The gramicidin ion channel: A model membrane protein

Biochimica et Biophysica Acta - Biomembranes

Volumn 1768, Issue 9, 2007, Pages 2011-2025

  Kelkar, Devaki A ^a   Chattopadhyay, Amitabha ^a  

^a CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

Gramicidin; Ion Channel; Lipid protein interaction; Membrane Interface; Tryptophan

Indexed keywords

GRAMICIDIN; ION CHANNEL; MEMBRANE PROTEIN; TRYPTOPHAN;

CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; DIMERIZATION; FLUORESCENCE; MEMBRANE CHANNEL; PRIORITY JOURNAL; PROTEIN LIPID INTERACTION; REVIEW; SPECTROSCOPY; X RAY ANALYSIS;

CELL MEMBRANE; GRAMICIDIN; ION CHANNEL GATING; ION CHANNELS; LIPID BILAYERS; MODELS, BIOLOGICAL;

EID: 34548481061     PISSN: 00052736     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbamem.2007.05.011     Document Type: Review

References (214)

1. Cooper E.C., and Jan L.Y. Ion channel genes and human neurological disease: recent progress, prospects and challenges. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 4759-4766
2. Jentsch T.J., Hübner C.A., and Fuhrmann J.C. Ion channels: function unravelled by dysfunction. Nat. Cell Biol. 6 (2004) 1039-1047
3. Stutts M.J., Canessa C.M., Olsen J.C., Hamrick M., Cohn J.A., Rossier B.C., and Boucher RC. CFTR as a cAMP-dependent regulator of sodium channels. Science 269 (1995) 847-850
4. Kornak U., Kasper D., Bösl M.R., Kaiser E., Schweizer M., Schulz A., Friedrich W., Delling G., and Jentsch T.J. Loss of the ClC-7 chloride channel leads to osteoporosis in mice and man. Cell 104 (2001) 205-215
5. + channel mutated in a form of dominant deafness, is expressed in the inner ear and the central auditory pathway. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 4333-4338
6. Cirelli C., Bushey D., Hill S., Kreber R., Ganetzky B., and Tononi G. Reduced sleep in Drosophila Shaker mutants. Nature 434 (2005) 1087-1092
7. Doyle D.A., Cabral J.M., Pfuetzner R.A., Kuo A., Gulbis J.M., Cohen S.L., Chait B.T., and MacKinnon R. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280 (1998) 69-77
8. Dutzler R., Campbell E.B., Cadene M., Chait B.T., and MacKinnon R. X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity. Nature 415 (2002) 287-294
9. + channel. Nature 423 (2003) 33-41
10. MacKinnon R. Nobel lecture. Potassium channels and the atomic basis of selective ion conduction. Biosci. Rep. 24 (2004) 75-100
11. Jackson M.B. Advances in ion channel structure. Trends Neurosci. 24 (2004) 291
12. Bezanilla F. The voltage-sensor structure in a voltage-gated channel. Trends. Biochem. Sci. 30 (2005) 166-168
13. + channels. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 5020-5025
14. Miloshevsky G.V., and Jordan P.C. Permeation in ion channels: the interplay of structure and theory. Trends Neurosci. 27 (2004) 308-314
15. Koeppe R.E., and Andersen O.S. Engineering the gramicidin channel. Annu. Rev. Biophys. Biomol. Struct. 25 (1996) 231-258
16. Sarges R., and Witkop B. The structure of valine- and isoleucine-gramicidin A. J. Am. Chem. Soc. 87 (1965) 2011-2020
17. Hladky S.B., and Haydon D.A. Ion transfer across lipid membranes in the presence of gramicidin A: I. Studies of the unit conductance channel. Biochim. Biophys. Acta 274 (1972) 294-312
18. Mukherjee S., and Chattopadhyay A. Motionally restricted tryptophan environments at the peptide-lipid interface of gramicidin channels. Biochemistry 33 (1994) 5089-5097
19. Segrest J.P., and Feldman R.J. Membrane proteins: amino acid sequence and membrane penetration. J. Mol. Biol. 87 (1974) 853-858
20. Kemp G., Jacobson K.A., and Wennera C.E. Solution and interfacial properties of gramicidin pertinent to its effect on membranes. Biochim. Biophys. Acta 255 (1972) 493-501
21. Dubos R.J., and Cattaneo C. Studies on a bactericidal agent extracted from a soil bacillus: III. Preparation and activity of a protein-free fraction. J. Exp. Med. 70 (1939) 249-256
22. Hotchkiss R.D., and Dubos R.J. Bactericidal fractions from an aerobic sporulating bacillus. J. Biol. Chem. 136 (1940) 803-804
23. Moberg C.L., and Cohn Z.A. René Jules Dubos. Sci. Am. 264 (1991) 66-74
24. Van Epps H.L. René Dubos: unearthing antibiotics. J. Exp. Med. 203 (2006) 259
25. Killian J.A. Gramicidin and gramicidin-lipid interactions. Biochim. Biophys. Acta 1113 (1992) 391-425
26. Mitchell J.B.O., and Smith J. d-amino acid residues in peptides and proteins. Proteins 50 (2003) 563-571
27. Andersen O.S., Saberwal G., Greathouse D.V., and Koeppe R.E. Gramicidin channels a solvable membrane-protein folding problem. Ind. J. Biochem. Biophys. 33 (1996) 331-342
28. Edwards S., Corry B., Kuyucak S., and Chung S.-H. Continuum electrostatics fails to describe ion permeation in the gramicidin channel. Biophy. J. 83 (2002) 1348-1360
