Coarse-grained molecular dynamics study of membrane fusion: Curvature effects on free energy barriers along the stalk mechanism

Journal of Chemical Physics

Volumn 143, Issue 24, 2015, Pages

  Kawamoto, Shuhei ^a   Klein, Michael L ^b   Shinoda, Wataru ^a  

^a NAGOYA UNIVERSITY   (Japan)

^b Temple University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL MEMBRANES; CONFORMATIONS; CONTINUUM MECHANICS; ENERGY BARRIERS; LIPIDS; MOLECULAR DYNAMICS;

COARSE-GRAINED MOLECULAR DYNAMICS; CONFORMATIONAL CHANGE; CONTINUUM MODELING; DIFFERENT GEOMETRY; DIMYRISTOYLPHOSPHATIDYLCHOLINE; MEMBRANE CURVATURE; PHOSPHATIDYLETHANOLAMINE; POTENTIAL METHODS;

FREE ENERGY;

DIMYRISTOYLPHOSPHATIDYLCHOLINE; DIOLEOYL PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLETHANOLAMINE;

CHEMICAL PHENOMENA; CHEMISTRY; MOLECULAR DYNAMICS; THERMODYNAMICS;

DIMYRISTOYLPHOSPHATIDYLCHOLINE; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MOLECULAR DYNAMICS SIMULATION; PHOSPHATIDYLETHANOLAMINES; THERMODYNAMICS;

EID: 84944673903     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4933087     Document Type: Article

References (68)

