sarazin, Catherine
Lins, Laurence ; Université de Liège - ULiège > Département GxABT > Chimie des agro-biosystèmes
Dauchez, Manuel
Language :
English
Title :
LIMONADA: A database dedicated to the simulation of biological membranes.
Publication date :
2021
Journal title :
Journal of Computational Chemistry
ISSN :
0192-8651
eISSN :
1096-987X
Publisher :
John Wiley & Sons, Hoboken, United States - New Jersey
K. Jacobson, O. G. Mouritsen, R. G. W. Anderson, Nat. Cell Biol. 2007, 9, 7.
G. van Meer, D. R. Voelker, G. W. Feigenson, Nat. Rev. Mol. Cell Biol. 2008, 9, 112.
T. Kobayashi, A. K. Menon, Curr. Biol. 2018, 28, R386.
H. I. Ingólfsson, T. S. Carpenter, H. Bhatia, P.-T. Bremer, S. J. Marrink, F. C. Lightstone, Biophys. J. 2017, 113, 2271.
J.-L. Cacas, C. Buré, K. Grosjean, P. Gerbeau-Pissot, J. Lherminier, Y. Rombouts, E. Maes, C. Bossard, J. Gronnier, F. Furt, L. Fouillen, V. Germain, E. Bayer, S. Cluzet, F. Robert, J.-M. Schmitter, M. Deleu, L. Lins, F. Simon-Plas, S. Mongrand, Plant Physiol. 2016, 170, 367.
A. Y. Andreyev, E. Fahy, Z. Guan, S. Kelly, X. Li, J. G. McDonald, S. Milne, D. Myers, H. Park, A. Ryan, B. M. Thompson, E. Wang, Y. Zhao, H. A. Brown, A. H. Merrill, C. R. H. Raetz, D. W. Russell, S. Subramaniam, E. A. Dennis, J. Lipid Res. 2010, 51, 2785.
J. L. Sampaio, M. J. Gerl, C. Klose, C. S. Ejsing, H. Beug, K. Simons, A. Shevchenko, Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 1903.
C. S. Ejsing, J. L. Sampaio, V. Surendranath, E. Duchoslav, K. Ekroos, R. W. Klemm, K. Simons, A. Shevchenko, Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 2136.
T. Harayama, H. Riezman, Nat. Rev. Mol. Cell Biol. 2018, 19, 281.
A. D. Dupuy, D. M. Engelman, Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 2848.
A. L. Duncan, T. Reddy, H. Koldsø, J. Hélie, P. W. Fowler, M. Chavent, M. S. P. Sansom, Sci. Rep. 2017, 7, 16647.
T. Ryan, J. Myers, D. Holowka, B. Baird, W. Webb, Science 1988, 239, 61.
M. Javanainen, H. Hammaren, L. Monticelli, J.-H. Jeon, M. S. Miettinen, H. Martinez-Seara, R. Metzler, I. Vattulainen, Faraday Discuss. 2013, 161, 397.
R. Friedman, S. Khalid, C. Aponte-Santamaría, E. Arutyunova, M. Becker, K. J. Boyd, M. Christensen, J. T. S. Coimbra, S. Concilio, C. Daday, F. J. van Eerden, P. A. Fernandes, F. Gräter, D. Hakobyan, A. Heuer, K. Karathanou, F. Keller, M. J. Lemieux, S. J. Marrink, E. R. May, A. Mazumdar, R. Naftalin, M. Pickholz, S. Piotto, P. Pohl, P. Quinn, M. J. Ramos, B. Schiøtt, D. Sengupta, L. Sessa, S. Vanni, T. Zeppelin, V. Zoni, A.-N. Bondar, C. Domene, J. Membr. Biol. 2018, 251, 609.
S. J. Marrink, V. Corradi, P. C. T. Souza, H. I. Ingólfsson, D. P. Tieleman, M. S. P. Sansom, Chem. Rev. 2019, 119, 6184.