29. Chung S.-H., and Kuyucak S. Recent advances in ion channel research. Biochim. Biophys. Acta 1565 (2002) 267-286
30. Roux B. Computational studies of the gramicidin channel. Acc. Chem. Res. 35 (2002) 366-375
31. Allen T.W., Andersen O.S., and Roux B. Molecular dynamics-potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Biophys. Chem. 124 (2006) 251-267
32. (l,d) helix. Proc. Natl. Acad. Sci. U. S. A. 68 (1971) 672-676
33. Ramachandran G.N., and Chandrasekaran R. Conformation of peptide chains containing both l- and d-residues: part I-helical structures with alternating l- and d-residues with special reference to the ld-ribbon and the ld-helices. Indian J. Biochem. Biophys. 9 (1972) 1-11
34. Veatch W.R., Fossel E.T., and Blout E.R. The conformation of gramicidin A. Biochemistry 13 (1974) 5249-5256
35. Wallace B.A. Gramicidin channels and pores. Annu. Rev. Biophys. Biophys. Chem. 19 (1990) 127-157
36. Hotchkiss R.D., and Dubos R.J. Fractionation of the bactericidal agent from cultures of a soil bacillus. J. Biol. Chem. 132 (1940) 791-792
37. Koeppe R.E., Hodgson K.O., and Stryer L. Helical channels in crystals of gramicidin a and of a cesium-gramicidin a complex: an X-ray diffraction study. J. Mol. Biol. 121 (1978) 41-54
38. Koeppe R.E., Berg J.M., Hodgson K.O., and Stryer L. Gramicidin a crystals contain two cation binding sites per channel. Nature 279 (1979) 723-725
39. Wallace B.A., and Ravikumar K. The gramicidin pore: crystal structure of a cesium complex. Science 241 (1988) 182-187
40. Langs D.A. Three-dimensional structure at 0.86 Å of the uncomplexed form of the transmembrane ion channel peptide gramicidin A. Science 241 (1988) 188-191
41. 5.6) structure of gramicidin A: alternate patterns of helical association and deformation. Proc. Natl. Acad. Sci. U. S. A. 88 (1991) 5345-5349
42. Wallace B.A. Crystallographic studies of a transmembrane ion channel, gramicidin A. Prog. Biophys. Mol. Biol. 57 (1992) 59-69
43. l,d and the β helix by electrical measurements with lipid bilayer membranes. Proc. Natl. Acad. Sci. U. S. A. 74 (1977) 2402-2406
44. Veatch W.R., Mathies R., Eisenberg M., and Stryer L. Simultaneous fluorescence and conductance studies of planar bilayer membranes containing a highly active and fluorescent analog of gramicidin A. J. Mol. Biol. 99 (1975) 75-92
45. Venkatachalam C.M., and Urry D.W. Theoretical conformational analysis of the gramicidin A transmembrane channel: I. Helix sense and energetics of head-to-head dimerization. J. Comp. Chem. 4 (1983) 461-469
46. O'Connell A.M., Koeppe R.E., and Andersen O.S. Kinetics of gramicidin channel formation in lipid bilayers: transmembrane monomer association. Science 250 (1990) 1256-1259
47. (l,d) helices. Proc. Natl. Acad. Sci. U. S. A. 68 (1971) 1907-1911
48. Myers V.B., and Haydon D.A. Ion transfer across lipid membranes in the presence of gramicidin A.II. The ion selectivity. Biochim. Biophys. Acta 274 (1972) 313-322
49. 1H-NMR study of gramicidin A transmembrane ion channel. Head-to-head right-handed, single stranded helices. FEBS Lett. 186 (1985) 168-174
50. Ketchem R.R., Hu W., and Cross T.A. High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR. Science 261 (1993) 1457-1460
51. Ketchem R.R., Roux B., and Cross T.A. High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints. Structure 5 (1997) 1655-1669
52. Sychev S.V., Barsukov L.I., and Ivanov V.T. The double ππ5.6 helix of gramicidin A predominates in unsaturated lipid membranes. Eur. Biophys. J. 22 (1993) 279-288
53. Killian J.A., Prasad K.U., Hains D., and Urry D.W. The membrane as an environment of minimal interconversion. A circular dichroism study on the solvent dependence of the conformational behavior of gramicidin in diacylphosphatidylcholine model membranes. Biochemistry 27 (1988) 4848-4855
54. Zein M., and Winter R. Effect of temperature, pressure and lipid acyl chain length on the structure and phase behaviour of phospholipid-gramicidin bilayers. Phys. Chem. Chem. Phys. 2 (2000) 4545-4551
55. Kelkar D.A., and Chattopadhyay A. Modulation of gramicidin channel conformation and organization by hydrophobic mismatch in saturated phosphatidylcholine bilayers. Biochim. Biophys. Acta 1768 (2007) 1103-1113
56. LoGrasso P.V., Moll F., and Cross T.A. Solvent history dependence of gramicidin A conformations in hydrated lipid bilayers. Biophys. J. 54 (1988) 259-267
57. Wimley W.C., and White S.H. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat. Struct. Biol. 3 (1996) 842-848
58. Chothia C. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105 (1976) 1-14
59. Burley S.K., and Petsko G.A. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science 229 (1985) 23-28
