Microsecond Molecular Dynamics Simulations of Lipid Mixing

Langmuir

Volumn 30, Issue 40, 2014, Pages 11993-12001

  Hong, Chunkit ^a   Tieleman, D Peter ^b   Wang, Yi ^a  

^a CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CHOLESTEROL; LIPIDS; MAMMALS; MIXING; MIXTURES; MOLECULAR DYNAMICS;

DIRECT MEASUREMENT; LATERAL DISTRIBUTIONS; LOW SALT CONCENTRATION; MAMMALIAN MEMBRANES; MOLECULAR DYNAMICS SIMULATIONS; NACL CONCENTRATION; SPECIAL-PURPOSE MACHINES; WATER PERMEABILITY;

LIPID BILAYERS;

1-PALMITOYL-2-OLEOYLGLYCERO-3-PHOSPHOGLYCEROL; 1-PALMITOYL-2-OLEOYLPHOSPHATIDYLCHOLINE; 1-PALMITOYL-2-OLEOYLPHOSPHATIDYLETHANOLAMINE; CHOLESTEROL; LIPID BILAYER; PHOSPHATIDYLCHOLINE; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; SODIUM CHLORIDE; WATER;

CHEMISTRY; CONFORMATION; LIPID BILAYER; MOLECULAR DYNAMICS; THERMODYNAMICS; TIME FACTOR;

CHOLESTEROL; LIPID BILAYERS; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; PHOSPHATIDYLCHOLINES; PHOSPHATIDYLETHANOLAMINES; PHOSPHATIDYLGLYCEROLS; SODIUM CHLORIDE; THERMODYNAMICS; TIME FACTORS; WATER;

EID: 84909989886     PISSN: 07437463     EISSN: 15205827     Source Type: Journal    
DOI: 10.1021/la502363b     Document Type: Article

References (61)