1. S. W. Hui, T. P. Stewart, L. T. Boni, and P. L. Yeagle, Science 212, 921 (1981). 10.1126/science.7233185
2. H. Noguchi and T. Masako, J. Chem. Phys. 115, 9547 (2001). 10.1063/1.1414314
3. D. P. Siegel, Biophys. J. 65, 2124 (1993). 10.1016/S0006-3495(93)81256-6
4. P. M. Kasson and V. S. Pande, PLoS Comput. Biol. 3, e220 (2007). 10.1371/journal.pcbi.0030220
5. P. M. Kasson, N. W. Kelley, N. Singhal, M. Vrljic, A. T. Brunger, and V. S. Pande, Proc. Natl. Acad. Sci. U. S. A. 103, 11916 (2006). 10.1073/pnas.0601597103
6. L. Chernomordik, Chem. Phys. Lipids 81, 203 (1996). 10.1016/0009-3084(96)02583-2
7. L. V. Chernomordik, E. Leikina, V. Frolov, P. Bronk, and J. Zimmerberg, J. Cell Biol. 136, 81 (1997). 10.1083/jcb.136.1.81
8. L. V. Chernomordik and M. M. Kozlov, Annu. Rev. Biochem. 72, 175 (2003). 10.1146/annurev.biochem.72.121801.161504
9. M. E. Haque, T. J. McIntosh, and B. R. Lentz, Biochemistry 40, 4340 (2001). 10.1021/bi002030k
10. D. P. Siegel and R. M. Epand, Biophys. J. 73, 3089 (1997). 10.1016/S0006-3495(97)78336-X
11. Z. Khattari, S. Köhler, Y. Xu, S. Aeffner, and T. Salditt, Biochim. Biophys. Acta 1848, 41 (2015). 10.1016/j.bbamem.2014.08.010
12. S. Aeffner, T. Reusch, B. Weinhausen, and T. Salditt, Proc. Natl. Acad. Sci. U. S. A. 109, E1609 (2012). 10.1073/pnas.1119442109
13. D. P. Siegel, Biophys. J. 76, 291 (1999). 10.1016/S0006-3495(99)77197-3
14. Y. Kozlovsky, A. Efrat, D. P. Siegel, and M. M. Kozlov, Biophys. J. 87, 2508 (2004). 10.1529/biophysj.103.038075
15. D. P. Siegel, Biophys. J. 95, 5200 (2008). 10.1529/biophysj.108.140152
16. V. S. Malinin and B. R. Lentz, Biophys. J. 86, 2951 (2004). 10.1016/S0006-3495(04)74346-5
17. S. May, Biophys. J. 83, 2969 (2002). 10.1016/S0006-3495(02)75303-4
18. Y. Kozlovsky and M. M. Kozlov, Biophys. J. 82, 882 (2002). 10.1016/S0006-3495(02)75450-7
19. Y. Kozlovsky, L. V. Chernomordik, and M. M. Kozlov, Biophys. J. 83, 2634 (2002). 10.1016/S0006-3495(02)75274-0
20. A. Callan-Jones, B. Sorre, and P. Bassereau, Cold Spring Harbor Perspect. Biol. 3, 1 (2011). 10.1101/cshperspect.a004648
21. B. Sorre, A. Callan-Jones, J. B. Manneville, P. Nassoy, J. F. Joanny, J. Prost, B. Goud, and P. Bassereau, Proc. Natl. Acad. Sci. U. S. A. 106, 5622 (2009). 10.1073/pnas.0811243106
22. R. Aurélien, C. Damien, N. Pierre, P. Jacques, B. Patricia, and G. Bruno, EMBO J. 24, 1537 (2005). 10.1038/sj.emboj.7600631
23. I. R. Cooke and M. Deserno, Biophys. J. 91, 487 (2006). 10.1529/biophysj.105.078683
24. H. J. Risselada, S. J. Marrink, and M. Müller, Phys. Rev. Lett. 106, 148102 (2011). 10.1103/PhysRevLett.106.148102
25. W. Shinoda and M. L. Klein, Pure Appl. Chem. 86, 215 (2014). 10.1515/pac-2014-5023
26. S. L. Leikin, M. M. Kozlov, L. V. Chernomordik, V. S. Markin, and Y. A. Chizmadzhev, J. Theor. Biol. 129, 411 (1987). 10.1016/S0022-5193(87)80021-8
27. M. M. Kozlov and L. V. Chernomordik, Biophys. J. 75, 1384 (1998). 10.1016/S0006-3495(98)74056-1
28. A. Efrat, L. V. Chernomordik, and M. M. Kozlov, Biophys. J. 92, L61 (2007). 10.1529/biophysj.106.103341
29. P. I. Kuzmin, J. Zimmerberg, Y. A. Chizmadzhev, and F. S. Cohen, Proc. Natl. Acad. Sci. U. S. A. 98, 7235 (2001). 10.1073/pnas.121191898
30. K. Katsov, M. Müller, and M. Schick, Biophys. J. 87, 3277 (2004). 10.1529/biophysj.103.038943
31. K. Katsov, M. Müller, and M. Schick, Biophys. J. 90, 915 (2006). 10.1529/biophysj.105.071092
32. J. Y. Lee and M. Schick, Biophys. J. 92, 3938 (2007). 10.1529/biophysj.106.097063
33. M. Müller, Y. G. Smirnova, G. Marelli, M. Fuhrmans, and A.-C. Shi, Phys. Rev. Lett. 108, 228103 (2012). 10.1103/PhysRevLett.108.228103
34. A. Grafmüller, J. Shillcock, and R. Lipowsky, Biophys. J. 96, 2658 (2009). 10.1016/j.bpj.2008.11.073