60. Burley S.K., and Petsko G.A. Weakly polar interactions in proteins. Adv. Protein Chem. 39 (1988) 125-189
61. Fonseca V., Daumas P., Ranjalahy-Rasoloarijao L., Heitz F., Lazaro R., Trudelle Y., and Andersen O.S. Gramicidin channels that have no tryptophan residues. Biochemistry 31 (1992) 5340-5350
62. Andersen O.S., Greathouse D.V., Providence L.L., Becker M.D., and Koeppe R.E. Importance of tryptophan dipoles for protein function: 5-fluorination of tryptophans in gramicidin A channels. J. Am. Chem. Soc. 120 (1998) 5142-5146
63. Yau W.-M., Wimley W.C., Gawrisch K., and White S.H. The preference of tryptophan for membrane interfaces. Biochemistry 37 (1998) 14713-14718
64. Cotten M., Xu F., and Cross T.A. Protein stability and conformational rearrangements in lipid bilayers: linear gramicidin, a model system. Biophys. J. 73 (1997) 614-623
65. Salom D., Baño M.C., Braco L., and Abad C. HPLC demonstration that an all Trp → Phe replacement in gramicidin A results in a conformational rearrangement from beta-helical monomer to double-stranded dimer in model membranes. Biochem. Biophys. Res. Commun. 209 (1995) 466-473
66. Salom D., Pérez-Payá E., Pascal J., and Abad C. Environment- and sequence-dependent modulation of the double-stranded to single-stranded conformational transition of gramicidin A in membranes. Biochemistry 37 (1998) 14279-14291
67. Townsley L.E., Tucker W.A., Sham S., and Hinton J.F. Structures of gramicidin A, B, and C incorporated into sodium dodecyl sulfate micelles. Biochemistry 40 (2001) 11676-11686
68. Rawat S.S., Kelkar D.A., and Chattopadhyay A. Effect of structural transition of the host assembly on dynamics of an ion channel peptide: a fluorescence approach. Biophys. J. 89 (2005) 3049-3058
69. Salom D., Abad C., and Braco L. Characterization of gramicidin A in an inverted micellar environment. A combined high-performance liquid chromatographic and spectroscopic study. Biochemistry 31 (1992) 8072-8079
70. Kelkar D.A., and Chattopadhyay A. Effect of graded hydration on the organization and dynamics of an ion channel: a fluorescence approach. Biophys. J. 88 (2005) 1070-1080
71. Greathouse D.V., Koeppe R.E., Providence L.L., Shobana S., and Andersen O.S. Design and characterization of gramicidin channels. Methods Enzymol. 294 (1999) 525-550
72. Hu W., and Cross T.A. Tryptophan hydrogen bonding and electric dipole moments: functional roles in the gramicidin channel and implications for membrane proteins. Biochemistry 34 (1995) 14147-14155
73. Koeppe R.E., Sun H., van der Wel P.C.A., Scherer E.M., Pulay P., and Greathouse D.V. Combined experimental/theoretical refinement of indole ring geometry using deuterium magnetic resonance and ab initio calculations. J. Am. Chem. Soc. 125 (2003) 12268-12276
74. Durkin J.T., Koeppe R.E., and Andersen O.S. Energetics of gramicidin hybrid channel formation as a test for structural equivalence. Side-chain substitutions in the native sequence. J. Mol. Biol. 211 (1990) 221-234
75. 6.3-helical gramicidin channels between sequence-substituted gramicidin analogues. Biophys. J. 62 (1992) 145-159
76. Cifu A.S., Koeppe R.E., and Andersen O.S. On the supramolecular organization of gramicidin channels. The elementary conducting unit is a dimer. Biophys. J. 61 (1992) 189-203
77. Bransburg-Zabary S., Kessel A., Gutman M., and Ben-Tal N. Stability of an ion channel in lipid bilayers: implicit solvent model calculations with gramicidin. Biochemistry 41 (2002) 6946-6954
78. Jude A.R., Greathouse D.V., Koeppe R.E., Providence L.L., and Andersen O.S. Modulation of gramicidin channel structure and function by the aliphatic "spacer" residues 10, 12, and 14 between the tryptophans. Biochemistry 38 (1999) 1030-1039
79. Koeppe R.E., Hatchett J., Jude A.R., Providence L.L., Andersen O.S., and Greathouse D.V. Neighboring aliphatic/aromatic side chain interactions between residues 9 and 10 in gramicidin channels. Biochemistry 39 (2000) 2235-2242
80. Miloshevsky G.V., and Jordan P.C. Gating gramicidin channels in lipid bilayers: reaction coordinates and the mechanism of dissociation. Biophys. J. 86 (2004) 92-104
81. Durkin J.T., Providence L.L., Koeppe R.E., and Andersen O.S. Energetics of heterodimer formation among gramicidin analogues with an NH2-terminal addition or deletion. Consequences of missing a residue at the join in the channel. J. Mol. Biol. 231 (1993) 1102-1121
82. Jude A.R., Greathouse D.V., Leister M.C., and Koeppe R.E. Steric interactions of valines 1, 5, and 7 in [valine 5, d-alanine 8] gramicidin A channels. Biophys. J. 77 (1999) 1927-1935
83. Oiki S., Koeppe R.E., and Andersen O.S. Voltage-dependent gating of an asymmetric gramicidin channel. Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 2121-2125
