Distribution and favorable binding sites of pyrroloquinoline and its analogues in a lipid bilayer studied by molecular dynamics simulations

Biophysical Chemistry

Volumn 136, Issue 2-3, 2008, Pages 128-135

  Kyrychenko, Alexander ^a   Waluk, Jacek ^b  

^a V N KARAZIN KHARKIV NATIONAL UNIVERSITY   (Ukraine)

^b INSTITUTE OF PHYSICAL CHEMISTRY   (Poland)

Author keywords

Fluorescence probe; Lipid bilayer; Molecular dynamics simulation; Proton transfer

Indexed keywords

11H DIPYRIDO[2,3 A]CARBAZOLE; 1H PYRROLO[3,2 H]QUINOLINE; 7 AZAINDOLE; CARBAZOLE DERIVATIVE; DIPALMITOYLPHOSPHATIDYLCHOLINE; INDOLE DERIVATIVE; PYRROLOQUINOLINE; QUINOLINE DERIVATIVE;

ARTICLE; BINDING SITE; DIPOLE; FLUORESCENCE; HYDROGEN BOND; HYDROPHOBICITY; LIPID BILAYER; MEMBRANE BINDING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTON TRANSPORT;

BINDING SITES; COMPUTER SIMULATION; HYDROGEN BONDING; LIPID BILAYERS; MOLECULAR STRUCTURE; PROTONS; PYRROLES; QUINOLINES; SOLVENTS; WATER;

EID: 46049106926     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2008.05.006     Document Type: Article

References (64)

