Gramicidin channels

IEEE Transactions on Nanobioscience

Volumn 4, Issue 1, 2005, Pages 10-19

  Andersen, Olaf S ^a   Koeppe II, Roger E ^b   Roux, Benoît ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b UNIVERSITY OF ARKANSAS   (United States)

Author keywords

Kinetics of ion permeation; Molecular dynamics; Single channel electrophysiology; Structure function studies

Indexed keywords

AMINO ACIDS; BIOLOGICAL MEMBRANES; DIMERIZATION; ELECTROPHYSIOLOGY; HYDROGEN BONDS; MOLECULAR DYNAMICS; PHOSPHOLIPIDS; POSITIVE IONS; PROTEINS; REACTION KINETICS; WATER;

GRAMICIDIN CHANNELS; KINETICS OF ION PERMEATION; SINGLE-CHANNEL ELECTROPHYSIOLOGY; STRUCTURE-FUNCTION STUDIES;

ANTIBIOTICS;

GRAMICIDIN; ION CHANNEL;

ANIMAL; BIOLOGICAL MODEL; CELL MEMBRANE PERMEABILITY; CELL MEMBRANE POTENTIAL; CHANNEL GATING; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; LIPID BILAYER; METABOLISM; PHYSIOLOGY; PROTEIN CONFORMATION; REVIEW; STRUCTURE ACTIVITY RELATION;

ANIMALS; CELL MEMBRANE PERMEABILITY; GRAMICIDIN; HUMANS; ION CHANNEL GATING; ION CHANNELS; LIPID BILAYERS; MEMBRANE POTENTIALS; MODELS, BIOLOGICAL; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 15244354798     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2004.842470     Document Type: Article

References (118)