84. Woolley G.A., Zunic V., Karanicolas J., Jaikaran A.S.I., and Starostin A.V. Voltage-dependent behavior of a ball-and-chain gramicidin channel. Biophys. J. 73 (1997) 2465-2475
85. Bamberg E., and Janko K. The action of a carbonsuboxide dimerized gramicidin A on lipid bilayer membranes. Biochim. Biophys. Acta 465 (1977) 486-499
86. Rudnev V.S., Ermishkin L.N., Fonina L.A., and Rovin Y.G. The dependence of the conductance and lifetime of gramicidin channels on the thickness and tension of lipid bilayers. Biochim. Biophys. Acta 642 (1981) 196-202
87. Stankovic C.J., Heinemann S.H., Delfino J.M., Sigworth F.J., and Schreiber S.L. Transmembrane channels based on tartaric acid-gramicidin A hybrids. Science 244 (1989) 813-817
88. Stankovic C.J., Heinemann S.H., and Schreiber S.L. Immobilizing the gate of a tartaric acid-gramicidin A hybrid channel molecule by rational design. J. Am. Chem. Soc. 112 (1990) 3702-3704
89. Stankovic C.J., Heinemann S.H., and Schreiber S.L. Photo-modulated ion channels based on covalently linked gramicidins. Biochim. Biophys. Acta 1061 (1991) 163-170
90. Cukierman S. Flying protons in linked gramicidin A channels, Israel. J. Chem. 39 (1999) 419-426
91. Cukierman S., Quigley E.P., and Crumrine D.S. Proton conduction in gramicidin A and in its dioxolane-linked dimer in different lipid bilayers. Biophys. J. 73 (1997) 2489-2502
92. Quigley E.P., Quigley P., Cukierman S., and Crumrine D.S. The conduction of protons in different stereoisomers of dioxolane-linked gramicidin A channels. Biophys. J. 77 (1999) 2479-2491
93. Crouzy S., Woolf T.B., and Roux B. A molecular dynamics study of gating in dioxolane-linked gramicidin A channels. Biophys. J. 67 (1994) 1370-1386
94. Armstrong K.M., Quigley E.P., Quigley P., Crumrine D.S., and Cukierman S. Covalently linked gramicidin channels: effects of linker hydrophobicity and alkaline metals on different stereoisomers. Biophys. J. 80 (2001) 1810-1818
95. Ring A. Brief closures of gramicidin A channels in lipid bilayer membranes. Biochim. Biophvs. Acta 856 (1986) 646-653
96. Sigworth F.J., Urry D.W., and Prasad K.U. Open channel noise. III. High-resolution recordings show rapid current fluctuations in gramicidin A and four chemical analogues. Biophys. J. 52 (1987) 1055-1064
97. Armstrong K.M., and Cukierman S. On the origin of closing flickers in gramicidin channels: a new hypothesis. Biophys. J. 82 (2002) 1329-1337
98. Prasad K.U., Trapane T.L., Busath D., Szabo G., and Urry D.W. Synthesis and characterization of (1-13C) Phe9 gramicidin A. Effects of side chain variations. Int. J. Pept. Protein Res. 22 (1983) 341-347
99. Daumas P., Heitz F., Ranjalahy-Rasoloarijao L., and Lazaro R. Gramicidin A analogs: influence of the substitution of the tryptophans by naphthylalanines. Biochimie 71 (1989) 77-81
100. Becker M.D., Greathouse D.V., Koeppe R.E., and Andersen O.S. Amino acid sequence modulation of gramicidin channel function: effects of tryptophan-to-phenylalanine substitutions on the single-channel conductance and duration. Biochemistry 30 (1991) 8830-8839
101. Bamberg E., Noda K., Gross E., and Lauger P. Single-channel parameters of gramicidin A, B, and C. Biochim. Biophys. Acta 419 (1976) 223-228
102. Busath D.D., and Waldbillig R.C. Photolysis of gramicidin A channels in lipid bilayers. Biochim. Biophys. Acta 736 (1983) 28-38
103. Jones D., Hayon E., and Busath D. Tryptophan photolysis is responsible for gramicidin-channel inactivation by ultraviolet light. Biochim. Biophys. Acta 861 (1986) 62-66
104. Busath D.D., and Hayon E. Ultraviolet flash photolysis of gramicidin-doped lipid bilayers. Biochim. Biophys. Acta 944 (1988) 73-78
105. Strässle M., Stark G., Wilhelm M., Daumas P., Heitz F., and Lazaro R. Radiolysis and photolysis of ion channels formed by analogues of gramicidin A with a varying number of tryptophan residues. Biochim. Biophys. Acta 980 (1989) 305-314
106. Sobko A.A., Vigasina M.A., Rokitskaya T.I., Kotova E.A., Zakharov S.D., Cramer W.A., and Antonenko Y.N. Chemical and photochemical modification of colicin E1 and gramicidin A in bilayer lipid membranes. J. Membr. Biol. 199 (2004) 51-62
107. Weiler-Feilchenfeld H., Pullman A., Berthod H., and Giessner-Prettre C. Experimental and quantum-chemical studies of the dipole moments of quinoline and indole. J. Mol. Struct. 6 (1970) 297-304
108. Ross J.B.A., Szabo A.G., and Hogue C.W.V. Enhancement of protein spectra with tryptophan analogs: fluorescence spectroscopy of protein-protein and protein-nucleic acid interactions. Methods Enzymol. 278 (1997) 151-190
