Effect of hydrophobic mismatch on domain formation and peptide sorting in the multicomponent lipid bilayers in the presence of immobilized peptides

Journal of Chemical Physics

Volumn 141, Issue 7, 2014, Pages

  Liang, Qing ^a,b   Wu, Qing Yan ^a   Wang, Zhi Yong ^c  

^a ZHEJIANG NORMAL UNIVERSITY   (China)

^b NINGBO UNIVERSITY   (China)

^c CHONGQING UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CELL MEMBRANES; HYDROPHOBICITY; MOLECULAR DYNAMICS; PEPTIDES;

COARSE-GRAINED MOLECULAR DYNAMICS SIMULATIONS; EXTRACELLULAR MATRICES; HYDROPHOBIC MISMATCH; IMMOBILIZED PEPTIDE; LATERAL DIFFUSION; PEPTIDE IMMOBILIZATION; PROTEINS/PEPTIDES; TRANSMEMBRANE PROTEINS;

LIPID BILAYERS;

1,2-LINOLEOYLPHOSPHATIDYLCHOLINE; CHOLESTEROL; DIPALMITOYLPHOSPHATIDYLCHOLINE; IMMOBILIZED PROTEIN; LIPID BILAYER; PEPTIDE; PHOSPHATIDYLCHOLINE;

CELL MEMBRANE; CHEMICAL PHENOMENA; CHEMISTRY; LIPID BILAYER; MOLECULAR DYNAMICS; PROTEIN CONFORMATION;

1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE; CHOLESTEROL; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; IMMOBILIZED PROTEINS; LIPID BILAYERS; MEMBRANE MICRODOMAINS; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PHOSPHATIDYLCHOLINES; PROTEIN CONFORMATION;

EID: 84906535688     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4891931     Document Type: Article

References (68)

