Partitioning and localization of environment-sensitive 2-(2′-pyridyl) - and 2-(2′-pyrimidyl)-indoles in lipid membranes: A joint refinement using fluorescence measurements and molecular dynamics simulations

Journal of Physical Chemistry B

Volumn 114, Issue 42, 2010, Pages 13574-13584

  Kyrychenko, Alexander ^a,b,c   Wu, Feiyue ^d   Thummel, Randolph P ^d   Waluk, Jacek ^e   Ladokhin, Alexey S ^b  

^a V N KARAZIN KHARKIV NATIONAL UNIVERSITY   (Ukraine)

^b UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

^c Ukrainian American Laboratory of Computational Chemistry   (Ukraine)

^d University of Houston   (United States)

^e INSTITUTE OF PHYSICAL CHEMISTRY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; HYDROGEN; HYDROGEN BONDS; LIPID BILAYERS; LIPOSOMES; MOLECULAR DYNAMICS; MOLECULES; PHOSPHOLIPIDS; SOLUTIONS;

AQUEOUS ENVIRONMENT; AQUEOUS SOLUTIONS; ATOMISTIC MOLECULAR DYNAMICS; BI-LAYER; BLUE SHIFT; BULK WATER; EMISSION MAXIMA; ENERGY PROFILE; ENVIRONMENT-SENSITIVE; EQUILIBRIUM CONDITIONS; FLUORESCENCE ENHANCEMENT; FLUORESCENCE MEASUREMENTS; FLUORESCENCE QUENCHING; FREE REGION; HYDROGEN BONDING INTERACTIONS; HYDROGEN BONDINGS; INDOLE DERIVATIVES; LIPID COMPOSITION; LIPID MEMBRANES; LOCAL STRUCTURE; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; NON-POLAR; PASSIVE DIFFUSIONS; PHOSPHOLIPID VESICLES; POLAR APROTIC SOLVENT; PROBE MOLECULES; PYRIDYL; SOLVATION DYNAMICS; STEADY-STATE FLUORESCENCE INTENSITY; UMBRELLA SAMPLING; WATER MOLECULE;

FLUOROPHORES;

EID: 77958502212     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp106981c     Document Type: Article

References (76)