109. Ross J.B.A., Rusinova E., Luck L.A., and Rousslang K.W. Spectral enhancement of proteins by in vivo incorporation of tryptophan analogues. In: Lakowicz J.R. (Ed). Topics in Fluorescence Spectroscopy, Volume 6: Protein Fluorescence (2000), Kluwer Academic/Plenum Publishers, New York 17-42
110. 13 gramicidin A channels. Biophys. J. 75 (1998) 2830-2844
111. 13 gramicidin A currents. Biophys. J. 81 (2001) 1245-1254
112. Phillips L.R., Cole C.D., Hendershot R.J., Cotten M., Cross T.A., and Busath D.D. Noncontact dipole effects on channel permeation: III. Anomalous proton conductance effects in gramicidin. Biophys. J. 77 (1999) 2492-2501
113. Dorigo A.E., Anderson D.G., and Busath D.D. Noncontact dipole effects on channel permeation: II. Trp conformations and dipole potentials in gramicidin A. Biophsy. J. 76 (1999) 1897-1908
114. Cole C.D., Frost A.S., Thompson N., M.Cotten T.A., and Cross D.D. Noncontact dipole effects on channel permeation. VI. 5F- and 6F-Trp gramicidin channel currents. Biophys. J. 83 (2002) 1974-1986
115. Gowen J.A., Markham J.C., Morrison S.E., Cross T.A., Busath D.D., Mapes E.J., and Schumaker M.F. The role of Trp side chains in tuning single proton conduction through gramicidin channels. Biophys. J. 83 (2002) 880-898
116. Anderson D.G., Shirts R.B., Cross T.A., and Busath D.D. Noncontact dipole effects on channel permeation: V. Computed potentials for fluorinated gramicidin. Biophys. J. 81 (2001) 1255-1264
117. Rokitskaya T.I., Antonenko Y.N., and Kotova E.A. Effect of the dipole potential of a bilayer lipid membrane on gramicidin channel dissociation kinetics. Biophys. J. 73 (1997) 850-854
118. Duffin R.L., Garrett M.P., Flake K.B., Durrant J.D., and Busath D.D. Modulation of lipid bilayer interfacial dipole potential by phloretin, RH421, and 6-ketocholestanol as probed by gramicidin channel conductance. Langmuir 19 (2003) 3561
119. Anderson D.G., Shirts R.B., Cross T.A., and Busath D.D. Noncontact dipole effects on channel permeation: V. Computed potentials for fluorinated gramicidin. Biophys. J. 81 (2001) 1255-1264
120. Cotten M., Tian C., Busath D.D., Shirts R.B., and Cross T.A. Modulating dipoles for structure-function correlations in the gramicidin A channel. Biochemistry 38 (1999) 9185-9197
121. Jordan J.B., Easton P.L., and Hinton J.F. Effects of phenylalanine substitutions in gramicidin A on the kinetics of channel formation in vesicles and channel structure in SDS micelles. Biophys. J. 88 (2005) 224-234
122. Hu W., Lee K.-C., and Cross T.A. Tryptophans in membrane proteins: indole ring orientations and functional implications in the gramicidin channel. Biochemistry 32 (1993) 7035-7047
123. Hu W., Lazo N.D., and Cross T.A. Tryptophan dynamics and structural refinement in a lipid bilayer environment: solid state NMR of the gramicidin channel. Biochemistry 34 (1995) 14138-14146
124. Hu W., and Cross T.A. Tryptophan hydrogen bonding and electric dipole moments: functional roles in the gramicidin channel and implications for membrane proteins. Biochemistry 34 (1995) 14147-14155
125. Allen T.W., Andersen O.S., and Roux B. Structure of gramicidin A in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data. J. Am. Chem. Soc. 125 (2003) 9868-9877
126. Chiu S.W., Subramaniam S., and Jakobsson E. Simulation study of a gramicidin/lipid bilayer system in excess water and lipid: I. Structure of the molecular complex. Biophys. J. 76 (1999) 1929-1938
127. Rawat S.S., Kelkar D.A., and Chattopadhyay A. Monitoring gramicidin conformations in membranes: a fluorescence approach. Biophys. J. 87 (2004) 831-843
128. Woolf T.B., and Roux B. Structure, energetics, and dynamics of lipid-protein interactions: a molecular dynamics study of the gramicidin A channel in a DMPC bilayer. Proteins 24 (1996) 92-114
129. Macdonald P.M., and Seelig J. Dynamic properties of gramicidin A in phospholipid membranes. Biochemistry 27 (1988) 2357-2364
130. Bingham N.C., Smith N.E.C., Cross T.A., and Busath D.D. Molecular dynamics simulations of trp side-chain conformational flexibility in the gramicidin A channel. Biopolymers 71 (2003) 593-600
131. 19F-labeled tryptophan in gramicidin A in oriented membranes. Biophys. J. 83 (2002) 3336-3350
132. Burger K., Gimpl G., and Fahrenholz F. Regulation of receptor function by cholesterol. Cell. Mol. Life Sci. 57 (2000) 1577-1592
133. Lee A.G. Lipid-protein interactions in biological membranes: a structural perspective. Biochim. Biophys. Acta 1612 (2003) 1-40
134. Lee A.G. How lipids affect the activities of integral membrane proteins. Biochim. Biophys. Acta 1666 (2004) 62-87
135. Pucadyil T.J., and Chattopadhyay A. Role of cholesterol in the function and organization of G-protein coupled receptors. Prog. Lipid Res. 45 (2006) 295-333
