Molecular dynamics simulations of DPPC bilayers using "lIME", a new coarse-grained model

Journal of Physical Chemistry B

Volumn 117, Issue 17, 2013, Pages 5019-5030

  Curtis, Emily M ^a   Hall, Carol K ^a  

^a North Carolina State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIME; MOLECULAR DYNAMICS; PHOSPHOLIPIDS;

ATOMISTIC SIMULATIONS; BILAYER THICKNESS; COARSE GRAINED MODELS; DISCONTINUOUS MOLECULAR DYNAMICS SIMULATIONS; ENERGETIC PARAMETERS; LIQUID-CRYSTALLINE PHASE; MOLECULAR DYNAMICS SIMULATIONS; MULTI-SCALE MODELING;

COMPUTER SIMULATION;

EID: 84877052967     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp309712b     Document Type: Article

References (66)

1. Bennun, S.; Hoopes, M.; Xing, C.; Faller, R. Chem. Phys. Lipids 2009, 159, 59-66
2. Meer, G.; Voelker, D.; Feigenson, G. Nat. Rev. Mol. Cell Biol. 2008, 9, 112-124
3. Phillips, R.; Ursell, T.; Wiggins, P.; Sens, P. Nature. 2009, 459, 379-385
4. Karve, S.; Bandekar, A.; Ali, M.; Sofou, S. Biomaterials 2010, 31, 4409-4416
5. Schroeder, A.; Levins, C.; Cortez, C.; Langer, R.; Anderson, D. J. Int. Med. 2009, 267, 9-21
6. Almeida, A.; Souto, E. Adv. Drug Delivery Rev. 2007, 59, 478-479
7. Sharma, A.; Mayhew, E.; Straubinger, R. Cancer Res. 1993, 53, 5877-5881
8. Sharma, A.; Straubinger, R. Pharm. Res. 1994, 11, 889-896
9. Skubitz, K. Cancer Invest. 2003, 21, 167-176
10. Gabizon, A. Cancer Invest. 2001, 19, 424-436
11. Colbern, G.; Hiller, A.; Musterer, R.; Pegg, E.; Henderson, I.; Working, P. J. Liposome Res. 1999, 9, 523-538
12. Song, H.; Zhang, J.; Han, Z.; Zhang, X.; Li, Z.; Zhang, L.; Fu, M.; Lin, C.; Ma, J. Cancer Chemother. Pharmacol. 2006, 57, 591-598
13. Pandit, S.; Jakobsson, E.; Scott, H. Biophys. J. 2004, 87, 3312-3322
14. Latour, R. Biointerphases 2008, 3, 2-12
15. Curtis, E.; Hall, C. Unpublished.
16. Bemporad, D.; Essex, J.; Luttman, C. J. Phys. Chem. B 2004, 108, 4875-4884
17. Heine, D.; Rammohan, A.; Balakrishnan, J. Mol. Simul. 2007, 33, 391-397
18. Rog, T.; Murzyn, K.; Pasenkiewicz-Gierula, M. Acta Biochim. Pol. 2003, 50, 789-798
19. Feller, S.; Gawrisch, K.; MacKerell, A. J. Am. Chem. Soc. 2002, 124, 318-326
20. Feller, S.; MacKerell, A. J. Phys. Chem. B 2000, 104, 7510-7515
21. Rosso, L.; Gould, I. J. Comput. Chem. 2008, 29, 24-37
22. Oostenbring, C.; Villa, A.; Mark, A.; Van Gunsteren, W. J. Comput. Chem. 2004, 25, 1656-1675
23. Hess, B.; Kutzner, C.; Van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435-447
24. Van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A.; Berendsen, H. J. Comput. Chem. 2005, 26, 1701-1719
25. Kukol, A. J. Chem. Theory Comput. 2009, 5, 615-626
26. De Vries, A.; Mark, A.; Marrink, S. J. Am. Chem. Soc. 2004, 126, 4488-4489
27. Orsi, M.; Haubertin, D.; Sanderson, W.; Essex, J. J. Phys. Chem. B 2008, 112, 802-815
28. Marrink, S.; de Vries, A.; Mark, A. J. Phys. Chem. B 2004, 108, 750-760
