Chapter 4 Molecular Dynamics Simulation of Lipid-Protein Interactions

Current Topics in Membranes

Volumn 60, Issue , 2008, Pages 111-130

  Sapay, Nicolas ^a   Tieleman, D Peter ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 45849125767     PISSN: 10635823     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1063-5823(08)00004-5     Document Type: Review

References (63)

1. Aliste M.P., MacCallum J.L., and Tieleman D.P. Biochemistry 42 (2003) 8976-8987
2. Aliste M.P., and Tieleman D.P. BMC Biochem. 6 (2005) 30
3. Allen T.W., Andersen O.S., and Roux B. Biophys. Chem. 124 (2006) 251-267
4. Anézo C., de Vries A.H., Höltje H.D., Tieleman D.P., and Marrink S.J. J. Phys. Chem. B 107 (2003) 9424-9433
5. Ash W.L., Zlomislic M.R., Oloo E.O., and Tieleman D.P. Biochim. Biophys. Acta (BBA) Biomembranes 1666 (2004) 158-189
6. Ayton G.S., and Voth G.A. J. Struct. Biol. 157 (2007) 570-578
7. Bandyopadhyay S., Tarek M., and Klein M.L. J. Phys. Chem. B 103 (1999) 10075-10080
8. Bechinger B., Aisenbrey C., and Bertani P. Biochim. Biophys. Acta (BBA) Biomembranes 1666 (2004) 190
9. Benz R.W., Castro-Roman F., Tobias D.J., and White S.H. Biophys. J. 88 (2005) 805-817
10. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., and Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B. (Ed). Intermolecular Forces (1981), Reidel, Dordrecht 331-342
11. Berger O., Edholm O., and Jahnig F. Biophys. J. 72 (1997) 2002-2013
12. Betanzos M., Chiang C.S., Guy H.R., and Sukharev S. Nat. Struct. Mol. Biol. 9 (2002) 704-710
13. Bockmann R.A., and Grubmuller H. Nat. Struct. Mol. Biol. 9 (2002) 198-202
14. Bockmann R.A., and Grubmuller H. Angew. Chem. Int. Ed. Engl. 43 (2004) 1021-1024
15. Bockmann R.A., Hac A., Heimburg T., and Grubmuller H. Biophys. J. 85 (2003) 1647-1655
16. Case D.A., Cheatham T.E., Darden T., Gohlke H., Luo R., Merz K.M., Onufriev A., Simmerling C., Wang B., and Woods R.J. J. Comput. Chem. 26 (2005) 1668-1688
17. Chandrasekhar I., Kastenholz M., Lins R.D., Oostenbrink C., Schuler L.D., Tieleman D.P., and van Gunsteren W.F. Eur. Biophys. J. 32 (2003) 67-77
18. Chiu S.W., Clark M.M., Jakobsson E., Subramaniam S., and Scott H.L. J. Phys. Chem. B 103 (1999) 6323-6327
19. Forrest L.R., and Sansom M.S. Curr. Opin. Struct. Biol. 10 (2000) 174-181
20. Grossfield A., Feller S.E., and Pitman M.C. Proc. Natl. Acad. Sci. 103 (2006) 4888-4893
21. Grossfield A., Feller S.E., and Pitman M.C. Proteins Struct. Funct. Bioinform. 67 (2007) 31-40
22. Gumbart J., Wang Y., Aksimentiev A., Tajkhorshid E., and Schulten K. Curr. Opin. Struct. Biol. 15 (2005) 423-431
23. Gumbart J., Wiener M.C., and Tajkhorshid E. Biophys, J. 93 (2007) 496-504
24. Hess B., and van der Vegt N.F.A. J. Phys. Chem. B 110 (2006) 17616-17626
25. Jakobsson E. Trends Biochem. Sci. 22 (1997) 339-344
26. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. J. Chem. Phys. 79 (1983) 926-935
27. Jorgensen W.L., Maxwell D.S., and Tirado-Rives J. J. Am. Chem. Soc. 118 (1996) 11225-11236
28. Kandt C., Ash W.L., and Tieleman D.P. Methods 41 (2007) 475-488
29. Killian J.A., and Nyholm T.K. Curr. Opin. Struct. Biol. 16 (2006) 473-479
30. Klauda J.B., Kucerka N., Brooks B.R., Pastor R.W., and Nagle J.F. Biophys. J. 90 (2006) 2796-2807