1. Taylor, C. L.; El-Bayoumi, M. A.; Kasha, M. Proc. Natl. Acad. Sci. U.S.A. 1969, 63, 253-260
2. Zimmer, M. Chem. Rev. 2002, 102, 759-781
3. Pakhomov, A. A.; Martynov, V. I. Chem. Biol. 2008, 15, 755-764
4. Vendrell, O.; Gelabert, R.; Moreno, M.; Lluch, J. M. J. Phys. Chem. B 2008, 112, 13443-13452
5. Herbich, J.; Hung, C. Y.; Thummel, R. P.; Waluk, J. J. Am. Chem. Soc. 1996, 118, 3508-3518
6. Waluk, J. Acc. Chem. Res. 2003, 36, 832-838
7. Kyrychenko, A.; Herbich, J.; Wu, F.; Thummel, R. P.; Waluk, J. J. Am. Chem. Soc. 2000, 122, 2818-2827
8. Kijak, M.; Petkova, I.; Toczek, M.; Wiosna-Sałyga, G.; Zielińska, A.; Herbich, J.; Thummel, R. P.; Waluk, J. Acta Phys. Pol., A 2007, 112, S105-S120
9. Petkova, I.; Mudadu, M. S.; Singh, A.; Thummel, R. P.; van Stokkum, I. H. M.; Buma, W. J.; Waluk, J. J. Phys. Chem. A 2007, 111, 11400-11409
10. Wiosna-Sałyga, G.; Nosenko, Y.; Kijak, M.; Thummel, R. P.; Brutschy, B.; Waluk, J. J. Phys. Chem. A 2010, 114, 3270-3279
11. Nosenko, Y.; Wiosna-Sałyga, G.; Kunitski, M.; Petkova, I.; Singh, A.; Buma, W. J.; Thummel, R. P.; Brutschy, B.; Waluk, J. Angew. Chem., Int. Ed. 2008, 47, 6037-6040
12. Vetokhina, V.; Kijak, M.; Wiosna-Sałyga, G.; Thummel, R. P.; Herbich, J.; Waluk, J. Photochem. Photobiol. Sci. 2010, 9, 923-930
13. Kyrychenko, A.; Waluk, J. In Challenges and Advances in Computational Chemistry and Physics; Kinetics and Dynamics: from Nano- to Bio-Scale; Paneth, P.; Dybala-Defratyka, A., Eds.; Springer Science+Business Media B.V.: New York, 2010, Vol. 12, pp 35 - 75.
14. Kyrychenko, A.; Herbich, J.; Izydorzak, M.; Gil, M.; Dobkowski, J.; Wu, F. Y.; Thummel, R. P.; Waluk, J. Isr. J. Chem. 1999, 39, 309-318
15. Nosenko, Y.; Kunitski, M.; Riehn, C.; Thummel, R. P.; Kyrychenko, A.; Herbich, J.; Waluk, J.; Brutschy, B. J. Phys. Chem. A 2008, 112, 1150-1156
16. Kyrychenko, A.; Herbich, J.; Izydorzak, M.; Wu, F.; Thummel, R. P.; Waluk, J. J. Am. Chem. Soc. 1999, 121, 11179-11188
17. Kijak, M.; Zielińska, A.; Thummel, R. P.; Herbich, J.; Waluk, J. Chem. Phys. Lett. 2002, 366, 329-335
18. Smirnov, A. V.; English, D. S.; Rich, R. L.; Lane, J.; Teyton, L.; Schwabacher, A. W.; Luo, S.; Thornburg, R. W.; Petrich, J. W. J. Phys. Chem. B 1997, 101, 2758-2769
19. Kelepouris, L.; Blanchard, G. J. J. Phys. Chem. B 2002, 106, 6600-6608
20. Kelepouris, L.; Blanchard, G. J. J. Phys. Chem. B 2003, 107, 1079-1087
21. Mukherjee, T. K.; Ahuja, P.; Koner, A. L.; Datta, A. J. Phys. Chem. A 2005, 109, 12567-12573
22. Mukherjee, T. K.; Panda, D.; Datta, A. J. Phys. Chem. A 2005, 109, 18895-18901
23. Kwon, O. H.; Jang, D. J. J. Phys. Chem. B 2005, 109, 8049-8052
24. Kwon, O. H.; Jang, D. J. J. Phys. Chem. B 2005, 109, 20479-20484
25. Demchenko, A. P.; Mély, Y.; Duportail, G.; Klymchenko, A. S. Biophys. J. 2010, 96, 3461-3470
26. Tieleman, D. P. Proc. Aust. Physiol. Soc. 2006, 37, 3715-27
27. Berkowitz, M. L.; Bostick, D. L.; Pandit, S. Chem. Rev. 2006, 106, 1527-1539
28. Vácha, R.; Siu, S. W. I.; Petrov, M.; Böckmann, R. A.; Jurkiewicz, P.; Barucha-Kraszewska, J.; Hof, M.; Berkowitz, M. L.; Jungwirth, P. J. Phys. Chem. B 2009, 113, 7235-7243
29. Vácha, R.; Jurkiewicz, P.; Petrov, M.; Berkowitz, M. L.; Böckmann, R. A.; Barucha-Kraszewska, J.; Hof, M.; Jungwirth, P. J. Phys. Chem. B 2010, 114, 9504-9509
30. Xiang, T.-X.; Anderson, B. D. Adv. Drug Delivery Rev. 2006, 58, 1357-1378
31. Boggara, M. B.; Krishnamoorti, R. Biophys. J. 2010, 98, 586-595
32. Högberg, C. J.; Maliniak, A.; Lyubartsev, A. P. Biophys. Chem. 2007, 125, 416-424
33. Koubi, L.; Tarek, M.; Klein, M. L.; Scharf, D. Biophys. J. 2000, 78, 800-811
34. Koubi, L.; Saiz, L.; Tarek, M.; Scharf, D.; Klein, M. L. J. Phys. Chem. B 2003, 107, 14500-14508