1. Waluk J. Hydrogen-bonding-induced phenomena in bifunctional heteroazaaromatics. Acc. Chem. Res. 36 (2003) 832-838
2. Herbich J., Dobkowski J., Thummel R.P., Henge V., and Waluk J. Intermolecular excited-state double proton transfer in dipyridocarbazole:alcohol complexes. J. Phys. Chem., A 101 (1997) 5839-5845
3. Kyrychenko A., Herbich J., Izydorzak M., Gil M., Dobkowski J., Wu F.Y., Thummel R.P., and Waluk J. Photoinduced double proton transfer: inter- and intramolecular cases. Isr. J. Chem. 39 (1999) 309-318
4. Kyrychenko A., Herbich J., Izydorzak M., Wu F., Thummel R.P., and Waluk J. Role of ground state structure in photoinduced tautomerization in bifunctional proton donor-acceptor molecules: 1H-Pyrrolo[3,2-h]quinoline and related compounds. J. Am. Chem. Soc. 121 (1999) 11179-11188
5. del Valle J.C., Dominguez E., and Kasha M. Competition between dipolar relaxation and double proton transfer in the electronic spectroscopy of pyrroloquinolines. J. Phys. Chem., A 103 (1999) 2467-2475
6. Marks D., Zhang H., Borowicz P., Waluk J., and Glasbeek M. (Sub)picosecond fluorescence upconversion studies of intermolecular proton transfer of dipyrido[2,3-a:3',2'-i]carbazole and related compounds. J. Phys. Chem., A 104 (2000) 7167-7175
7. Kyrychenko A., Stepanenko Y., and Waluk J. Molecular dynamics and DFT studies of intermolecular hydrogen bonds between bifunctional heteroazaaromatic molecules and hydroxylic solvents. J. Phys. Chem., A 104 (2000) 9542-9555
8. Kijak M., Zielińska A., Thummel R.P., Herbich J., and Waluk J. Photoinduced double proton transfer in water complexes of 1H-pyrrolo[3,2-h]quinoline and dipyrido[2,3-a:3',2'-i]carbazole. Chem. Phys. Lett. 366 (2002) 329-335
9. Herbich J., Kijak M., Luboradzki R., Gil M., Zielińska A., Hu Y.Z., Thummel R.P., and Waluk J. In search for phototautomerization in solid dipyrido[2,3-a:3',2'-i] carbazole. J. Photochem. Photobiol., A Chem. 154 (2002) 61-68
10. Kyrychenko A., and Waluk J. Excited-state proton transfer through water bridges and structure of hydrogen-bonded complexes in 1H-pyrrolo[3,2-h]quinoline: adiabatic time-dependent density functional theory study. J. Phys. Chem., A 110 (2006) 11958-11967
11. Taylor C.A., El-Bayoumi M.A., and Kasha M. Excited-state two proton tautomerism in hydrogen-bonded N-heterocyclic base pairs. Proc. Natl. Acad. Sci. U. S. A. 63 (1969) 253-260
12. Avouris P., Yang L.L., and El-Bayoumi M.A. Excited-state interactions of 7-azaindole with alcohol and water. Photochem. Photobiol. 24 (1976) 211-216
13. Chou P.-T. The host/guest type of excited-state proton transfer; a general review. J. Chin. Chem. Soc. 48 (2001) 651-682
14. Wei C.-Y., Yu W.-S., Chou P.-T., Hung F.-T., Chang C.-P., and Lin T.-C. Conjugated dual hydrogen-bond mediating proton-transfer reaction in 3-hydroxyisoquinoline. J. Phys. Chem., B 102 (1998) 1053-1064
15. Chou P.-T., Wei C.-Y., Wang C.R.C., Hung F.-T., and Chang C.-P. Proton-transfer tautomerism of 7-hydroxyquinolines mediated by hydrogen-bonded complexes. J. Phys. Chem., A 103 (1999) 1939-1949
16. Geerlings J.D., and Varma C.A.G.O. Active participation of solvent molecules in photoinduced enol-keto tautomerisation of 7-hydroxyquinoline with a mobile proton carrier as substituent. J. Photochem. Photobiol., A Chem. 129 (1999) 129-135
17. Kohtani S., Tagami A., and Nakagaki N. Excited-state proton transfer of 7-hydroxyquinoline in a non-polar medium: mechanism of triple proton transfer in the hydrogen-bonded system. Chem. Phys. Lett. 316 (2000) 88-93
18. n clusters. J. Phys. Chem., A 106 (2002) 5591-5599
19. Tanner C., Thut M., Steinlin A., Manca C., and Leutwyler S. Excited-state hydrogen-atom transfer along solvent wires: water molecules stop the transfer. J. Phys. Chem., A 110 (2006) 1758-1766
20. Kwon O.H., Kim T.G., Lee Y.S., and Jang D.J. Biphasic tautomerization dynamics of excited 7-hydroxyquinoline in reverse micelles. J. Phys. Chem., B 110 (2006) 11997-12004
21. Angulo G., Organero J.A., Carranza M.A., and Douhal A. Probing the behavior of confined water by proton-transfer reactions. J. Phys. Chem., B 110 (2006) 24231-24237
22. Herbich J., Waluk J., Thummel R.P., and Hung C.Y. Mechanisms of fluorescence quenching by hydrogen-bonding in various azaaromatics. J. Photochem. Photobiol., A Chem. 80 (1994) 157-160
23. Herbich J., Hung C.Y., Thummel R.P., and Waluk J. Solvent controlled excited-state behavior: 2-(2'-pyridyl) indoles in alcohols. J. Am. Chem. Soc. 118 (1996) 3508-3518
24. Kyrychenko A., Herbich J., Wu F., Thummel R.P., and Waluk J. Solvent-induced syn-anti rotamerization of 2-(2'-pyridyl) indole and the structure of its alcohol complexes. J. Am. Chem. Soc. 122 (2000) 2818-2827
25. Smedarchina Z., Siebrand W., Fernández-Ramos A., Gorb L., and Leszczynski J. A direct-dynamics study of proton transfer through water bridges in guanine and 7-azaindole. J. Chem. Phys. 112 (2000) 566-573
26. Fernández-Ramos A., Smedarchina Z., Siebrand W., and Zgierski M. Dynamics of the water-catalyzed phototautomerization of 7-azaindole. J. Chem. Phys. 114 (2001) 7510-7526
27. Nosenko Y., Kunitski M., Thummel R.P., Kyrychenko A., Herbich J., Waluk J., Riehn C., and Brutschy B. Detection and structural characterization of clusters with ultrashort-lived electronically excited states: IR absorption detected by femtosecond. J. Am. Chem. Soc. 128 (2006) 10000-10001
28. Nosenko Y., Kyrychenko A., Thummel R.P., Waluk J., Brutschy B., and Herbich J. Fluorescence quenching in cyclic hydrogen-bonded complexes of 1H-pyrrolo[3,2-h]quinoline with methanol: cluster size effect. Phys. Chem. Chem. Phys. 9 (2007) 3276-3285
29. n = 1,2 complexes. J. Phys. Chem., A 112 (2008) 1150-1156
