On the orientation of a designed transmembrane peptide: Toward the right tilt angle?

Journal of the American Chemical Society

Volumn 129, Issue 49, 2007, Pages 15174-15181

  Özdirekcan, Suat ^a   Etchebest, Catherine ^b   Killian, J Antoinette ^a   Fuchs, Patrick F J ^b  

^a UTRECHT UNIVERSITY   (Netherlands)

^b INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; HYDROPHOBICITY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE;

AZIMUTHAL ROTATION; TILT ANGLES; TRANSMEMBRANE PEPTIDES;

PEPTIDES;

MEMBRANE PROTEIN; PEPTIDE;

ANISOTROPY; ARTICLE; CHEMICAL ANALYSIS; HYDROPHOBICITY; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PROTEIN STRUCTURE; SOLID STATE;

1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE; ALGORITHMS; COMPUTER SIMULATION; DIMYRISTOYLPHOSPHATIDYLCHOLINE; LIPID BILAYERS; MEMBRANE PROTEINS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; THERMODYNAMICS;

EID: 37049023237     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja073784q     Document Type: Article

References (52)

1. Isaiah, T.; Arkin, I. T.; Brunger, A. T. Biochim. Biophys. Acta 1998, 1429, 113-128.
2. Landolt-Marticorena, C.; Williams, K. A.; Deber, C. M.; Reithmeier, R. A. J. Mol. Biol. 1993, 229, 602-608.
3. Reithmeier, R. A. Curr. Opin. Struct. Biol. 1995, 5, 491-500.
4. Sakai, H.; Tsukihara, T. J. Biochem. (Tokyo) 1998, 124, 1051-1059.
5. von Heijne, G. Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 167-192.
6. Wallin, E.; Tsukihara, T.; Yoshikawa, S.; von Heijne, G.; Elofsson, A. Protein Sci. 1997, 6, 808-815.
7. Dumas, F.; Lebrun, M. C.; Tocanne, J. F. FEBS Lett. 1999, 458, 271-277.
8. Killian, J. A. Biochim. Biophys. Acta 1998, 1376, 401-415.
9. Lee, A. G. Biochim. Biophys. Acta. 2003, 1612, 1-40.
10. de Planque, M. R.; Killian, J. A. Mol. Membr. Biol. 2003, 20, 271-284.
11. Demmers, J. A.; van Duijn, E.; Haverkamp, J.; Greathouse, D. V.; Koeppe, R. E., II; Heck, A. J.; Killian, J. A. J. Biol. Chem. 2001, 276, 34501-34508.
12. Davis, J. H.; Clare, D. M.; Hodges, R. S.; Bloom, M. Biochemistry 1983, 22, 5298-5305.
13. de Planque, M. R.; Bonev, B. B.; Demmers, J. A.; Greathouse, D. V.; Koeppe, R. E., II; Separovic, F.; Watts, A.; Killian, J. A. Biochemistry 2003, 42, 5341-5348.
14. Killian, J. A. FEBS Lett. 2003, 555, 134-138.
15. Killian, J. A.; Nyholm, T. K. Curr. Opin. Struct. Biol. 2006, 16, 473-479.
16. Ren, J.; Lew, S.; Wang, J.; London, E. Biochemistry 1999, 38, 5905-5912.
17. Zhang, Y. P.; Lewis, R. N.; Hodges, R. S.; McElhaney, R. N. Biochemistry 1995, 34, 2362-2371.
18. de Planque, M. R.; Greathouse, D. V.; Koeppe, R. E., II; Schafer, H.; Marsh, D.; Killian, J. A. Biochemistry 1998, 37, 9333-9345.
19. Strandberg, E.; Özdirekcan, S.; Rijkers, D. T.; van der Wel, P. C.; Koeppe, R. E., II; Liskamp, R. M.; Killian, J. A. Biophys. J. 2004, 86, 3709-3721.
20. Özdirekcan, S.; Rijkers, D. T.; Liskamp, R. M.; Killian, J. A. Biochemistry 2005, 44, 1004-1012.
21. Goodyear, D. J.; Sharpe, S.; Grant, C. W.; Morrow, M. R. Biophys. J. 2005, 88, 105-117.