136. Woolley G.A., and Wallace B.A. Membrane protein structure: lessons from gramicidin. In: White S.H. (Ed). Membrane Protein Structure: Experimental Approaches (1994), Oxford Univ. Press, New York 314-334
137. Kelkar D.A., and Chattopadhyay A. Membrane interfacial localization of aromatic amino acids and membrane protein function. J. Biosci. 31 (2006) 297-302
138. Hollerbach U., Chen D.P., Busath D.D., and Eisenberg B. Predicting function from structure using the Poisson-Nernst-Planck equations: sodium current in the gramicidin A channel. Langmuir 16 (2000) 5509-5514
139. Pasqual-Ronchetti I., Spisni A., Casali E., Masotti L., and Urry D.W. Gramicidin A induces lysolecithin to form bilayers. Biosci. Rep. 3 (1983) 127-133
140. Killian J.A., de Kruijff B., van Echteld C.J., Verkleij A.J., Leunissen-Bijvelt J., and de Gier J. Mixtures of gramicidin and lysophosphatidylcholine form lamellar structures. Biochim. Biophys. Acta 728 (1983) 141-144
141. Killian J.A., and Urry D.W. Conformation of gramicidin in relation to its ability to form bilayers with lysophosphatidylcholine. Biochemistry 27 (1988) 7295-7301
142. Brasseur R., Cabiaux V., Killian J.A., de Kruijff B., and Ruysschaert J.M. Orientation of gramicidin A at the lysophosphatidylcholine/water interface: a semi-empirical conformational analysis. Biochim. Biophys. Acta 855 (1986) 317-324
143. Aranda F.J., Killian J.A., and de Kruijff B. Importance of the tryptophans of gramicidin for its lipid structure modulating activity in lysophosphatidylcholine and phosphatidylethanolamine model membranes. A comparative study employing gramicidin analogs and a synthetic α-helical hydrophobic polypeptide. Biochim. Biophys. Acta 901 (1987) 217-228
144. van Echteld C.J.A., de Kruijff B., Verkleij A.J., Leunissen-Bijvelt J., and de Gier J. Gramicidin induces the formation of non-bilayer structures in phosphatidylcholine dispersions in a fatty acid chain length dependent way. Biochim. Biophys. Acta 692 (1982) 126-138
145. Szule J.A., and Rand R.P. The effects of gramicidin on the structure of phospholipid assemblies. Biophys. J. 85 (2003) 1702-1712
146. Tournois H., Leunissen-Bijvelt J., Haest C.W., de Gier J., and de Kruijff B. Gramicidin-induced hexagonal HII phase formation in erythrocyte membranes. Biochemistry 26 (1987) 6613-6621
147. Tournois H., Henseleit U., deGier J., de Kruijff B., and Haest C.W. Relationship between gramicidin conformation dependent induction of phospholipid transbilayer movement and hexagonal HII phase formation in erythrocyte membranes. Biochim. Biophys. Acta 946 (1988) 173-177
148. Killian J.A., and de Kruijff B. Importance of hydration for gramicidin-induced hexagonal HII phase formation in dioleoylphosphatidylcholine model membranes. Biochemistry 24 (1985) 7890-7898
149. Killian J.A., Burger K.N.J., and de Kruijff B. Phase separation and hexagonal HII phase formation by gramicidins A, B and C in dioleoylphosphatidylcholine model membranes. A study on the role of the tryptophan residues. Biochim. Biophys. Acta 897 (1987) 269-284
150. α and peptide-rich HII phase coexistence in gramicidin A′/phospholipid dispersions. Biochemistry 33 (1994) 12945-12953
151. Watnick P.I., Chan S.I., and Dea P. Hydrophobic mismatch in gramicidin A′/lecithin systems. Biochemistry 29 (1990) 6215-6621
152. Cornell B.A., Weir L.E., and Separovic F. The effect of gramicidin A on phospholipid bilayers. Eur. Biophys. J. 16 (1988) 113-119
153. Killian J.A., Prasad K.U., Urry D.W., and de Kruijff B. A mismatch between the length of gramicidin and the lipid acyl chains is a prerequisite of HII phase formation in phosphatidylcholine model membranes. Biochim. Biophys. Acta 978 (1989) 341-345
154. Tuornois H., Fabrie C.H., Burger K.N., Mandersloot J., Hilgers P., van Dalen H., de Gier J., and de Kruijff B. Gramicidin A induced fusion of large unilamellar dioleoylphosphatidylcholine vesicles and its relation to the induction of type II nonbilayer structures. Biochemistry 29 (1990) 8297-8307
155. Chattopadhyay A., and Raghuraman H. Application of fluorescence spectroscopy to membrane protein structure and dynamics. Curr. Sci. 87 (2004) 175-180
156. Cox K.J., Ho C., Lombardi J.V., and Stubbs C.D. Gramicidin conformational studies with mixed-chain unsaturated phospholipid bilayer systems. Biochemistry 31 (1992) 1112-1118
157. Baño M.C., Braco L., and Abad C. Conformational transitions of gramicidin A in phospholipid model membranes. A high-performance liquid chromatography assessment. Biochemistry 30 (1991) 886-894
158. Kirby E.P., and Steiner R.F. Influence of solvent and temperature upon the fluorescence of indole derivatives. J. Phys. Chem. 74 (1970) 4480-4490