29. Marrink, S.; Risselada, H.; Yefimov, S.; Tieleman, D.; de Vries, A. J. Phys. Chem. B 2007, 111, 7812-7824
30. Risselada, H.; Marrink, S. Proc. Natl. Acad. Sci. 2008, 105, 17367-17372
31. Orsi, M.; Michel, J.; Essex, J. J. Phys.: Condens. Matter 2010, 22, 1-15
32. Orsi, M.; Essex, J. PLoS ONE 2011, 6, 1-22
33. Orsi, M.; Essex, J. Faraday Discuss. 2013, 10.1039/C2FD20110K
34. DeNicola, A.; Zhao, Y.; Kawakatsu, T.; Roccatano, D.; Milano, G. J. Chem. Theory Comput. 2011, 7, 2947-2962
35. Wang, Z.; Deserno, M. J. Phys. Chem. B 2010, 114, 11207-11220
36. Phillips, J.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
37. MacKerell, A.; Banavali, N.; Foloppe, N. Biopolymers 2000, 56, 257-265
38. Lyubartsev, A.; Laaksonen, A. Comput. Phys. Commun. 2000, 128, 565-589
39. Lyubartsev, A. Eur. Biophys. J. 2005, 35, 53-61
40. Izvekov, S.; Voth, G. J. Phys. Chem. B 2009, 113, 4443-4455
41. Reith, D.; Putz, M.; Muller-Plathe, F. J. Comput. Chem. 2003, 24, 1624-1636
42. Chennamsetty, N.; Bock, H.; Gubbins, K. J. Chem. Phys. 2006, 124, 074105-1-074105-12
43. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38
44. Smith, S. W.; Hall, C. K.; Freeman, B. D. J. Comput. Phys. 1997, 134, 16-30
45. Alder, B. J.; Wainwright, T. E. J. Chem. Phys. 1959, 31, 459-466
46. Rapaport, D. C. J. Phys. A: Math. Gen. 1978, 11, L213-L217
47. Rapaport, D. C. J. Chem. Phys. 1979, 71, 3299-3303
48. Andersen, H. C. J. Chem. Phys. 1980, 72, 2384-2393
49. Berendsen, H.; Postma, J.; Van Gunsteren, W.; DiNola, A.; Haak, J. J. Chem. Phys. 1984, 81, 3684-3690
50. Nguyen, H. D.; Hall, C. K. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 16180-16185
51. Khan, M.; Herbordt, M. J. Comput. Phys. 2011, 230, 6563-6582
52. Hill, T. L. Introduction to Statistical Thermodynamics; Addison Wesley Publishing Company, Inc.: Reading, MA, 1960.
53. Kucerka, N.; Tristram-Nagle, St.; Nagle, J. Biophys. J. 2006, 90, L83-L85
54. Kucerka, N.; Nagle, J.; Sachs, J.; Feller, S.; Pencer, J.; Jackson, A.; Katsaras, J. Biophys. J. 2008, 95, 2356-2367
55. Tristra-Nagle, S.; Zhang, R.; Suter, R.; Worthington, C.; Sun, W.; Nagle, J. Biophys. J. 1993, 64, 1097-1109
56. Marrink, S.; Risselada, J.; Mark, A. Chem. Phys. Lipids 2005, 135, 223-244
57. Biltonen, R.; Lichtenberg, D. Chem. Phys. Lipids 1993, 64, 129-142
58. Nagle, J.; Tristram-Nagle, S. Biochim. Biophys. Acta 2000, 1469, 159-195
59. Wang, Z.; Deserno, M. New J. Phys. 2010, 12, 1-25
60. Leekumjorn, S.; Sum, A. Biochim. Biophys. Acta 2007, 1768, 354-365
61. Liu, J.; Conboy, J. Biophys. J. 2005, 89, 2522-2532
62. Liu, J.; Conboy, J. J. Am. Chem. Soc. 2004, 126, 8376-8377
63. John, K.; Schreiber, S.; Kubelt, J.; Herrman, A.; Muller, P. Biophys. J. 2002, 83, 3315-3323
64. Norberg, J.; Nilsson, L. Biophys. J. 2000, 79, 1537-1553
65. Kenkare, N.; Hall, C.; Khan, S. J. Chem. Phys. 2000, 113, 404-418
66. Shultz, A.; Hall, C.; Genzer, J. J. Chem. Phys. 2004, 120, 2049-2055