22. Im, W.; Brooks, C. L., III. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6771-6776.
23. Kandasamy, S. K.; Larson, R. G. Biophys. J. 2006, 90, 2326-2343.
24. Petrache, H. I.; Zuckerman, D. M.; Sachs, J. N.; Killian, J. A.; Koeppe, R. E.; Woolf, T. B. Langmuir 2002, 18, 1340-1351.
25. de Planque, M. R.; Goormaghtigh, E.; Greathouse, D. V.; Koeppe, R. E., II; Kruijtzer, J. A.; Liskamp, R. M.; de Kruijff, B.; Killian, J. A. Biochemistry 2001, 40, 5000-5010.
26. Nyholm, T. K.; Ozdirekcan, S.; Killian, J. A. Biochemistry 2007, 46, 1457-1465.
27. Sparr, E.; Ash, W. L.; Nazarov, P. V.; Rijkers, D. T.; Hemminga, M. A.; Tieleman, D. P.; Killian, J. A. J. Biol. Chem. 2005, 280, 39324-39331.
28. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43-56.
29. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317.
30. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. J. Comput. Chem. 2005, 26, 1701-1718.
31. Berger, O.; Edholm, O.; Jahnig, F. Biophys. J. 1997, 72, 2002-2013.
32. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Interaction models for water in relation to protein hydration. In Intermolecular Forces; Pullman, B., Ed.; Reidel: Dordrecht, 1981; pp 331-342.
33. van Gunsteren, W. F.; Berendsen, H. J. C. Groningen Molecular Simulation (GROMOS) Library Manual; Biomos: Groningen, 1987.
34. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463-1472.
35. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952-962.
36. Berendsen, H. J. C.; Postma, J. P. M.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
37. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. J. Chem. Phys. 1995, 102, 5451-5459.
38. Hunenberger, P. H.; van Gunsteren, W. F. J. Chem. Phys. 1998, 108, 6117-6134.
39. Smith, P. E.; van Gunsteren, W. F. J. Chem. Phys. 1994, 100, 3169-3174.
40. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092.
41. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
42. Anézo, C.; de Vries, A. H.; Höltje, H.-D.; Tieleman, D. P.; Marrink, S. J. J. Phys. Chem. B 2003, 107, 9424-9433.
43. van der Wel, P. C.; Strandberg, E.; Killian, J. A.; Koeppe, R. E., II. Biophys. J. 2002, 83, 1479-1488.
44. de Planque, M. R.; Kruijtzer, J. A.; Liskamp, R. M.; Marsh, D.; Greathouse, D. V.; Koeppe, R. E., II; de Kruijff, B.; Killian, J. A. J. Biol. Chem. 1999, 274, 20839-20846.
45. Naarmann, N.; Bilgicer, B.; Kumar, K.; Steinem, C. Biochemistry 2005, 44, 5188-5195.
46. Nielsen, R. D.; Che, K.; Gelb, M. H.; Robinson, B. H. J. Am. Chem. Soc. 2005, 127, 6430-6442.
47. Özdirekcan, S.; Nyholm, T.; Raja, M.; Rijkers, D.; Liskamp, R.; Killian, J. A. Biophys. J. 2007, in press.
48. Bond, P. J.; Holyoake, J.; Ivetac, A.; Khalid, S.; Sansom, M. S. J. Struct. Biol. 2007, 157, 593-605.
49. Ramamoorthy, A.; Kandasamy, S. K.; Lee, D. K.; Kidambi, S.; Larson, R. G. Biochemistry 2007, 46, 965-975.
50. Sengupta, D.; Meinhold, L.; Langosch, D.; Ullmann, G. M.; Smith, J. C. Proteins 2005, 58, 913-922.
51. Park, S. H.; Opella, S. J. J. Mol. Biol. 2005, 350, 310-318.
52. Gibbons, W. J., Jr.; Karp, E. S.; Cellar, N. A.; Minto, R. E.; Lorigan, G. A. Biophys. J. 2006, 90, 1249-1259.