1. Tieleman, D. P.; Marrink, S.-J.; Berendsen, H. J. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems Biochim. Biophys. Acta, Biomembr. 1997, 1331, 235 - 270
2. Pastor, R. W.; Venable, R. M.; Feller, S. E. Lipid bilayers, NMR relaxation, and computer simulations Acc. Chem. Res. 2002, 35, 438 - 446
3. Saiz, L.; Klein, M. L. Computer simulation studies of model biological membranes Acc. Chem. Res. 2002, 35, 482 - 489
4. Marrink, S. J.; de Vries, A. H.; Tieleman, D. P. Lipids on the move: simulations of membrane pores, domains, stalks and curves Biochim. Biophys. Acta 2009, 1788, 149 - 168
5. Hénin, J.; Shinoda, W.; Klein, M. L. Models for phosphatidylglycerol lipids put to a structural test J. Phys. Chem. B 2009, 113, 6958 - 6963
6. Vattulainen, I.; Rog, T. Lipid simulations: a perspective on lipids in action Cold Spring Harb Perspect Biol. 2011, 3, a004655
7. Bennett, W.; Tieleman, D. P. Computer simulations of lipid membrane domains Biochim. Biophys. Acta, Biomembr. 2013, 1828, 1765 - 1776
8. Klauda, J. B.; Venable, R. M.; Freites, J. A.; O'Connor, J. W.; Tobias, D. J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A. D., Jr.; Pastor, R. W. Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types J. Phys. Chem. B 2010, 114, 7830 - 7843
9. Klauda, J. B.; Monje, V.; Kim, T.; Im, W. Improving the CHARMM force field for polyunsaturated fatty acid chains J. Phys. Chem. B 2012, 116, 9424 - 9431
10. Pastor, R. W.; MacKerell, A. D. Development of the CHARMM force field for lipids J. Phys. Chem. Lett. 2011, 2, 1526 - 1532
11. Jambeck, J. P. M.; Lyubartsev, A. P. An extension and further validation of an all-atomistic force field for biological membranes J. Chem. Theory Comput. 2012, 8, 2938 - 2948
12. Dickson, C. J.; Madej, B. D.; Skjevik, Å. A.; Betz, R. M.; Teigen, K.; Gould, I. R.; Walker, R. C. Lipid14: The Amber lipid force field J. Chem. Theory Comput. 2014, 10, 865 - 879
13. Maciejewski, A.; Pasenkiewicz-Gierula, M.; Cramariuc, O.; Vattulainen, I.; Rog, T. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration J. Phys. Chem. B 2014, 118, 4571 - 4581
14. Pandit, S. A.; Bostick, D.; Berkowitz, M. L. Mixed bilayer containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine: lipid complexation, ion binding, and electrostatics Biophys. J. 2003, 85, 3120 - 3131
15. Gurtovenko, A. A.; Patra, M.; Karttunen, M.; Vattulainen, I. Cationic DMPC/DMTAP lipid bilayers: molecular dynamics study Biophys. J. 2004, 86, 3461 - 3472
16. Murzyn, K.; Róg, T.; Pasenkiewicz-Gierula, M. Phosphatidylethanolamine-phosphatidylglycerol bilayer as a model of the inner bacterial membrane Biophys. J. 2005, 88, 1091 - 1103
17. Broemstrup, T.; Reuter, N. Molecular dynamics simulations of mixed acidic/zwitterionic phospholipid bilayers Biophys. J. 2010, 99, 825 - 833
18. Janosi, L.; Gorfe, A. A. Simulating POPC and POPC/POPG bilayers: Conserved packing and altered surface reactivity J. Chem. Theory Comput. 2010, 6, 3267 - 3273
19. Yin, F.; Kindt, J. T. Atomistic simulation of hydrophobic matching effects on lipid composition near a helical peptide embedded in mixed-lipid bilayers J. Phys. Chem. B 2010, 114, 8076 - 8080
20. Pandit, K. R.; Klauda, J. B. Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain Biochim. Biophys. Acta, Biomembr. 2012, 1818, 1205 - 1210
21. Nielsen, S. O.; Lopez, C. F.; Srinivas, G.; Klein, M. L. Coarse grain models and the computer simulation of soft materials J. Phys.: Condens. Matter 2004, 16, R481 - R512
22. Chang, R.; Ayton, G. S.; Voth, G. A. Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations J. Chem. Phys. 2005, 122, 244716 - 244728
23. Izvekov, S.; Voth, G. A. Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers J. Chem. Theory Comput. 2006, 2, 637 - 648
24. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H. The MARTINI force field: coarse grained model for biomolecular simulations J. Phys. Chem. B 2007, 111, 7812 - 7824
25. Baoukina, S.; Mendez-Villuendas, E.; Tieleman, D. P. Molecular view of phase coexistence in lipid monolayers J. Am. Chem. Soc. 2012, 134, 17543 - 17553
26. Marrink, S. J.; Mark, A. E. The mechanism of vesicle fusion as revealed by molecular dynamics simulations J. Am. Chem. Soc. 2003, 125, 11144 - 11145
27. Marrink, S. J.; Mark, A. E. Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles J. Am. Chem. Soc. 2003, 125, 15233 - 15242
28. Marrink, S. J.; Tieleman, D. P. Perspecitve on the Martini model Chem. Soc. Rev. 2013, 42, 6801 - 6822
29. Coppock, P. S.; Kindt, J. T. Atomistic simulations of mixed-lipid bilayers in gel and fluid phases Langmuir 2009, 25, 352 - 359
30. de Joannis, J.; Coppock, P. S.; Yin, F.; Mori, M.; Zamorano, A.; Kindt, J. T. Atomistic simulation of cholesterol effects on miscibility of saturated and unsaturated phospholipids: implications for liquid-ordered/liquid-disordered phase coexistence J. Am. Chem. Soc. 2011, 133, 3625 - 3634
31. Shaw, D. E.; et al. International Symposium on Computer Architecture, ACM, 2007; pp 1 - 12.