1. K. Simons and E. Ikonen, Nature (London) 387, 569 (1997). 10.1038/42408
2. D. Lingwood and K. Simons, Science 327, 46 (2010). 10.1126/science. 1174621
3. E. Sackmann, Science 271, 43 (1996). 10.1126/science.271.5245.43
4. M. Tanaka and E. Sackmann, Nature (London) 437, 656 (2005). 10.1038/nature04164
5. F. Roder, O. Birkholz, O. Beutel, D. Paterok, and J. Piehler, J. Am. Chem. Soc. 135, 1189 (2013). 10.1021/ja310186g
6. C. Dietrich, L. Bagatolli, Z. Volovyk, N. Thompson, M. Levi, K. Jacobson, and E. Gratton, Biophys. J. 80, 1417 (2001). 10.1016/S0006-3495(01)76114-0
7. T. Baumgart, S. T. Hess, and W. W. Webb, Nature (London) 425, 821 (2003). 10.1038/nature02013
8. T. Baumgart, A. T. Hammond, P. Sengupta, S. T. Hess, D. A. Holowka, B. A. Baird, and W. W. Webb, Proc. Natl. Acad. Sci. U.S.A. 104, 3165 (2007). 10.1073/pnas.0611357104
9. D. Lingwood, J. Ries, P. Schwille, and K. Simons, Proc. Natl. Acad. Sci. U.S.A. 105, 10005 (2008). 10.1073/pnas.0804374105
10. H.-J. Kaiser, D. Lingwood, I. Levental, J. L. Sampaio, L. Kalvodova, L. Rajendran, and K. Simons, Proc. Natl. Acad. Sci. U.S.A. 106, 16645 (2009). 10.1073/pnas.0908987106
11. G. W. Feigenson, Biochim. Biophys. Acta, Biomembr. 1788, 47 (2009). 10.1016/j.bbamem.2008.08.014
12. E. L. Elson, E. Fried, J. E. Dolbow, and G. M. Genin, Annu. Rev. Biophys. 39, 207 (2010). 10.1146/annurev.biophys.093008.131238
13. L. J. Pike, J. Lipid Res. 47, 1597 (2006). 10.1194/jlr.E600002-JLR200
14. L. J. Pike, J. Lipid Res. 50, S323 (2009). 10.1194/jlr.R800040-JLR200
15. P. Sharma, R. Varma, R. Sarasij, Ira, K. Gousset, G. Krishnamoorthy, M. Rao, and S. Mayor, Cell 116, 577 (2004). 10.1016/S0092-8674(04)00167-9
16. K. G. N. Suzuki, R. S. Kasai, K. M. Hirosawa, Y. L. Nemoto, M. Ishibashi, Y. Miwa, T. K. Fujiwara, and A. Kusumi, Nat. Chem. Biol. 8, 774 (2012). 10.1038/nchembio.1028
17. M. E. Fastenberg, H. Shogomori, X. Xu, D. A. Brown, and E. London, Biochemistry 42, 12376 (2003). 10.1021/bi034718d
18. K. Bacia, C. G. Schuette, N. Kahya, R. Jahn, and P. Schwille, J. Biol. Chem. 279, 37951 (2004). 10.1074/jbc.M407020200
19. A. T. Hammond, F. A. Heberle, T. Baumgart, D. Holowka, B. Baird, and G. W. Feigenson, Proc. Natl. Acad. Sci. U.S.A. 102, 6320 (2005). 10.1073/pnas.0405654102
20. H. Shogomori, A. T. Hammond, A. G. Ostermeyer-Fay, D. J. Barr, G. W. Feigenson, E. London, and D. A. Brown, J. Biol. Chem. 280, 18931 (2005). 10.1074/jbc.M500247200
21. F. J.-M. de Meyer, M. Venturoli, and B. Smit, Biophys. J. 95, 1851 (2008). 10.1529/biophysj.107.124164
22. D. A. Pantano and M. L. Klein, J. Phys. Chem. B 113, 13715 (2009). 10.1021/jp901840u
23. B. West, F. L. Brown, and F. Schmid, Biophys. J. 96, 101 (2009). 10.1529/biophysj.108.138677
24. H.-J. Kaiser, A. Orłowski, T. Róg, T. K. M. Nyholm, W. Chai, T. Feizi, D. Lingwood, I. Vattulainen, and K. Simons, Proc. Natl. Acad. Sci. U.S.A. 108, 16628 (2011). 10.1073/pnas.1103742108
25. T. Kim and W. Im, Biophys. J. 99, 175 (2010). 10.1016/j.bpj.2010.04.015
26. E. Strandberg, S. Esteban-Martín, A. S. Ulrich, and J. Salgado, Biochim. Biophys. Acta, Biomembr. 1818, 1242 (2012). 10.1016/j.bbamem.2012.01. 023
27. F. A. Heberle, R. S. Petruzielo, J. Pan, P. Drazba, N. Kučerka, R. F. Standaert, G. W. Feigenson, and J. Katsaras, J. Am. Chem. Soc. 135, 6853 (2013). 10.1021/ja3113615
28. E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, Science 313, 1642 (2006). 10.1126/science.1127344
29. C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff, S. Polyakova, V. N. Belov, B. Hein, C. von Middendorff, A. Schönle, and S. W. Hell, Nature (London) 457, 1159 (2009). 10.1038/nature07596
30. K. Simons and M. J. Gerl, Nat. Rev. Mol. Cell Biol. 11, 688 (2010). 10.1038/nrm2977
31. C. Kuo and R. M. Hochstrasser, J. Am. Chem. Soc. 133, 4664 (2011). 10.1021/ja1099193
32. D. M. Owen, D. J. Williamson, A. Magenau, and K. Gaus, Nat. Commun. 3, 1256 (2012). 10.1038/ncomms2273
33. A. Toulmay and W. A. Prinz, J. Cell Biol. 202, 35 (2013). 10.1083/jcb.201301039