1. F. M. Harold and J. R. Baarda, "Gramicidin, valinomycin, and cation permeability of Streptococcus faecalis," J. Bacteriol., vol. 94, pp. 53-60, 1967.
2. S. B. Hladky and D. A. Haydon, "Discreteness of conductance change in bimolecular lipid membranes in the presence of certain antibiotics," Nature, vol. 225, pp. 451-453, 1970.
3. (L,D) helix," Proc. Nat. Acad. Sci. USA, vol. 68, pp. 672-676, 1971.
4. _, "Protein conformation in biomembranes: optical rotation and absorption of membrane suspensions," Biochim. Biophys. Acta, vol. 265, pp. 115-168, 1972.
5. M. S. Weiss, A. Kreusch, E. Schiltz, U. Nestel, W. Welte, J. Weckesser, and G. E. Schulz, "The structure of porin from Rhodobacter capsulatus at 1.8 Å resolution," FEBS Lett., vol. 280, pp. 379-382, 1991.
6. S. W. Cowan et al., "Crystal structures explain functional properties of two E. coli porins," Nature, vol. 358, pp. 727-733, 1992.
7. + conduction and selectivity," Science, vol. 280, pp. 69-77, 1998.
8. G. Chang, R. H. Spencer, A. T. Lee, M. T. Barclay, and D. C. Rees, "Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel," Science, vol. 282, pp. 2220-2226, 1998.
9. R. B. Bass, P. Strop, M. Barclay, and D. C. Rees, "Crystal structure of Escherichia coli MscS, a voltage-modulated and mechanosensitive channel," Science, vol. 298, pp. 1582-1587, 2002.
10. Y. Jiang, A. Lee, J. Chen, M. Cadene, B. T. Chait, and R. MacKinnon, "The open pore conformation of potassium channels," Nature, vol. 417, pp. 523-526, 2002.
11. + channel," Nature, vol. 423, pp. 33-41, 2003.
12. A. Kuo et al., "Crystal structure of the potassium channel KirBac 1.1 in the closed state," Science, vol. 300, pp. 1922-1926, 2003.
13. A. Miyazawa, Y. Fujiyoshi, and N. Unwin, "Structure and gating mechanism of the acetylcholine receptor pore," Nature, vol. 423, pp. 949-955, 2003.
14. R. Sarges and B. Witkop, "Gramicidin A. V. The structure of valine- and isoleucine-gramicidin A," J. Amer. Chem. Soc., vol. 87, pp. 2011-2019, 1965.
15. G. N. Ramachandran and R. Chandrasekaran, "Studies on dipeptide conformation and on peptides with sequences of alternating L and D residues with special reference to antibiotic and ion transport peptides," Prog. Peptides Res., vol. 2, pp. 195-215, 1972.
16. W. R. Veatch, E. T. Fossel, and E. R. Blout, "The conformation of gramicidin A," Biochemistry, vol. 13, pp. 5249-5256, 1974.
17. W. R. Veatch and E. R. Blout, "The aggregation of gramicidin a in solution," Biochemistry, vol. 13, pp. 5257-5264, 1974.
18. V. F. Bystrov and A. S. Arseniev, "Diversity of the gramicidin A spatial structure: two-dimensional proton NMR study in solution," Tetrahedron, vol. 44, pp. 925-940, 1988.
19. D. A. Langs, "Three-dimensional structure at 0.86 Å of the uncomplexed form of the transmembrane ion channel peptide gramicidin A," Science, vol. 241, pp. 188-191, 1988.
20. B. M. Burkhart, N. Li, D. A. Langs, W. A. Pangborn, and W. L. Duax, "The conducting form of gramicidin A is a right-handed double-stranded double helix," Proc. Nat. Acad. Sci. USA, vol. 95, pp. 12950-12955, 1998.
21. N. Abdul-Manan and J. F. Hinton, "Conformational states of gramicidin A along the pathway to the formation of channels in model membranes determined by 2D NMR and circular dichroism spectroscopy," Biochemistry, vol. 33, pp. 6773-6783, 1994.
22. S. B. Hladky and D. A. Haydon, "Ion transfer across lipid membranes in the presence of gramicidin A. I. Studies of the unit conductance channel," Biochim. Biophys. Acta, vol. 274, pp. 294-312, 1972.
23. V. B. Myers and D. A. Haydon, "Ion transfer across lipid membranes in the presence of gramicidin A. II. Ion selectivity," Biochim. Biophys. Acta, vol. 274, pp. 313-322, 1972.
24. A. Finkelstein, "Aqueous pores created in thin lipid membranes by the antibiotics nystatin, amphotericin B and gramicidin A. Implications for pores in plasma membranes," in Drugs and Transport Processes, B. A. Callingham, Ed. London, U.K.: MacMillan, 1974, pp. 241-250.
25. L,D and the β helix by electrical measurements with lipid bilayer membranes," Proc. Nat. Acad. Sci. USA, vol. 74, pp. 2402-2406, 1977.