31. Lee A.G. Biochim. Biophys. Acta 1666 (2004) 62-87
32. Lennard-Jones J.E. Proc. R. Soc. London A 106 (1924) 463-477
33. Leontiadou H., Mark A.E., and Marrink S.J. J. Am. Chem. Soc. 128 (2006) 12156-12161
34. MacCallum J.L., Bennett W.F., and Tieleman D.P. J. Gen. Physiol. 129 (2007) 371-377
35. MacCallum J.L., and Tieleman D.P. J. Comput. Chem. 24 (2003) 1930-1935
36. MacCallum J.L., and Tieleman D.P. J. Am. Chem. Soc. 128 (2006) 125-130
37. MacKerell Jr. A.D., Bashford D., Bellott D., Dunbrack Jr. R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher III W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., and Karplus M. J. Phys. Chem. B 102 (1998) 3586-3616
38. MacKerell Jr. A.D., Feig M., and Brooks III C.L. J. Am. Chem. Soc. 126 (2004) 698-699
39. Marrink S.J., Risselada H.J., Yefimov S., Tieleman D.P., and de Vries A.H. J. Phys. Chem. B 111 (2007) 7812-7824
40. Mátyus E., Kandt C., and Tieleman D.P. Curr. Med. Chem. 14 (2007) 2789-2798
41. Pastor R.W., Venable R.M., and Feller S.E. Acc. Chem. Res. 35 (2002) 438-446
42. Periole X., Huber T., Marrink S.J., and Sakmar T.P. J. Am. Chem. Soc. 129 (2007) 10126-10132
43. Pertsin A., Platonov D., and Grunze M. Langmuir 23 (2007) 1388-1393
44. Ponder J.W., and Case D.A. Protein Simul. 66 (2003) 27-85
45. Radzicka A., and Wolfenden R. Biochemistry 27 (1988) 1664-1670
46. Ryckaert J.P., and Bellemans A. Faraday Discuss. Chem. Soc. 66 (1978) 95-106
47. Scheraga H.A., Khalili M., and Liwo A. Ann. Rev. Phys. Chem. 58 (2007) 57-83
48. Scott W.R.P., Hünenberger P.H., Tironi I.G., Mark A.E., Billeter S.R., Fennen J., Torda A.E., Huber T., Krüger P., and van Gunsteren W.F. J. Phys. Chem. A 103 (1999) 3596-3607
49. Shirts M.R., and Pande V.S. J. Chem. Phys. 122 (2005) 144107
50. Shirts M.R., Pitera J.W., Swope W.C., and Pande V.S. J. Chem. Phys. 119 (2003) 5740 10.1063/11587119
51. Sonne J., Jensen M.O., Hansen F.Y., Hemmingsen L., and Peters G.H. Biophys. J. 92 (2007) 4157-4167
52. Sonne J., Kandt C., Peters G.H., Hansen F.Y., Jensen M.O., and Tieleman D.P. Biophys. J. 92 (2007) 2727-2734
53. Tieleman D.P., Berendsen H.J., and Sansom M.S. Biophys. J. 76 (1999) 1757-1769
54. Tieleman D.P., Hess B., and Sansom M.S.P. Biophys. J. 83 (2002) 2393-2407
55. Tieleman D.P., MacCallum J.L., Ash W.L., Kandt C., Xu Z., and Monticelli L. J. Phys. Condens. Matter 18 (2006) S1221-S1234
56. Tieleman D.P., Marrink S.J., and Berendsen H.J. Biochim. Biophys. Acta 1331 (1997) 235-270
57. Tieleman D.P., Sansom M.S., and Berendsen H.J. Biophys. J. 76 (1999) 40-49
58. van Gunsteren W.F., Billeter S.R., Eising A.A., Hünenberger P.H., Krüger P., Mark A.E., Scott W.R.P., and Tironi I.G. Biomolecular Simulation: The GROMOS96 Manual and User Guide (1996), Vdf Hochschulverlag AG an der ETH Zürich, Zürich
59. Vigh L., Escriba P.V., Sonnleitner A., Sonnleitner M., Piotto S., Maresca B., Horvath I., and Harwood J.L. Prog. Lipid Res. 44 (2005) 303-344
60. Villa A., and Mark A.E. J. Comput. Chem. 23 (2002) 548-553
61. Wohlert J., and Edholm O. J. Chem. Phys. 125 (2006) 204703
62. Wolfenden R. J. Gen. Physiol. 129 (2007) 357-362
63. Xu Z.T., Luo H.H., and Tieleman D.P. J. Comput. Chem. 28 (2007) 689-697