F. J. van Eerden, D. H. de Jong, A. H. de Vries, T. A. Wassenaar, S. J. Marrink, Biochim. Biophys. Acta, Biomembr. 2015, 1848, 1319.
N. Flinner, E. Schleiff, PLoS One 2015, 10, e0133999.
H. Koldsø, D. Shorthouse, J. Hélie, M. S. P. Sansom, PLoS Comput. Biol. 2014, 10, e1003911.
J. B. Klauda, J. Chem. Phys. 2018, 149, 220901.
H. I. Ingólfsson, M. N. Melo, F. J. van Eerden, C. Arnarez, C. A. Lopez, T. A. Wassenaar, X. Periole, A. H. de Vries, D. P. Tieleman, S. J. Marrink, J. Am. Chem. Soc. 2014, 136, 14554.
A. Singharoy, C. Maffeo, K. H. Delgado-Magnero, D. J. K. Swainsbury, M. Sener, U. Kleinekathöfer, J. W. Vant, J. Nguyen, A. Hitchcock, B. Isralewitz, I. Teo, D. E. Chandler, J. E. Stone, J. C. Phillips, T. V. Pogorelov, M. I. Mallus, C. Chipot, Z. Luthey-Schulten, D. P. Tieleman, C. N. Hunter, E. Tajkhorshid, A. Aksimentiev, K. Schulten, Cell 2019, 179, 1098.
A. N. Leonard, E. Wang, V. Monje-Galvan, J. B. Klauda, Chem. Rev. 2019, 119, 6227.
J. B. Klauda, R. M. Venable, J. A. Freites, J. W. O'Connor, D. J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A. D. MacKerell, R. W. Pastor, J. Phys. Chem. B 2010, 114, 7830.
S. J. Marrink, A. H. de Vries, A. E. Mark, J. Phys. Chem. B 2004, 108, 750.
C. Oostenbrink, A. Villa, A. E. Mark, W. F. van Gunsteren, J. Comput. Chem. 2004, 25, 1656.
J. Domański, P. J. Stansfeld, M. S. P. Sansom, O. Beckstein, J. Membr. Biol. 2010, 236, 255.
L. Li, J. Han, Z. Wang, J. Liu, J. Wei, S. Xiong, Z. Zhao, Int. J. Mol. Sci. 2014, 15, 10492.
E. Fahy, S. Subramaniam, R. C. Murphy, M. Nishijima, C. R. H. Raetz, T. Shimizu, F. Spener, G. van Meer, M. J. O. Wakelam, E. A. Dennis, J. Lipid Res. 2009, 50 Suppl, S9.
L. Aimo, R. Liechti, N. Hyka-Nouspikel, A. Niknejad, A. Gleizes, L. Götz, D. Kuznetsov, F. P. A. David, F. G. van der Goot, H. Riezman, L. Bougueleret, I. Xenarios, A. Bridge, Bioinformatics 2015, 31, 2860.
K. Watanabe, E. Yasugi, M. Oshima, Trends Glycosci. Glycotechnol. 2000, 12, 175.
M. R. Molenaar, A. Jeucken, T. A. Wassenaar, C. H. A. van de Lest, J. F. Brouwers, J. B. Helms, Gigascience 2019, 8, giz061. https://doi.org/10.1093/gigascience/giz061.
N. M. O'Boyle, M. Banck, C. A. James, C. Morley, T. Vandermeersch, G. R. Hutchison, Aust. J. Chem. 2011, 3, 33.
A. S. Rose, P. W. Hildebrand, Nucleic Acids Res. 2015, 43, W576.
A. S. Rose, A. R. Bradley, Y. Valasatava, J. M. Duarte, A. Prlić, P. W. Rose, Bioinformatics 2018, 34, 3755.
S. Buchoux, Bioinformatics 2017, 33, 133.
O. H. S. Ollila, G. Pabst, Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2512.
F. Furt, F. Simon-Plas, S. Mongrand, in The Plant Plasma Membrane, Vol. 19 (Eds: A. Murphy, B. Schulz, W. Peer), Springer, Berlin, Heidelberg 2011, p. 3.