159. Beechem J.M., and Brand L. Time-resolved fluorescence of proteins. Annu. Rev. Biochem. 54 (1985) 43-71
160. Cavatorta P., Spisni A., Casali E., Lindner L., Masotti L., and Urry D.W. Intermolecular interactions of gramicidin A′ transmembrane channels incorporated into lysophosphatidylcholine lipid systems. Biochim. Biophys. Acta 689 (1982) 113-120
161. Scarlata S.F. The effects of viscosity on gramicidin tryptophan rotational motion. Biophys. J. 54 (1988) 1149-1157
162. Scarlata S.F. Effect of increased chain packing on gramicidin-lipid interactions. Biochemistry 30 (1991) 9853-9859
163. Camaleño-Delango J.-M., Zhao X.K., and Fendler J.H. Intrinsic gramicidin fluorescence lifetimes in bilayer lipid membranes and in vesicles. Can. J. Chem. 68 (1990) 888-896
164. Shobini J., Mishra A.K., and Chandra N. Conformation of gramicidin-A in CTAB micellar media. J. Photochem. Photobiol., B 70 (2003) 117-124
165. Kelkar D.A., and Chattopadhyay A. Monitoring ion channel conformations in membranes utilizing a novel dual fluorescence quenching approach. Biochem. Biophys. Res. Commun. 343 (2006) 483-488
166. Chattopadhyay A., and Rawat S.S. Wavelength-selective fluorescence in ion channels formed by gramicidin A in membranes. J. Chem. Sci. 119 (2007) 135-140
167. Demchenko A.P. The red-edge effects: 30 years of exploration. Luminescence 17 (2002) 19-42
168. Chattopadhyay A. Exploring membrane organization and dynamics by the wavelength-selective fluorescence approach. Chem. Phys. Lipids 122 (2003) 3-17
169. Raghuraman H., Kelkar D.A., and Chattopadhyay A. Novel insights into protein structure and dynamics utilizing the red edge excitation shift approach. In: Geddes C.D., and Lakowicz J.R. (Eds). Reviews in Fluorescence 2005 vol. 2 (2005), Springer, New York 199-222
170. Rawat S.S., and Chattopadhyay A. Structural transition in the micellar assembly: a fluorescence study. J. Fluoresc. 9 (1999) 233-244
171. Elliott J.R., Needham D., Dilger J.P., and Haydon D.A. The effects of bilayer thickness and tension on gramicidin single-channel lifetime. Biochim. Biophys. Acta 735 (1983) 95-103
172. Lundbæk J.A., Birn P., Girshman J., Hansen A.J., and Andersen O.S. Membrane stiffness and channel function. Biochemistry 35 (1996) 3825-3830
173. Huang H.W. Deformation free energy of bilayer membrane and its effect on gramicidin channel lifetime. Biophys. J. 50 (1986) 1061-1070
174. Helfrich P., and Jakobsson E. Calculation of deformation energies and conformations in lipid membranes containing gramicidin channels. Biophys. J. 57 (1990) 1075-1084
175. Lundbæk J.A., Birn P., Hansen A.J., Søgaard R., Nielsen C., Girshman J., Bruno M.J., Tape S.E., Egebjerg J., Greathouse D.V., Mattice G.L., Koeppe R.E., and Andersen O.S. Regulation of sodium channel function by bilayer elasticity: the importance of hydrophobic coupling. Effects of micelle-forming amphiphiles and cholesterol. J. Gen. Physiol. 123 (2004) 599-621
176. Lundbæk J.A., and Andersen O.S. Lysophospholipids modulate channel function by altering the mechanical properties of lipid bilayers. J. Gen. Physiol. 104 (1996) 645-673
177. Lundbæk J.A., Maer A.M., and Andersen O.S. Lipid bilayer electrostatic energy, curvature stress, and assembly of gramicidin channels. Biochemistry 36 (1997) 5695-5701
178. Hamill O.P., and Martinac B. Molecular basis of mechanotransduction in living cells. Physiol. Rev. 81 (2001) 685-740
179. Martinac B., and Hamill O.P. Gramicidin A channels switch between stretch activation and stretch inactivation depending on bilayer thickness. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 4308-4312
180. Needham D., and Nunn R.S. Elastic deformation and failure of lipid bilayer membranes containing cholesterol. Biophys. J. 58 (1990) 997-1009
181. Needham D. Cohesion and permeability of lipid bilayer vesicles. In: Simon S.A., and Disalvo E.A. (Eds). Permeability and Stability of Bilayers (1995), CRC Press, Boca Raton, FL 49-76
182. Lundbæk J.A., Andersen O.S., Werge T., and Nielsen C. Cholesterol-induced protein sorting: an analysis of energetic feasibility. Biophys. J. 84 (2003) 2080-2089
183. Simon S.A., McIntosh T.J., and Latorre R. Influence of cholesterol on water penetration into bilayers. Science 216 (1982) 65-67
184. Nezil F.A., and Bloom M. Combined influence of cholesterol and synthetic amphiphillic peptides upon bilayer thickness in model membranes. Biophys. J. 61 (1992) 1176-1182
185. Elliott J.R., Needham D., Dilger J.P., Brandt O., and Haydon D.A. A quantitative explanation of the effects of some alcohols on gramicidin single-channel lifetime. Biochim. Biophys. Acta 814 (1985) 401-404
186. Schagina L.V., Blaskó K., Grinfeldt A.E., Korchev Y.E., and Lev A.A. Cholesterol-dependent gramicidin A channel inactivation in red blood cell membranes and lipid bilayer membranes. Biochim. Biophys. Acta 978 (1989) 145-150