32. Humphrey, W.; Dalke, A.; Schulten, K. VMD-visual molecular dynamics J. Mol. Graphics 1996, 14, 33 - 38
33. Jo, S.; Kim, T.; Iyer, V. G.; Im, W. CHARMM-GUI: A Web-based graphical user interface for CHARMM J. Comput. Chem. 2008, 29, 1859 - 1865
34. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable molecular dynamics with NAMD J. Comput. Chem. 2005, 26, 1781 - 1802
35. Lim, J. B.; Rogaski, B.; Klauda, J. B. Update of the cholesterol force field parameters in CHARMM J. Phys. Chem. B 2011, 116, 203 - 210
36. Andersen, H. C. Rattle: A "velocity" version of the shake algorithm for molecular dynamics calculations J. Chem. Phys. 1983, 52, 24 - 34
37. Miyamoto, S.; Kollman, P. A. SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 1993, 13, 952 - 962
38. Darden, T.; York, D.; Pedersen, L. G. Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089 - 10092
39. Chodera, J. D.; Swope, W. C.; Pitera, J. W.; Seok, C.; Dill, K. A. Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations J. Chem. Theory Comput. 2007, 3, 26 - 41
40. Ester, M.; Kriegel, H.-P.; Sander, J.; Xu, X. A density-based algorithm for discovering clusters in large spatial databases with noise Proc. 2nd Int. Conf. Knowledge Discovery Data Mining 1996, 96, 226 - 231
41. Aksimentiev, A.; Schulten, K. Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability and the electrostatic potential map Biophys. J. 2005, 88, 3745 - 3761
42. Wang, Y.; Markwick, P. R. L.; de Oliveira, C. A. F.; McCammon, J. A. Enhanced lipid diffusion and mixing in accelerated molecular dynamics J. Chem. Theory Comput. 2011, 7, 3199 - 3207
43. Coppock, P. S.; Kindt, J. T. Atomistic simulations of mixed-lipid bilayers in gel and fluid phases Langmuir 2009, 25, 352 - 359
44. Zhao, W.; Róg, T.; Gurtovenko, A. A.; Vattulainen, I.; Karttunen, M. Role of phosphatidylglycerols in the stability of bacterial membranes Biochimie 2008, 90, 930 - 938
45. Chiu, S. W.; Jakobsson, E.; Mashl, R. J.; Scott, H. L. Cholesterol-induced modifications in lipid bilayers: a simulation study Biophys. J. 2002, 83, 1842 - 1853
46. Pandit, S.; Bostick, D.; Berkowitz, M. Complexation of phosphatidylcholine lipids with cholesterol Biophys. J. 2004, 86, 1345 - 1356
47. Berkowitz, M. L. Detailed molecular dynamics simulations of model biological membranes containing cholesterol Biochim. Biophys. Acta, Biomembr. 2009, 1788, 86 - 96
48. Róg, T.; Pasenkiewicz-Gierula, M.; Vattulainen, I.; Karttunen, M. Ordering effects of cholesterol and its analogues Biochim. Biophys. Acta, Biomembr. 2009, 1788, 97 - 121
49. Kaiser, H.-J.; Orłowski, A.; Róg, T.; Nyholm, T. K.; Chai, W.; Feizi, T.; Lingwood, D.; Vattulainen, I.; Simons, K. Lateral sorting in model membranes by cholesterol-mediated hydrophobic matching Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 16628 - 16633
50. Jeon, J.-H.; Monne, H. M.-S.; Javanainen, M.; Metzler, R. Anomalous diffusion of phospholipids and cholesterols in a lipid bilayer and its origins Phys. Rev. Lett. 2012, 109, 188103
51. Sodt, A. J.; Sandar, M. L.; Gawrisch, K.; Pastor, R. W.; Lyman, E. The molecular structure of the liquid ordered phase of lipid bilayers J. Am. Chem. Soc. 2014, 136, 725 - 732
52. Ali, M. R.; Cheng, K. H.; Huang, J. Assess the nature of cholesterol-lipid interactions through the chemical potential of cholesterol in phosphatidylcholine bilayers Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 5372 - 5377
53. Mátyus, E.; Kandt, C.; Tieleman, D. Computer simulation of antimicrobial peptides Curr. Med. Chem. 2007, 14, 2789 - 2798
54. Herce, H. D.; García, A. E. Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 20805 - 20810
55. Pan, J.; Tieleman, D.; Nagle, J.; Kucerka, N.; Tristram-Nagle, S. Alamethicin in lipid bilayers: combined use of X-ray scattering and MD simulations Biochim. Biophys. Acta, Biomembr. 2009, 1788, 1387 - 1397
56. Wang, Y.; Schlamadinger, D. E.; Kim, J. E.; McCammon, J. A. Comparative molecular dynamics simulation of the antimicrobial peptide CM15 in model lipid bilayers Biochim. Biophys. Acta, Biomembr. 2012, 1818, 1402 - 1409
57. Böckmann, R. A.; Hac, A.; Heimburg, T.; Grubmüller, H. Effect of sodium chloride on a lipid bilayer Biophys. J. 2003, 85, 1647 - 1655
58. Venable, R. M.; Luo, Y.; Gawrisch, K.; Roux, B.; Pastor, R. W. Simulations of anionic lipid membranes: Development of interaction-specific ion parameters and validation using NMR data J. Phys. Chem. B 2013, 117, 10183 - 10192
59. Marrink, S.; Berendsen, H. Simulation of water transport through a lipid membrane J. Phys. Chem. 1994, 98, 4155 - 68
60. Swift, R.; Amaro, R. E. Back to the future: can physical models of passive membrane permeability help reduce drug candidate attrition and move us beyond QSPR? Chem. Biol. Drug Des. 2013, 81, 61 - 71
61. Comer, J.; Schulten, K.; Chipot, C. Calculation of lipid-bilayer permeabilities using an average force J. Chem. Theory Comput. 2014, 10, 554 - 564