26. W. Veatch and L. Stryer, "The dimeric nature of the gramicidin A transmembrane channel: conductance and fluorescence energy transfer studies of hybrid channels," J. Mol. Biol., vol. 113, pp. 89-102, 1977.
27. S. Weinstein, B. A. Wallace, E. R. Blout, J. S. Morrow, and W. Veatch, "Conformation of gramicidin A channel in phospholipid vesicles: a carbon-13 and fluorine-19 nuclear magnetic resonance study," Proc. Nat. Acad. Sci. USA, vol. 76, pp. 4230-4234, 1979.
28. S. Weinstein, B. A. Wallace, J. S. Morrow, and W. R. Veatch, "Conformation of the gramicidin A transmembrane channel: a 13C nuclear magnetic resonance study of 13C-enriched gramicidin in phosphatidyl-choline vesicles," J. Mol. Biol., vol. 143, pp. 1-19, 1980.
29. O. S. Andersen and R. E. Koeppe II, "Molecular determinants of channel function," Physiol. Rev., vol. 72, pp. S89-S158, 1992.
30. A. S. Arseniev, I. L. Barsukov, V. F. Bystrov, and Y. A. Ovchinnikov, "Spatial structure of a gramicidin A transmembrane ion channel. NMR analysis in micelles," Biol. Membr., vol. 3, pp. 437-462, 1986.
31. R. R. Ketchem, B. Roux, and T. A. Cross, "High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints," Structure, vol. 5, pp. 1655-1669, 1997.
32. L. E. Townsley, W. A. Tucker, S. Sham, and J. F. Hinton, "Structures of gramicidins A, B, and C incorporated into sodium dodecyl sulfate micelles," Biochemistry, vol. 40, pp. 11676-11686, 2001.
33. T. W. Allen, O. S. Andersen, and B. Roux, "The structure of gramicidin A in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data," J. Amer. Chem. Soc., vol. 125, pp. 9868-9878, 2003.
34. A. S. Arseniev, A. L. Lomize, I. L. Barsukov, and V. F. Bystrov, "Gramicidin A transmembrane ion-channel. Three-dimensional structure reconstruction based on NMR spectroscopy and energy refinement," Biol. Membr., vol. 3, pp. 1077-1104, 1986.
35. R. R. Ketchem, W. Hu, and T. A. Cross, "High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR," Science, vol. 261, pp. 1457-1460, 1993.
36. + block and permeation in a K+ channel of known structure," J. Gen. Physiol., vol. 120, p. 323, Aug 26, 2002.
37. + channel: re-examination of the surface charge hypothesis," J. Gen. Physiol., vol. 121, pp. 375-398, 2003.
38. A. M. O'Connell, R. E. Koeppe II, and O. S. Andersen, "Kinetics of gramicidin channel formation in lipid bilayeis: transmembrane monomer association," Science, vol. 250, pp. 1256-1259, 1990.
39. J. T. Durkin, L. L. Providence, R. E. Koeppe II, and O. S. Andersen, "Formation of non-β-helical gramicidin channels between sequence-substituted gramicidin analogues," Biophys. J., vol. 62, pp. 145-159, 1992.
40. O. S. Andersen et al., "Gramicidin channel controversy - The structure in a lipid environment," Nature Struct. Biol., vol. 6, p. 609, 1999.
41. D. Salom, M. C. Bańo, L. Braco, and C. Abad, "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., vol. 209, pp. 466-473, 1995.
42. D. Salom, E. Perez-Paya, J. Pascal, and C. Abad, "Environment- and sequence-dependent modulation of the double-stranded to single-stranded conformational transition of gramicidin A in membranes," Biochemistry, vol. 37, pp. 14279-14291, 1998.
43. J. A. Killian and G. von Heijne, "How proteins adapt to a membrane-water interface," Trends Biochem. Sci., vol. 25, pp. 429-434, 2000.
44. B. A. Cornell, F. Separovic, A. J. Baldassi, and R. Smith, "Conformation and orientation of gramicidin A in oriented phospholipid bilayers measured by solid state carbon-13 NMR," Biophys. J., vol. 53, pp. 67-76, 1988.
45. L. K. Nicholson, F. Moll, T. E. Mixon, P. V. LoGrasso, J. C. Lay, and T. A. Cross, "Solid-state 15N NMR of oriented lipid bilayer bound gramicidin A′," Biochemistry, vol. 26, pp. 6621-6626, 1987.
46. 2 H NMR study," Biochemistry, vol. 31, pp. 11283-11290, 1992.
47. F. Separovic, R. Pax, and B. Cornell, "NMR order parameter analysis of a peptide plane aligned in a lyotropic liquid crysta," Mol. Phys., vol. 78, pp. 357-369, 1993.
48. R. E. Koeppe II, H. Sun, P. C. van der Wel, E. M. Scherer, P. Pulay, and D. V. Greathouse, "Combined experimental/theoretical refinement of indole ring geometry using deuterium magnetic resonance and ab initio calculations," J. Amer. Chem. Soc., vol. 125, pp. 12 268-12 276, 2003.