34. M. P. Clausen and B. C. Lagerholm, Nano Lett. 13, 2332 (2013). 10.1021/nl303151f
35. E. Klotzsch and G. J. Schütz, Philos. Trans. R. Soc. B 368, 20120033 (2013). 10.1098/rstb.2012.0033
36. J. C. Chang and S. J. Rosenthal, ACS Chem. Neurosci. 3, 737 (2012). 10.1021/cn3000845
37. D. M. Owen, A. Magenau, D. Williamson, and K. Gaus, BioEssays 34, 739 (2012). 10.1002/bies.201200044
38. J. F. Frisz, K. Lou, H. A. Klitzing, W. P. Hanafin, V. Lizunov, R. L. Wilson, K. J. Carpenter, R. Kim, I. D. Hutcheon, J. Zimmerberg, P. K. Weber, and M. L. Kraft, Proc. Natl. Acad. Sci. U.S.A. 110, E613 (2013). 10.1073/pnas.1216585110
39. P. Lajoie and I. R. Nabi, Int. Rev. Cell Mol. Biol. 282, 135 (2010). 10.1016/S1937-6448(10)82003-9
40. N. L. Andrews, K. A. Lidke, J. R. Pfeiffer, A. R. Burns, S. Bridget, J. M. Oliver, and D. S. Lidke, Nat. Cell Biol. 10, 955 (2008). 10.1038/ncb1755
41. G. Chichili and W. Rodgers, Cell. Mol. Life Sci. 66, 2319 (2009). 10.1007/s00018-009-0022-6
42. D. H. de Jong, C. A. Lopez, and S. J. Marrink, Faraday Discuss. 161, 347 (2013). 10.1039/c2fd20086d
43. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, in Molecular Biology of the Cell, 5th ed. (Garland Science, New York, 2007), pp. 629-650.
44. J. Dinic, P. Ashrafzadeh, and I. Parmryd, Biochim. Biophys. Acta, Biomembr. 1828, 1102 (2013). 10.1016/j.bbamem.2012.12.004
45. M. V. Gudheti, N. M. Curthoys, T. J. Gould, D. Kim, M. S. Gunewardene, K. A. Gabor, J. A. Gosse, C. H. Kim, J. Zimmerberg, and S. T. Hess, Biophys. J. 104, 2182 (2013). 10.1016/j.bpj.2013.03.054
46. F. Heinemann, S. K. Vogel, and P. Schwille, Biophys. J. 104, 1465 (2013). 10.1016/j.bpj.2013.02.042
47. T. Witkowski, R. Backofen, and A. Voigt, Phys. Chem. Chem. Phys. 14, 14509 (2012). 10.1039/c2cp41274h
48. T. Fischer, H. Jelger Risselada, and R. L. C. Vink, Phys. Chem. Chem. Phys. 14, 14500 (2012). 10.1039/c2cp41417a
49. J. Ehrig, E. P. Petrov, and P. Schwille, Biophys. J. 100, 80 (2011). 10.1016/j.bpj.2010.11.002
50. B. B. Machta, S. Papanikolaou, J. P. Sethna, and S. L. Veatch, Biophys. J. 100, 1668 (2011). 10.1016/j.bpj.2011.02.029
51. T. Fischer and R. L. C. Vink, J. Chem. Phys. 134, 055106 (2011). 10.1063/1.3530587
52. M. Laradji and G. MacNevin, J. Chem. Phys. 119, 2275 (2003). 10.1063/1.1585011
53. G. S. Grest and D. J. Srolovitz, Phys. Rev. B 32, 3014 (1985). 10.1103/PhysRevB.32.3014
54. M. F. Gyure, S. T. Harrington, R. Strilka, and H. E. Stanley, Phys. Rev. E 52, 4632 (1995). 10.1103/PhysRevE.52.4632
55. 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
56. L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P. Tieleman, and S. J. Marrink, J. Chem. Theory Comput. 4, 819 (2008). 10.1021/ct700324x
57. X. Periole, and S.-J. Marrink, in Biomolecular Simulations, Methods in Molecular Biology Vol. 924, edited by L. Monticelli, and E. Salonen (Humana Press, 2013), pp. 533-565.
58. S. J. Marrink and D. P. Tieleman, Chem. Soc. Rev. 42, 6801 (2013). 10.1039/c3cs60093a
59. W. D. Bennett and D. P. Tieleman, Biochim. Biophys. Acta, Biomembr. 1828, 1765 (2013). 10.1016/j.bbamem.2013.03.004
60. H. J. Risselada and S. J. Marrink, Proc. Natl. Acad. Sci. U.S.A. 105, 17367 (2008). 10.1073/pnas.0807527105
61. D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, J. Comput. Chem. 26, 1701 (2005). 10.1002/jcc.20291
62. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 4, 435 (2008). 10.1021/ct700301q
63. S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl, Bioinformatics 29, 845 (2013). 10.1093/bioinformatics/btt055
64. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics 14, 33 (1996). 10.1016/0263-7855(96)00018-5
65. W. J. Allen, J. A. Lemkul, and D. R. Bevan, J. Comput. Chem. 30, 1952 (2009). 10.1002/jcc.21172
66. C. H. Bennett, J. Comput. Phys. 22, 245 (1976). 10.1016/0021-9991(76) 90078-4
67. L. Janosi, Z. Li, J. F. Hancock, and A. A. Gorfe, Proc. Natl. Acad. Sci. U.S.A. 109, 8097 (2012). 10.1073/pnas.1200773109
68. M. J. Saxton, Biophys. J. 55, 21 (1989). 10.1016/S0006-3495(89)82776-6