Location, tilt, and binding: A molecular dynamics study of voltage-sensitive dyes in biomembranes

Journal of Physical Chemistry B

Volumn 113, Issue 48, 2009, Pages 15807-15819

  Hinner, Marlon J ^a,b   Marrink, Siewert J ^a   De Vries, Alex H ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

AMPHIPHILES; FREE ENERGY; LIPIDS; MEMBRANES; MOLECULAR DYNAMICS; SIMULATORS;

ATOMISTIC SIMULATIONS; BINDING DATA; BINDING FREE ENERGY; BINDING MODES; BINDING STRENGTH; BIOMEMBRANES; BIOMOLECULAR SIMULATION; COARSE GRAINED MODELS; COARSE-GRAINED; CURRENT LIMITATION; EXPERIMENTAL DATA; FAST COMPUTATION; FREE ENERGY COMPUTATIONS; LIPID MEMBRANES; MEMBRANE BINDING; MOLECULAR PICTURES; PHARMACEUTICAL COMPOUNDS; STRUCTURAL CHANGE; STRUCTURAL VARIATIONS; UMBRELLA SAMPLING; VOLTAGE SENSITIVE DYES;

BINDING ENERGY;

EID: 72149121112     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp907981y     Document Type: Article

References (58)

1. Cohen, L. B.; Salzberg, B. M.; Grinvald, A. Annu. Rev. Neurosci. 1978, 1, 171.
2. Fluhler, E.; Burnham, V. G.; Loew, L. M. Biochemistry 1985, 24, 5749.
3. Grinvald, A.; Hildesheim, R. Nat. Rev. Neurosci. 2004, 5, 874.
4. Hübener, G.; Lambacher, A.; Fromherz, P. J. Phys. Chem. B 2003, 107, 7896.
5. Kuhn, B.; Fromherz, P. J. Phys. Chem. B 2003, 107, 7903.
6. Bedlack, R. S., Jr.; Wei, M.; Loew, L. M. Neuron 1992, 9, 393.
7. Gross, E.; Bedlack, R. S., Jr.; Loew, L. M. Biophys. J. 1994, 67, 208.
8. Buhler, R.; Sturmer, W.; Apell, H. J.; Lauger, P. J. Membr. Biol. 1991, 121, 141.
9. Betz, W. J.; Bewick, G. S. Science 1992, 255, 200.
10. Betz, W. J.; Mao, F.; Smith, C. B. Curr. Opin. Neurobiol. 1996, 6, 365.
11. Brumback, A. C.; Lieber, J. L.; Angleson, J. K.; Betz, W. J. Methods 2004, 33, 287.
12. Fromherz, P.; Röcker, C. Ber. Bunsen-Ges. Phys. Chem. 1994, 98, 128.
13. Hinner, M. J.; Hübener, G.; Fromherz, P. J. Phys. Chem. B 2004, 108, 2445.
14. Hinner, M. J.; Hübener, G.; Fromherz, P. ChemBioChem 2006, 7, 495.
15. Hinner, M. J. Genetically Targeted Staining of Cells with Voltage Sensitive Dyes using an Ecto-Enzyme. Ph.D. Thesis, Technische Universität München, 2005.
16. Pevzner, E.; Ehrenberg, B.; Loew, L. M. Spectrosc. Lett. 1993, 26, 1181.
17. Schote, U.; Seelig, J. Biochim. Biophys. Acta 1998, 1415, 135.
18. Lambacher, A.; Fromherz, P. J. Phys. Chem. B 2001, 105, 343.
19. Ries, R. S.; Choi, H.; Blunck, R.; Bezanilla, F.; Heath, J. R. J. Phys. Chem. B 2004, 108, 16040.
20. Visser, N. V.; Vanhoek, A.; Visser, A.; Frank, J.; Apell, H. J.; Clarke, R. J. Biochemistry 1995, 34, 11777.
21. Zouni, A.; Clarke, R. J.; Holzwarth, J. F. J. Phys. Chem. 1994, 98, 1732.
22. MacCallum, J. L.; Tieleman, D. P. Interactions between small molecules and lipid bilayers. In Curr. Top. Membr.; Feller, S. E., Ed.; Elsevier: 2008; Vol.60, pp 227-256.
23. Marrink, S. J.; Berendsen, H. J. C. J. Phys. Chem. 1994, 98, 4155.
24. MacCallum, J. L.; Tieleman, D. P. J. Am. Chem. Soc. 2006, 128, 125.
25. Ulander, J.; Haymet, A. D. J. Biophys. J. 2003, 85, 3475.
26. Marrink, S. J.; Berendsen, H. J. C. J. Phys. Chem. 1996, 100, 16729.