49. K. C. Lee, S. Huo, and T. A. Cross, "Lipid-peptide interface: valine conformation and dynamics in the gramicidin channel," Biochemistry, vol. 34, pp. 857-867, 1995.
50. R. E. Koeppe II, J. A. Killian, and D. V. Greathouse, "Orientations of the tryptophan 9 and 11 side chains of the gramicidin channel based on deuterium nuclear magnetic resonance spectroscopy," Biophys. J., vol. 66, pp. 14-24, 1994.
51. S. F. Scarlata, "The effects of viscosity on gramicidin tryptophan rotational motion," Biophys. J., vol. 54, pp. 1149-1157, 1988.
52. S. Mukherjee and A. Chattopadhyay, "Motionally restricted tryptophan environments at the peptide-lipid interface of gramicidin channels," Biochemistry, vol. 33, pp. 5089-5097, 1994.
53. D. V. Greathouse, J. F. Hinton, K. S. Kim, and R. E. Koeppe II, "Gramicidin A/short-chain phospholipid dispersions: chain length dependence of gramicidin conformation and lipid organization," Biochemistry, vol. 33, pp. 4291-4299, 1994.
54. O. G. Mouritsen and M. Bloom, "Mattress model of lipid-protein interactions in membranes," Biophys. J., vol. 46, pp. 141-153, 1984.
55. N. Mobashery, C. Nielsen, and O. S. Andersen, "The conformational preference of gramicidin channels is a function of lipid bilayer thickness," FEBS Lett., vol. 412, pp. 15-20, 1997.
56. T. P. Galbraith and B. A. Wallace, "Phospholipid chain length alters the equilibrium between pore and channel forms of gramicidin," Faraday Discuss., pp. 159-164, 1998.
57. H. W. Huang, "Deformation free energy of bilayer membrane and its effect on gramicidin channel lifetime," Biophys. J., vol. 50, pp. 1061-1070, 1986.
58. J. A. Lundbæk and O. S. Andersen, "Spring constants for channel-induced lipid bilayer deformations - estimates using gramicidin channels," Biophys. J., vol. 76, pp. 889-895, 1999.
59. M. C. Wiener and S. H. White, "Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of X-ray and neutron diffraction data. III. Complete structure," Biophys. J., vol. 61, pp. 437-447, 1992.
60. E. Lindahl and O. Edholm, "Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations," Biophys. J., vol. 79, p. 426, 2000.
61. C. Nielsen, M. Goulian, and O. S. Andersen, "Energetics of inclusion-induced bilayer deformations," Biophys. J., vol. 74, pp. 1966-1983, 1998.
62. J. R. Elliott, D. Needham, J. P. Dilger, and D. A. Haydon, "The effects of bilayer thickness and tension on gramicidin single-channel lifetime," Biochim. Biophys. Acta, vol. 735, pp. 95-103, 1983.
63. B. A. Cornell, F. Separovic, D. E. Thomas, A. R. Atkins, and R. Smith, "Effect of acyl chain length on the structure and motion of gramicidin A in lipid bilayers," Biochim. Biophys. Acta, vol. 985, pp. 229-232, 1989.
64. J. T. Durkin, R. E. Koeppe II, and O. S. Andersen, "Energetics of gramicidin hybrid channel formation as a test for structural equivalence. Side-chain substitutions in the native sequence," J. Mol. Biol., vol. 211, pp. 221-234, 1990.
65. 2 -terminal addition or deletion. Consequences of a missing residue at the join in channel," J. Mol. Biol., vol. 231, pp. 1102-1121, 1993.
66. J. L. Mazet, O. S. Andersen, and R. E. Koeppe II, "Single-channel studies on linear gramicidins with altered amino acid sequences. A comparison of phenylalanine, tryptophan, and tyrosine substitutions at positions 1 and 11," Biophys. J., vol. 45, pp. 263-276, 1984.
67. M. D. Becker, D. V. Greathouse, R. E. Koeppe II, and O. S. Andersen, "Amino acid sequence modulation of gramicidin channel function. Effects of tryptophan-to-phenylalanine substitutions on the single-channel conductance and duration," Biochemistry, vol. 30, pp. 8830-8839, 1991.
68. V. Fonseca, P. Daumas, L. Ranjalahy-Rasoloarijao, F. Heitz, R. Lazaro, Y. Trudelle, and O. S. Andersen, "Gramicidin channels that have no tryptophan residues," Biochemistry, vol. 31, pp. 5340-5350, 1992.
69. A. R. Jude, D. V. Greathouse, R. E. Koeppe II, L. L. Providence, and O. S. Andersen, "Modulation of gramicidin channel structure and function by the aliphatic 'spacer' residues 10, 12, and 14 between the tryptophans," Biochemistry, vol. 38, pp. 1030-1039, 1999.
