Analysis and evaluation of channel models: Simulations of alamethicin

Biophysical Journal

Volumn 83, Issue 5, 2002, Pages 2393-2407

  Peter Tieleman, D ^a   Hess, Berk ^b   Sansom, Mark S P ^c  

^a UNIVERSITY OF CALGARY   (Canada)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALAMETHICIN; AQUAPORIN; ION CHANNEL; PHOSPHATIDYLCHOLINE; ANTIINFECTIVE AGENT; CALCIUM; CALCIUM CHANNEL; PEPTIDE; POTASSIUM CHLORIDE;

ALGORITHM; ARTICLE; ARTIFACT REDUCTION; CHANNEL GATING; COVARIANCE; CRYSTAL STRUCTURE; ELECTRICITY; ION CONDUCTANCE; LIPID BILAYER; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; PERIODICITY; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; BIOPHYSICS; CELL MEMBRANE POTENTIAL; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; PH; PRESSURE; TEMPERATURE; TIME;

ALAMETHICIN; ALGORITHMS; ANTI-INFECTIVE AGENTS; BIOPHYSICS; CALCIUM; CALCIUM CHANNELS; COMPUTER SIMULATION; ELECTROSTATICS; HYDROGEN-ION CONCENTRATION; LIPID BILAYERS; MEMBRANE POTENTIALS; PEPTIDES; PHOSPHATIDYLCHOLINES; POTASSIUM CHLORIDE; PRESSURE; PROTEIN STRUCTURE, SECONDARY; TEMPERATURE; TIME FACTORS;

EID: 0036841855     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)75253-3     Document Type: Article

References (71)