27. Bemporad, D.; Luttmann, C.; Essex, J. W. Biophys. J. 2004, 87, 1.
28. MacCallum, J. L.; Bennett, W. F.; Tieleman, D. P. J. Gen. Physiol. 2007, 129, 371.
29. Tieleman, D. P.; Marrink, S. J. J. Am. Chem. Soc. 2006, 128, 12462.
30. Marrink, S. J.; de Vries, A. H.; Harroun, T. A.; Katsaras, J.; Wassall, S. R. J. Am. Chem. Soc. 2008, 130, 10.
31. Bennett, W. F.; MacCallum, J. L.; Hinner, M. J.; Marrink, S. J.; Tieleman, D. P. J. Am. Chem. Soc. 2009, 131, 12714.
32. Voth, G. A. Coarse-Graining of Condensed Phase and Biomolecular Systems, 1st ed.; CRC Press: 2009.
33. Muller, M.; Katsov, K.; Schick, M. Phys. Rep.-Rev. Sec. Phys. Lett. 2006, 434, 113.
34. Venturoli, M.; Sperotto, M. M.; Kranenburg, M.; Smit, B. Phys. Rep.-Rev. Sec. Phys. Lett. 2006, 437, 1.
35. Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; de Vries, A. H. J. Phys. Chem. B 2007, 111, 7812.
36. Oostenbrink, C.; Villa, A.; Mark, A. E.; Van Gunsteren, W. F. J. Comput. Chem. 2004, 25, 1656.
37. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187.
38. Van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701.
39. http://www.gromacs.org/.
40. Van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; Verlag der Fachvereine Hochschulverlag AG an der ETH Zurich: Zürich, 1996.
41. Thole, B. T.; Van Duijnen, P. T. Theor. Chim. Acta 1983, 63, 209.
42. GAMESS-UK is a package of ab initio programs. See: http://www.cfs.dl.ac. uk/gamess-uk/index.shtml. Guest, M. F.; Bush, I. J.; Van Dam, H. J. J.; Sherwood, P.; Thomas, J. M. H.; Van Lenthe, J. H.; Havenith, R. W. A.; Kendrick, J. Mol. Phys. 2005, 103, 719.
43. The POPC topology used in this work represents a stage in the development of a GROMOS 53A6 lipid library with modified parameters that reproduce the phase transition behavior of a wide range of lipids.
44. Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; D. Reidel Publishing Company: Dordrecht, The Netherlands, 1981; pp 331-342.
45. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463.
46. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952.
47. Van Gunsteren, W. F.; Berendsen, H. J. C. Angew. Chem., Int. Ed. Engl. 1990, 29, 992.
48. Tironi, I. G.; Sperb, R.; Smith, P. E.; Van Gunsteren, W. F. J. Chem. Phys. 1995, 102, 5451.
49. Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
50. Marrink, S. J.; de Vries, A. H.; Mark, A. E. J. Phys. Chem. B 2004, 108, 750.
51. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011.
52. Lasch, J. Biochim. Biophys. Acta 1995, 1241, 269.
53. Monticelli, L.; Kandasamy, S. K.; Periole, X.; Larson, R. G.; Tieleman, D. P.; Marrink, S. J. J. Chem. Theory Comput. 2008, 4, 819.
54. Bammel, B. P.; Hamilton, D. D.; Haugland, R. P.; Hopkins, H. P.; Schuette, J.; Szalecki, W.; Smith, J. C. Biochim. Biophys. Acta 1990, 1024, 61.
55. Rusu, C. F.; Lanig, H.; Othersen, O. G.; Kryschi, C.; Clark, T. J. Phys. Chem. B 2008, 112, 2445.
56. Grinvald, A.; Hildesheim, R.; Farber, I. C.; Anglister, L. Biophys. J. 1982, 39, 301.
57. Rohr, S.; Salzberg, B. M. Biophys. J. 1994, 67, 1301.
58. Rowe, E. S.; Zhang, F.; Leung, T. W.; Parr, J. S.; Guy, P. T. Biochemistry 1998, 37, 2430.