70. 2 in gramicidin channels," Biochemistry, vol. 34, pp. 6827-6837, 1995.
71. 15-gramicidin A incorporated into SDS micelles and PC/PG vesicles," Biochemistry, vol. 42, pp. 1401-1409, 2003.
72. D. G. Levitt, S. R. Elias, and J. M. Hautman, "Number of water molecules coupled to the transport of sodium, potassium and hydrogen ions via gramicidin, nonactin or valinomycin," Biochim. Biophys. Acta, vol. 512, pp. 436-451, 1978.
73. P. A. Rosenberg and A. Finkelstein, "Interaction of ions and water in gramicidin A channels: streaming potentials across lipid bilayer membranes," J. Gen. Physiol., vol. 72, pp. 327-340, 1978.
74. E. Neher, J. Sandblom, and G. Eisenman, "Ionic selectivity, saturation, and block in gramicidin A channels. II. Saturation behavior of single channel conductances and evidence for the existence of multiple binding sites in the channel," J. Membr. Biol., vol. 40, pp. 97-116, 1978.
75. O. S. Andersen, "Ion movement through gramicidin A channels. Single-channel measurements at very high potentials," Biophys. J., vol. 41, pp. 119-133, 1983.
76. B. A. Wallace, W. R. Veatch, and E. R. Blout, "Conformation of gramicidin A in phospholipid vesicles: circular dichroism studies of effects of ion binding, chemical modification, and lipid structure," Biochemistry, vol. 20, pp. 5754-5760, 1981.
77. F. Tian and T. A. Cross, "Cation transport: an example of structural based selectivity," J. Mol. Biol., vol. 285, pp. 1993-2003, 1999.
78. D. W. Urry, T. L. Trapane, C. M. Venkatachalam, and R. B. McMichens, "Ion interactions at membranous polypeptide sites using nuclear magnetic resonance: determining rate and binding constants and site locations," Methods Enzymol., vol. 171, pp. 286-342, 1989.
79. G. A. Olah, H. W. Huang, W. Liu, and Y. Wu, "Location of ion-binding sites in the gramicidin channel by X-ray diffraction," J. Mol. Biol., vol. 218, pp. 847-858, 1991.
80. L. V. Schagina, A. E. Grinfeldt, and A. A. Lev, "Interaction of cation fluxes in gramicidin A channels in lipid bilayer membranes," Nature, vol. 273, pp. 243-245, 1978.
81. H. A. Kramers, "Brownian motion in a field of force and the diffusion model of chemical reactions," Physica, vol. 7, pp. 284-304, 1940.
82. O. S. Andersen, "Kinetics of ion movement mediated by carriers and channels," Methods Enzymol., vol. 171, pp. 62-112, 1989.
83. B. Roux, T. W. Allen, T. W. Bernèche, and W. Im, "Theoretical and computational models of biological ion channels," Q. Rev. Biophys., vol. 37, pp. 15-103, 2004.
84. O. S. Andersen, "Ion movement through gramicidin A channels. Studies on the diffusion-controlled association step," Biophys. J., vol. 41, pp. 147-165, 1983.
85. _, "Ion movement through gramicidin A channels. Interfacial polarization effects on single-channel current measurements," Biophys. J., vol. 41, pp. 135-146, 1983.
86. E. Bamberg, K. Noda, E. Gross, and P. Läuger, "Single-channel parameters of gramicidin A, B, and C," Biochim. Biophys. Acta, vol. 419, pp. 223-228, 1976.
87. J. S. Morrow, W. R. Veatch, and L. Stryer, "Transmembrane channel activity of gramicidin A analogs: effects of modification and deletion of the amino-terminal residue," J. Mol. Biol., vol. 132, pp. 733-738, 1979.
88. F. Heitz, G. Spach, and Y. Trudelle, "Single channels of 9,11,13,15-destryptophyl-phenylalanyl-gramicidin A," Biophys, J., vol. 40, pp. 87-89, 1982.
89. E. W. B. Russell, L. B. Weiss, F. I. Navetta, R. E. Koeppe II, and O. S. Andersen, "Single-channel studies on linear gramicidins with altered amino acid side chains. Effects of altering the polarity of the side chain at position 1 in gramicidin A," Biophys. J., vol. 49, pp. 673-686, 1986.
90. R. E. Koeppe II, J.-L. Mazet, and O. S. Andersen, "Distinction between dipolar and inductive effects in modulating the conductance of gramicidin channels," Biochemistry, vol. 29, pp. 512-520, 1990.
91. O. S. Andersen, D. V. Greathouse, L. L. Providence, M. D. Becker, and R. E. Koeppe II, "Importance of tryptophan dipoles for protein function: 5-fluorination of tryptophans in gramicidin A channels," J. Amer. Chem. Soc., vol. 120, pp. 5142-5146, 1998.