187. Schagina L.V., Korchev Y.E., Grinfeldt A.E., Lev A.A., and Blaskó K. Sterol specific inactivation of gramicidin A induced membrane cation permeability. Biochim. Biophys. Acta 1109 (1992) 91-96
188. Mobashery N., Nielsen C., and Andersen O.S. The conformational preference of gramicidin channels is a function of lipid bilayer thickness. FEBS Lett. 412 (1997) 15-20
189. Arndt H.-D., Knoll A., and Koert U. Synthesis of minigramicidin ion channels and test of their hydrophobic match with the membrane. ChemBioChem 2 (2001) 221-222
190. Andersen O.S., Nielsen C., Maer A.M., Lundbæk J.A., Goulian M., and Koeppe R.E. Ion channels as tools to monitor lipid bilayer-membrane protein interactions: gramicidin channels as molecular force transducers. Methods Enzymol. 294 (1999) 208-224
191. Nielsen C., Goulian M., and Andersen O.S. Energetics of inclusion-induced bilayer deformations. Biophys. J. 74 (1998) 1966-1983
192. Lundbæk J.A., and Andersen O.S. Spring constants for channel-induced lipid bilayer deformations. Estimates using gramicidin channels. Biophys. J. 76 (1999) 889-895
193. Hwang T.-C., Koeppe R.E., and Andersen O.S. Genistein can modulate channel function by a phosphorylation-independent mechanism: importance of hydrophobic mismatch and bilayer mechanics. Biochemistry 42 (2003) 13646-13658
194. Liu L., Yang T., Bruno M.J., and Andersen O.S. Voltage-gated ion channels in nociceptors: modulation by cGMP. J. Neurophysiol. 92 (2004) 2323-2332
195. Suchyna T.M., Tape S.E., Koeppe R.E., Andersen O.S., Sachs F., and Gottlieb P.A. Bilayer-dependent inhibition of mechanosensitive channels by neuroactive peptide enantiomers. Nature 430 (2004) 235-240
196. Garcia M.L. Gate expectations. Nature 430 (2004) 153-155
197. Chattopadhyay A., and Kelkar D.A. Ion channels and d-amino acids. J. Biosci. 30 (2005) 147-149
198. Wallace B.A. Common structural features in gramicidin and other ion channels. BioEssays 22 (2000) 227-234
199. Wallace B.A. X-ray crystallographic structures of gramicidin and their relation to the Streptomyces lividans potassium channel structure. Novartis Foundation Symposium 225, Gramicidin and related ion channel forming peptides (1999), Wiley, Chichester 23-37
200. +-selectivity filter. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 17045-17049
201. Thundimadathil J., Roeske R.W., and Guo L. Conversion of a porin-like peptide channel into a gramicidin-like channel by glycine to d-alanine substitutions. Biophys. J. 90 (2006) 947-955
202. Arumugam S., Pascal S., North C.L., Hu W., Lee K.-C., Cotten M., Ketchem R.R., Xu F., Brenneman M., Kovacs F., Tian F., Wang A., Huo S., and Cross T.A. Conformational trapping in a membrane environment: a regulatory mechanism for protein activity?. Proc. Natl. Acad. Sci. U. S. A. 93 (1996) 5872-5876
203. Domene C., Vemparala S., Klein M.L., Vénien-Bryan C., and Doyle D.A. Role of aromatic localization in the gating process of a potassium channel. Biophys. J. 90 (2006) L01-L03
204. Miller A.S., and Falke J.J. Side chains at the membrane-water interface modulate the signaling state of a transmembrane receptor. Biochemistry 43 (2004) 1763-1770
205. Draheim R.R., Bormans A.F., Lai R.Z., and Manson M.D. Tryptophan residues flanking the second transmembrane helix (TM2) set the signaling state of the Tar chemoreceptor. Biochemistry 44 (2005) 1268-1277
206. Chiang C.S., Shirinian L., and Sukharev S. Capping transmembrane helices of MscL with aromatic residues changes channel response to membrane stretch. Biochemistry 44 (2005) 12589-12597
207. MacKinnon R., and von Heijne G. Membranes. Curr. Opin. Struct. Biol. 16 (2006) 431
208. Deisenhofer J., Epp O., Miki K., Huber R., and Michel H. X-ray structure analysis of a membrane protein complex. Electron density map at 3 Å resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. Nature 318 (1985) 618-624
209. Sui H., Han B.-G., Lee J.K., Walian P., and Jap B.K. Structural basis of water-specific transport through the AQP1 water channel. Nature 414 (2001) 872-878
210. Abramson J., Smirnova I., Kasho V., Verner G., Kaback H.R., and Iwata S. Structure and mechanism of the lactose permease of Escherichia coli. Science 301 (2003) 610-615
211. Bowie J.U. Are we destined to repeat history?. Curr. Opin. Struct. Biol. 10 (2000) 435-437
212. White S.H. The progress of membrane protein structure determination. Protein Sci. 13 (2004) 1948-1949
213. Miller G. The puzzling portrait of a pore. Science 300 (2003) 2020-2022
214. Sayle R.A., and Milner-White E.J. RasMol: biomolecular graphics for all. Trends Biochem. Sci. 20 (1995) 374-376