35. M. Fuhrmans, G. Marelli, Y. G. Smirnova, and M. Müller, Chem. Phys. Lipids 185, 109 (2015). 10.1016/j.chemphyslip.2014.07.010
36. H. J. Risselada, C. Kutzner, and H. Grubmüller, ChemBioChem 12, 1049 (2011). 10.1002/cbic.201100020
37. H. J. Risselada, G. Marelli, M. Fuhrmans, Y. G. Smirnova, H. Grubmüller, S. J. Marrink, and M. Müller, PLoS One 7, 38302 (2012). 10.1371/journal.pone.0038302
38. J. Yoo and Q. Cui, Biophys. J. 104, 128 (2013). 10.1016/j.bpj.2012.11.3813
39. M. Pannuzzo, D. H. De Jong, A. Raudino, and S. J. Marrink, J. Chem. Phys. 140, 124905 (2014). 10.1063/1.4869176
40. Y. Norizoe, K. C. Daoulas, and M. Müller, Faraday Discuss. 144, 369 (2010). 10.1039/B901657K
41. Y. G. Smirnova, S. J. Marrink, R. Lipowsky, and V. Knecht, J. Am. Chem. Soc. 132, 6710 (2010). 10.1021/ja910050x
42. H. J. Risselada, G. Bubnis, and H. Grubmüller, Proc. Natl. Acad. Sci. U. S. A. 111, 11043 (2014). 10.1073/pnas.1323221111
43. M. Nishizawa and K. Nishizawa, Biophys. J. 104, 1038 (2013). 10.1016/j.bpj.2013.01.022
44. S. Kawamoto and W. Shinoda, Soft Matter 10, 3048 (2014). 10.1039/c3sm52344f
45. W. Shinoda, R. DeVane, and M. L. Klein, J. Phys. Chem. B 114, 6836 (2010). 10.1021/jp9107206
46. W. Shinoda, R. DeVane, and M. L. Klein, Curr. Opin. Struct. Biol. 22, 175 (2012). 10.1016/j.sbi.2012.01.011
47. W. Shinoda, R. Devane, and M. L. Klein, Mol. Simul. 33, 27 (2007). 10.1080/08927020601054050
48. W. Shinoda, R. DeVane, and M. L. Klein, Soft Matter 4, 2454 (2008). 10.1039/b808701f
49. M. L. Klein and W. Shinoda, Science 321, 798 (2008). 10.1126/science.1157834
50. W. Shinoda, R. DeVane, and M. L. Klein, Soft Matter 7, 6178 (2011). 10.1039/c1sm05173c
51. See supplementary material at http://dx.doi.org/10.1063/1.4933087 E-JCPSA6-143-010598 for 1. a brief summary of the SDK-CG lipid model and 2. detailed analysis of each energy term contribution in continuum model.
52. A. MacKerell, D. Bashford, M. Bellott, R. Dunbrack, J. Evanseck, M. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. Lau, C. Mattos, S. Michnick, T. Ngo, D. Nguyen, B. Prodhom, W. Reiher, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 102, 3586 (1998). 10.1021/jp973084f
53. J. B. Klauda, R. M. Venable, J. A. Freites, J. W. O'Connor, D. J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A. D. MacKerell, and R. W. Pastor, J. Phys. Chem. B 114, 7830 (2010). 10.1021/jp101759q
54. X. He, W. Shinoda, R. DeVane, and M. L. Klein, Mol. Phys. 108, 2007 (2010). 10.1080/00268976.2010.503197
55. BT, which is small compared to the energy scale we discuss in the present paper.
56. M. Parrinello and A. Rahman, Phys. Rev. Lett. 45, 1196 (1980). 10.1103/PhysRevLett.45.1196
57. H. C. Andersen, J. Chem. Phys. 72, 2384 (1980). 10.1063/1.439486
58. S. Nosé, J. Chem. Phys. 81, 511 (1984). 10.1063/1.447334
59. W. G. Hoover, Phys. Rev. A 31, 1695 (1985). 10.1103/PhysRevA.31.1695
60. S. J. Plimpton, J. Comput. Phys. 117, 1 (1995). 10.1006/jcph.1995.1039
61. R. W. Hockney and J. W. Eastwood, Computer Simulation Using Particles (Taylor and Francis Group, 1988).
62. W. Shinoda, T. Nakamura, and S. O. Nielsen, Soft Matter 7, 9012 (2011). 10.1039/c1sm05404j
63. S. Kawamoto, T. Nakamura, S. O. Nielsen, and W. Shinoda, J. Chem. Phys. 139, 034108 (2013). 10.1063/1.4811677
64. M. Orsi, J. Michel, and J. W. Essex, J. Phys.: Condens. Matter 22, 155106 (2010). 10.1088/0953-8984/22/15/155106
65. D. Marsh, Biophys. J. 93, 3884 (2007). 10.1529/biophysj.107.107938
66. M. Schick, J. Stat. Phys. 142, 1317 (2011). 10.1007/s10955-010-0111-9
67. T. Nakamura and W. Shinoda, J. Chem. Phys. 138, 124903 (2013). 10.1063/1.4795579
68. C. K. Haluska, K. A. Riske, V. Marchi-Artzner, J. M. Lehn, R. Lipowsky, and R. Dimova, Proc. Natl. Acad. Sci. U. S. A. 103, 15841 (2006). 10.1073/pnas.0602766103