92. C. D. Cole, A. S. Frost, N. Thompson, M. Cotten, T. A. Cross, and D. D. Busath, "Noncontact dipole effects on channel permeation. VI. 5F-and 6F-Trp gramicidin channel currents," Biophys. J., vol. 83, pp. 1974-1986, 2002.
93. B. W. Urban, S. B. Hladky, and D. A. Haydon, "Ion movements in gramicidin pores. An example of single-file transport," Biochim. Biophys, Acta, vol. 602, pp. 331-354, 1980.
94. 13 gramicidin A channels," Biophys. J., vol. 75, pp. 2830-2844, 1998.
95. M. D. Becker, R. E. Koeppe II, and O. S. Andersen, "Amino acid substitutions and ion channel function: model-dependent conclusions," Biophys. J., vol. 62, pp. 25-27, 1992.
96. S. König, E. Sackmann, D. Richter, R. Zorn, C. Carlile, and T. M. Bayerl, "Molecular dynamics of water in oriented DPPC multilayers studied by quasielastic neutron scattering and deuterium-nuclear magnetic resonance relaxation," J Chem. Phys., vol. 100, pp. 3307-3316, 1994.
97. 4 cm/s," J. Phys. Chem., vol. 100, pp. 4622-4629, 1996.
98. A. Einstein, "Theoretische Betrachtungen über der Brownsche Bewegungen," Zeit. f. Elektrochemie, vol. 13, pp. 41-42, 1907.
99. R. Wolfenden and M. J. Snider, "The depth of chemical time and the power of enzymes as catalysts," Acc. Chem. Res., vol. 12, pp. 938-945, 2001.
100. T. Hanai, D. A. Haydon, and J. Taylor, "The variation of capacitance and conductance of bimolecular lipid membranes with area," J. Theor. Biol., vol. 9, pp. 433-443, 1965.
101. A. L. Hodgkin and B. Katz, "The effect of sodium ions on the electrical activity of the giant axon of the squid," J. Physiol., vol. 108, pp. 37-77, 1949.
102. O. S. Andersen, "Elementary aspects of acid-base permeation and pH regulation," Ann. New York Acad. Sci., vol. 574, pp. 333-353, 1989.
103. B. Roux, B. Prod'hom, and M. Karplus, "Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy," Biophys. J., vol. 68, pp. 876-892, 1995.
104. P. C. Jordan, "The total electrostatic potential in a gramicidin channel," J. Membr. Biol., vol. 78, pp. 91-102, 1984.
105. M. Sancho and G. Martinez, "Electrostatic modeling of dipole-ion interactions in gramicidin like channels," Biophys. J., vol. 60, pp. 81-88, 1991.
106. D. Caywood, J. Durrant, P. Morrison, and D. D. Busath, "The Trp potential deduced from gramicidin A/gramicidin M channels," Biophys. J., vol. 86, p. 55a, 2004.
107. S. Y. Noskov, S. Bernèche, and B. Roux, "Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands," Nature, vol. 431, pp. 830-834, 2004.
108. L,D-helices) as permselective transmembrane channels," in Proc. Jerusalem Symp. Quant. Chem. Biochem., vol. 5, 1973, pp. 723-736.
109. S. Edwards, B. Corry, S. Kuyucak, and S.-H. Chung, "Continuum electrostatics fails to describe ion permeation in the gramicidin channel," Biophys. J., vol. 83, p. 1348, 2002.
110. B. Roux, "Theoretical and computational models of ion channels," Curr. Opin. Struct. Biol., vol. 12, pp. 182-189, 2002.
111. T. W. Allen, T. Bastug, S. Kuyucak, and S.-H. Chung, "Gramicidin A channel as a test ground for molecular dynamics force fields," Biophys. J., vol. 84, p. 2159, 2003.
112. T. W. Allen, O. S. Andersen, and B. Roux, "Energetics of ion conduction through the gramicidin channel," Proc. Nat. Acad. Sci. USA, vol. 101, pp. 117-122, 2004.
113. P. H. Hünenberger and J. A. McCammon, "Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: a continuum electrostatics study," J. Chem. Phys., vol. 110, p. 1856, 1999.
114. + by gramicidin A," Biophys. J., vol. 56, pp. 171-182, 1989.
115. A. B. Mamanov, R. D. Coalson, A. Nitzan, and M. G. Kumikova, "The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents," Biophys. J., vol. 84, pp. 3646-3661, 2003.
116. G. Lamoureux and B. Roux, "Modeling induced polarizability with classical Drude oscillators: theory and molecular dynamics simulation algorithm.," J. Chem. Phys., pp. 3025-3039, 2003.
117. V. M. Anisimov, I. V. Vorobyov, G. Lamoureux, S. Noskov, B. Roux, and A. D. MacKerell Jr., "CHARMM all-atom polarizable force field parameter development for nucleic acids," Biophys. J., vol. 86, p. 415a, 2004.
118. G. Lamoureux, A. D. MacKerell Jr., and B. Roux, "A simple polarizable water model based on classical Drude oscillators," J. Chem. Phys., pp. 5185-5197, 2003.