35. Li, C.; Yi, M.; Hu, J.; Zhou, H.-X.; Cross, T. A. Biophys. J. 2008, 94, 1295-1302
36. Chew, C. F.; Guy, A.; Biggin, P. C. Biophys. J. 2008, 95, 5627-5636
37. dos Santos, D. J. V. A.; Eriksson, L. A. Biophys. J. 2006, 91, 2464-2474
38. MacCallum, J.; Tieleman, D. P. J. Am. Chem. Soc. 2005, 128, 125-130
39. Hoff, B.; Strandberg, E.; Ulrich, A. S.; Tieleman, D. P.; Posten, C. Biophys. J. 2005, 88, 1818-1827
40. Repáková, J.; Holopainen, J. M.; Karttunen, M.; Vattulainen, I. J. Phys. Chem. B 2006, 110, 15403-15410
41. Čurdová, J.; Čapková, P.; Plášek, J.; Repáková, J.; Vattulainen, I. J. Phys. Chem. B 2007, 111, 3640-3650
42. Repáková, J.; Čapková, P.; Holopainen, J. M.; Vattulainen, I. J. Phys. Chem. B 2004, 108, 13438-13448
43. Fraňová, M.; Repáková, J.; Čapková, P.; Holopainen, J. M.; Vattulainen, I. J. Phys. Chem. B 2010, 114, 2704-2711
44. Loura, L. M. S.; Ramalho, J. P. P. Biochim. Biophys. Acta 2007, 1768, 467-478
45. Loura, L. M. S.; Fernandes, F.; Fernandes, A. C.; Ramalho, J. P. P. Biochim. Biophys. Acta 2008, 1778, 491-501
46. Hinner, M. J.; Marrink, S. J.; de Vries, A. H. J. Phys. Chem. B 2009, 113, 15807-15819
47. Skaug, M. J.; Longo, M. L.; Faller, R. J. Phys. Chem. B 2009, 113, 8758-8766
48. Kyrychenko, A. Chem. Phys. Lett. 2010, 485, 95-99
49. Grossfield, A.; Woolf, T. B. Langmuir 2002, 18, 198-210
50. Norman, K. E.; Nymeyer, H. Biophys. J. 2006, 91, 2046-2054
51. Kyrychenko, A.; Waluk, J. Biophys. Chem. 2008, 136, 128-135
52. Hope, M. J.; Bally, M. B.; Mayer, L. D.; Janoff, A. S.; Cullis, P. R. Chem. Phys. Lipids 1986, 40, 89-107
53. Mayer, L. D.; Hope, M. J.; Cullis, P. R. Biochim. Biophys. Acta 1986, 858, 161-168
54. Bartlett, G. R. J. Biol. Chem. 1959, 234, 466-468
55. Thummel, R. P.; Hegde, V. J. Org. Chem. 1989, 54, 1720-1725
56. Wu, F.; Hardesty, J.; Thummel, R. P. J. Org. Chem. 1998, 63, 4055-4061
57. Berger, O.; Edholm, O.; Jähnig, F. Biophys. J. 1997, 72, 2002-2013
58. Kyrychenko, A.; Stepanenko, Y.; Waluk, J. J. Phys. Chem. A 2000, 104, 9542-9555
59. van der Spoel, D.; Lindahl, E.; Hess, B.; van Buuren, A. R.; Apol, E.; Meulenhoff, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Feenstra, K. A.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual version 3.3, 2005; www.gromacs.org.
60. Hermans, J.; Berendsen, H. J. C.; van Gunsteren, W. F.; Postma, J. P. M. Biopolymers 1984, 23, 1513-1518
61. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690
62. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092
63. Hees, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463-1472
64. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-317
65. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701-1718
66. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021
67. Bergman, D. L.; Laaksonen, L.; Laaksonen, A. J. Mol. Graph. Model. 1997, 15, 301 - 306.
68. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graph. 1996, 14, 33-38
69. Kyrychenko, A.; Waluk, J. J. Phys. Chem. A 2006, 110, 11958-11967
70. Nosenko, Y.; Kunitski, M.; Thummel, R. P.; Kyrychenko, A.; Herbich, J.; Waluk, J.; Riehn, C.; Brutschy, B. J. Am. Chem. Soc. 2006, 128, 10000-10001
71. Nosenko, Y.; Kyrychenko, A.; Thummel, R. P.; Waluk, J.; Brutschy, B.; Herbich, J. Phys. Chem. Chem. Phys. 2007, 9, 3276-3285
72. White, S. H.; Wimley, W. C.; Ladokhin, A. S.; Hristova, K. Methods Enzymol. 1998, 295, 62-87
73. Vijayan, R.; Biggin, P. C. Biophys. J.: Biophys. Lett. 2008, 95, L45-L47
74. Marrink, S. J.; Berendsen, H, J. C. J. Phys. Chem. 1994, 98, 4155-4168
75. Yau, W. M.; Wimley, W. C.; Gawrisch, K.; White, S. H. Biochem. 1998, 37, 14713-14718
76. MacCallum, J. L.; Bennett, W, F. D.; Tieleman, D. P. Biophys. J. 2008, 94, 3393-3404