30. Chattopadhyay A., and Mukherjee S. Red edge excitation shift of a deeply embedded membrane probe: implications in water penetration in the bilayer. J. Phys. Chem., B 103 (1999) 8180-8185
31. Ira, and Krishnamoorthy G. Probing the link between proton transport and water content in lipid membranes. J. Phys. Chem., B 105 (2001) 1484-1488
32. Klymchenko A.S., Duportail G., Demchenko A.P., and Mély Y. Bimodal distribution and fluorescence response of environment-sensitive probes in lipid bilayers. Biophys. J. 86 (2004) 2929-2941
33. Klymchenko A.S., Mély Y., Demchenko A.P., and Duportail G. Simultaneous probing of hydration and polarity of lipid bilayers with 3-hydroxyflavone fluorescent dyes. Biochim. Biophys. Acta 1665 (2004) 6-19
34. Lala A.K. Fluorescent and photoactivable probes in depth-dependent analysis of membranes. Chem. Phys. Lipids 116 (2002) 177-188
35. Maier O., Oberle V., and Hoekstra D. Fluorescent lipid probes: some properties and applications (a review). Chem. Phys. Lipids 116 (2002) 3-18
36. Jurkiewicz P., Sýkora J., Olżyńska A., Humpoličkova J., and Hof M. Solvent relaxation in phospholipid bilayers: principles and recent applications. J. Fluoresc. 15 (2005) 883-893
37. Tielaman D.P., Marrink S.J., and Berendsen H.J.C. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta 1331 (1997) 235-270
38. MacCallum J., and Tieleman D.P. Computer simulation of the distribution of hexane in a lipid bilayer: spatially resolved free energy, entropy, and enthalpy profiles. J. Am. Chem. Soc. 128 (2005) 125-130
39. Tieleman D.P. Computer simulations of transport through membranes: passive diffusion, pores, channels and transporters. Proceedings of Australian Physiological Society vol. 37 (2006) 15-27
40. Ulander J., and Haymet A.D.J. Permeation across hydrated DPPC lipid bilayers: simulation of the titrable amphiphilic drug valproic acid. Biophys. J. 85 (2003) 3475-3484
41. Xiang T.-X., and Anderson B.D. Liposomal drug transport: a molecular perspective from molecular dynamics simulations in lipid bilayers. Adv. Drug Deliv. Rev. 58 (2006) 1357-1378
42. 2H-NMR study and molecular dynamics simulation of the location, alignment, and mobility of pyrene in bilayers. Biophys. J. 88 (2005) 1818-1827
43. Čurdová J., Čapková P., Plášek J., Repáková J., and Vattulainen I. Free pyrene probes in gel and fluid membranes: perspective through atomistic simulations. J. Phys. Chem., B 111 (2007) 3640-3650
44. Kaiser R.D., and London E. Location of diphenylhexatriene (DPH) and its derivatives within membranes: comparison of different fluorescence quenching analyses of membrane depth. Biochemistry 37 (1998) 8180-8190
45. Repáková J., Čapková P., Holopainen J.M., and Vattulainen I. Distribution, orientation, and dynamics of DPH probes in DPPC bilayer. J. Phys. Chem., B 108 (2004) 13438-13448
46. Bemporad D., Essex J.W., and Luttmann C. Permeation of small molecules through a lipid bilayer: a computer simulation study. J. Phys. Chem., B 108 (2004) 4875-4884
47. Högberg C.J., Maliniak A., and Lyubartsev A.P. Dynamical and structural properties of charged and uncharged lidocaine in a lipid bilayer. Biophys. Chem. 125 (2007) 416-424
48. Koubi L., Tarek M., Klein M.L., and Scharf D. Distribution of halothane in a dipalmitoylphosphatidylcholine bilayer from molecular dynamics calculations. Biophys. J. 78 (2000) 800-811
49. Koubi L., Saiz L., Tarek M., Scharf D., and Klein M.L. Influence of anesthetic and nonimmobilizer molecules on the physical properties of a polyunsaturated lipid bilayer. J. Phys. Chem., B 107 (2003) 14500-14508
50. Yau W.M., Wimley W.C., Gawrisch K., and White S.H. The preference of tryptophan for membrane interfaces. Biochemistry 37 (1998) 14713-14718
51. Grossfield A., and Woolf T.B. Interaction of tryptophan analogs with POPC lipid bilayers investigated by molecular dynamics calculations. Langmuir 18 (2002) 198-210
52. Chattopadhyay A., Arora A., and Kelkar D.A. Dynamics of a membrane-bound tryptophan analog in environments of varying hydration: a fluorescence approach. Eur. Biophys. J. 35 (2005) 62-71
53. Gaede H.C., Yau W.M., and Gawrisch K. Electrostatic contributions to indole-lipid interactions. J. Phys. Chem., B 109 (2005) 13014-13023
54. Tieleman D.P., and Berendsen H.J.C. Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. J. Chem. Phys. 105 (1996) 4871-4880
55. Hermans J., Berendsen H.J.C., van Gunsteren W.F., and Postma J.P.M. A consistent empirical potential for water-protein interactions. Biopolymers 23 (1984) 1513-1518
56. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Dinola A., and Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
57. Darden T., York D., and Pedersen L. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
58. Anézo C., de Vries A.H., Höltje H.D., Tieleman D.P., and Marrink S.J. Methodological issues in lipid bilayer simulations. J. Phys. Chem., B 107 (2003) 9424-9433
59. Hees B., Bekker H., Berendsen H.J.C., and Fraaije J.G.E.M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18 (1997) 1463-1472
60. Lindahl E., Hess B., and van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7 (2001) 306-317
61. de Vries A.H., Chandrasekhar I., van Gunsteren W.F., and Hünenberger P.H. Molecular dynamics simulations of phospholipid bilayers: influence of artificial periodicity, system size, and simulation time. J. Phys. Chem., B 109 (2005) 11643-11652
62. Esbjörner E.K., Caesar C.E.B., Albinsson B., Lincoln P., and Nordén B. Tryptophan orientation in model membranes. Biochem. Biophys. Res. Commun. 361 (2007) 645-650
63. Norman K.E., and Nymeyer H. Indole localization in lipid membranes revealed by molecular simulation. Biophys. J. 91 (2006) 2046-2054
64. MacCallum J.L., Bennett W.F.D., and Tieleman D.P. Distribution of amino acids in a lipid bilayer from computer simulations. Biophys. J. 94 (2008) 3393-3404