Simulation of polyethylene glycol and calcium-mediated membrane fusion

Journal of Chemical Physics

Volumn 140, Issue 12, 2014, Pages

  Pannuzzo, Martina ^a   De Jong, Djurre H ^a   Raudino, Antonio ^b   Marrink, Siewert J ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF CATANIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CELL MEMBRANES; MOLECULAR DYNAMICS; POLYETHYLENE GLYCOLS; POSITIVE IONS;

ADHESION REGION; COARSE-GRAINED MOLECULAR DYNAMICS SIMULATIONS; DIVALENT CATION; NEGATIVELY CHARGED; NUCLEATION SITES; POLYETHYLENE GLYCOL (PEG); SYNERGISTIC EFFECT; THERMALLY DRIVEN;

CALCIUM;

CALCIUM; MACROGOL DERIVATIVE; WATER;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; LIPID BILAYER; MOLECULAR DYNAMICS;

CALCIUM; LIPID BILAYERS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; POLYETHYLENE GLYCOLS; WATER;

EID: 84897533441     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4869176     Document Type: Article

References (37)

1. W. Wickner and R. Schekman, Nat. Struct. Mol. Biol. 15, 658 (2008). 10.1038/nsmb.1451
2. S. Martens and H. T. McMahon, Nat. Rev. Mol. Cell. Biol. 9, 543 (2008). 10.1038/nrm2417
3. L. V. Chernomordik and M. M. Kozlov, Nat. Struct. Mol. Biol. 15, 675 (2008). 10.1038/nsmb.1455
4. J. C. Hay, EMBO Rep. 8, 236 (2007). 10.1038/sj.embor.7400921
5. P. K. Tarafdar, H. Chakraborty, S. M. Dennison, and B. R. Lentz, Biophys. J. 103, 1880 (2012). 10.1016/j.bpj.2012.09.030
6. A. Portis, C. Newton, W. Pangborn, and D. Papahadjopoulos, Biochemistry 18, 780 (1979). 10.1021/bi00572a007
7. B. R. Lentz, Eur. Biophys. J. 36, 315 (2007). 10.1007/s00249-006-0097-z
8. A. Raudino, M. Pannuzzo, and M. Karttunen, J. Chem. Phys. 136, 055101 (2012). 10.1063/1.3678836
9. W. Guo, P. J. Photos, and T. K. Vanderlick, Ind. Eng. Chem. Res. 45, 5512 (2006). 10.1021/ie0580755
10. A. J. Markvoort and S. J. Marrink, Curr. Top. Membr. 68, 259 (2011). 10.1016/B978-0-12-385891-7.00011-8
11. H. Ingolfsson, C. A. Lopez, J. J. Uusitalo, D. H. De Jong, S. Gopal, X. Periole, and S. J. Marrink, "The power of coarse-graining in biomolecular simulations," WIREs Comput. Mol. Sci. (published online). 10.1002/wcms.1169
12. S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, and A. H. De Vries, J. Phys. Chem. B. 111, 7812 (2007). 10.1021/jp071097f
13. H. Lee, A. H. de Vries, S. J. Marrink, and R. W. Pastor, J. Phys. Chem. B. 113, 13186 (2009). 10.1021/jp9058966
14. S. J. Marrink and D. P. Tieleman, Chem. Soc. Rev. 42, 6801 (2013). 10.1039/c3cs60093a
15. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 4, 435 (2008). 10.1021/ct700301q
16. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984). 10.1063/1.448118
17. G. Bussi, D. Donadio, and M. Parrinello, J. Chem. Phys. 126, 014101 (2007). 10.1063/1.2408420
18. M. Parrinello and J. Rahman, J. Appl. Phys. 52, 7182 (1981). 10.1063/1.328693
19. Y. Mao, Y. Du, X. Cang, J. Wang, Z. Chen, H. Yang, and H. Jiang, J. Phys. Chem. B. 117, 850 (2013). 10.1021/jp310163z
20. A. Martn-Molina, C. Rodrguez-Beas, and J. Faraudo, Biophys J. 102, 2095 (2012). 10.1016/j.bpj.2012.03.009
21. J. Schindler and H. G. Nothwang, Proteomics 6, 5409 (2006). 10.1002/pmic.200600243
22. A. Kukol, J. Chem. Theory Comput. 5, 615 (2009). 10.1021/ct8003468
23. A. Grafmüller, J. Shillcock, and R. Lipowsky, Phys. Rev. Lett. 98, 218101 (2007). 10.1103/PhysRevLett.98.218101
24. Z. K. Issa, C. W. Manke, B. P. Jena, and J. J. Potoff, J. Phys. Chem. B 114, 13249 (2010). 10.1021/jp105781z
25. A. Raudino and M. Pannuzzo, J. Chem. Phys. 132, 045103 (2010). 10.1063/1.3290823
26. A. Raudino, S. J. Marrink, and M. Pannuzzo, J. Chem. Phys. 138, 234901 (2013). 10.1063/1.4809993
27. S. W. Burgess, T. J. McIntosh, and B. R. Lentz, Biochemistry 31, 2653 (1992). 10.1021/bi00125a004
28. K. Arnold, O. Zschoering, D. Barthel, and W. Herold, Biochim. Biophys. Acta 1022, 303-310 (1990). 10.1016/0005-2736(90)90278-V
29. J. Y. Lehtonen and P. K. Kinnunen, Biophys. J. 68, 525-535 (1995). 10.1016/S0006-3495(95)80214-6
30. G. Moiset, A. D. Cirac, M. C. A. Stuart, S. J. Marrink, and D. Sengupta, PLoS One 8, e61541 (2013). 10.1371/journal.pone.0061541
31. K. Arnold, Handbook of Biological Physics, edited by R. Lipowsky and E. Sackmann (Elsevier, Amsterdam, 1995), pp. 903-957.
32. Y. G. Smirnova, S. J. Marrink, R. Lipowsky, and V. Knecht, J. Am. Chem. Soc. 132, 6710 (2010). 10.1021/ja910050x
33. D. Mirjanian, A. N. Dickey, J. H. Hoh, T. B. Woolf, and M. J. Stevens, J. Phys. Chem. B. 114, 11061 (2010). 10.1021/jp1055182
34. H. H. G. Tsai, W. F. Juang, C. M. Chang, T. Y. Hou, and J. B. Lee, Biochim. Biophys. Acta: Biomembranes 1828, 2729-2734 (2013). 10.1016/j.bbamem.2013.07.022
35. M. J. Hey, D. P. Jackson, and H. Yan, Polymer 46, 2567 (2005). 10.1016/j.polymer.2005.02.019
36. P. Thiyagarajan, D. J. Chaiko, and R. P. Hjelm, Macromolecules 28, 7730 (1995). 10.1021/ma00127a020
37. See supplementary material at http://dx.doi.org/10.1063/1.4869176 E-JCPSA6-140-052412 for the computational methods in detail and the reported results of performed control simulations.