1. Adcock, C., G. R. Smith, and M. S. P. Sansom. 1998. Electrostatics and the ion selectivity of ligand-gated channels. Biophys. J. 75:1211-1222.
2. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulation of Liquids. Oxford University Press, Oxford.
3. Bechinger, B. 1997. Structure and functions of channel-forming peptides: Magainins, cecropins, melittin and alamethicin. J. Membr. Biol. 156:197-211.
4. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
5. Berendsen, H. J. C., D. van der Spoel, and R. van Drunen. 1995. GROMACS: A message-passing parallel molecular dynamics implementation. Comp. Phys. Commun. 95:43-56.
6. Berger, O., O. Edholm, and F. Jahning. 1997. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidycholine at full hydration, constant pressure and constant temperature. Biophys. J. 72:2002-2013.
7. Bond, P. J., J. D. Faraldo-Gomez, and M. S. P. Sansom. 2002. OmpA: A pore or not a pore? Simulation and modeling studies. Biophys. J. 83:763-775.
8. Borisenko, V., M. S. P. Sansom, and G. A. Woolley. 2000. Protonation of lysine residues inverts cation/anion selectivity in a model channel. Biophys. J. 78:1335-1348.
9. Breed, J., P. C. Biggin, I. D. Kerr, O. S. Smart, and M. S. P. Sansom. 1997. Alamethicin channels: Modelling via restrained molecular dynamics simulations. Biochim. Biophys. Acta. 1325:235-249.
10. Cafiso, D. S. 1994. Alamethicin: A peptide model for voltage gating and protein membrane interactions. Annu. Rev. Biophys. Biomol. Struct. 23:141-165.
11. Capener, C. E., and M. S. P. Sansom. 2002. Molecular dynamics simulations of a K channel model: Sensitivity to changes in ions, waters, and membrane environment. J. Phys. Chem. B. 106:4543-4551.
12. Capener, C. E., I. H. Shrivastava, K. M. Ranatunga, L. R. Forrest, and M. S. P. Sansom. 2000. Homology modeling and molecular dynamics simulation studies of an inward rectifier potassium channel. Biophys. J. 78:2929-2942.
13. Chang, G., R. H. Spencer, A. T. Lee, M. T. Barclay, and D. C. Rees. 1998. Structure of the MscL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel. Science. 282:2220-2226.
14. Dieckmann, G. R., J. D. Lear, Q. Zhong, M. L. Klein, W. F. DeGrado, and K. A. Sharp. 1999. Exploration of the structural features defining the conduction properties of a synthetic ion channel. Biophys. J. 76:618-630.
15. Doering, C. R., and J. C. Gadoua. 1992. Resonant activation over a fluctuating barrier. Phys. Rev. Lett. 69:2318-2321.
16. Doyle, D. A., J. M. Cabral, R. A. Pfuetzner, A. Kuo, J. M. Gulbis, S. L. Cohen, B. T. Cahit, and R. MacKinnonl. 1998. The structure of the potassium channel: Molecular basis of K+ conduction and selectivity. Science. 280:69-77.
17. Duclohier, H., and H. Wroblewski. 2001. Voltage-dependent pore formation and antimicrobial activity by alamethicin and analogues. J. Membr. Biol. 184:1-12.
18. Dutzler, R., E. B. Campbell, M. Cadene, B. T. Chait, and R. MacKinnon. 2002. X-ray structure of a CLC chloride channel at 3.0 angstrom reveals the molecular basis of anion selectivity. Nature. 415:287-294.
19. Essmann, U., L. Perera, and M. L. Berkowitz. 1995. A smoth particle mesh ewald method. J. Chem. Phys. 103:8577-8593.
20. Feller, S. E., R. W. Pastor, A. Rojnuckarin, S. Bogusz, and B. R. Brooks. 1996. Effect of electrostatic force truncation on interfacial and transport-properties of water. J. Phys. Chem. 100:17011-17020.
21. Forrest, L. R., A. Kukol, I. T. Arkin, D. P. Tieleman, and M. S. P. Sansom. 2000. Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer. Biophys. J. 78:55-69.
22. Gibbs, N., R. B. Sessions, P. B. Williams, and C. E. Dempsey. 1997. Helix bending in alamethicin: Molecular dynamics simulations and amide hydrogen exchange in methanol. Biophys. J. 72:2490-2495.
23. Hanke, W., and G. Boheim. 1980. The lowest conductance state of the alamethicin pore. Biochim. Biophys. Acta. 596:456-462.
24. Hess, B. 2000. Similarities between principal components of protein dynamics and random diffusion. Phys. Rev. E. 62:8438-8448.
25. Hess, B. 2001. Convergence of sampling in protein simulations. Phys. Rev. E. 65:031910.
26. Hess, B. 2002. Determining the shear viscosity of model liquids from molecular dynamics simulations. J. Chem. Phys. 116:209-217.
27. Hess, B., H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije. 1997. LINCS: A linear constraint solver for molecular simulations. J. Comp. Chem. 18:1463-1472.
28. Hunenberger, P. H., and J. A. McCammon. 1999. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study. Biophys. Chem. 78:69-88.
29. Im, W., S. Seefeld, and B. Roux. 2000. Grand canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophys. J. 79:788-801.
30. Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
31. Kessel, A., D. S. Cafiso, and N. Ben-Tal. 2000. Continuum solvent model calculations of alamethicin-membrane interactions: Thermodynamic aspects. Biophys. J. 78:571-83.
32. Kraulis, P. J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24:946-950.
33. Kuyucak, S., O. S. Andersen, and Shin-Ho Chung. 2001. Models of permeation in ion channels. Rep. Prog. Phys. 64:1427-1472.
34. Law, R. J., L. R. Forrest, K. M. Ranatunga, P. LaRocca, D. P. Tieleman, and M. S. P. Sansom. 2000. Structure and dynamics of the pore-lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers, and transbilayer bundles. Proteins Struct. Funct. Genet. 39:47-55.
35. Law, R. J., D. P. Tieleman, and M. S. P. Sansom. Pores formed by the nicotinic receptor M2d peptide: A molecular dynamics study. Biophys. J. In press.
36. Lear, J. D., Z. R. Wasserman, and W. F. DeGrado. 1988. Synthetic amphiphilic peptide models for protein ion channels. Science. 240:1177-1181.
37. Levy, R. M., and E. Gallicchio. 1998. Computer simulations with explicit solvent: Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Ann. Rev. Phys. Chem. 49:531-567.
38. Parsegian, V. A. 1969. Energy of an ion crossing a low dielectric membrane: Solutions to four relevant electrostatic problems. Nature. 224:1197-1198.
39. Popot, J. L., and D. M. Engelman. 2000. Helical membrane protein folding, stability, and evolution. Ann. Rev. Biochem. 69:881-922.
40. Randa, H. S., L. R. Forrest, G. A. Voth, and M. S. P. Sansom. 1999. Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane. Biophys. J. 77:2400-2410.
41. Sansom, M. S. P. 1991. The biophysics of peptide models of ion channels. Prog. Biophys. Mol. Biol. 55:139-235.
42. Sansom, M. S. P. 1993a. Alamethicin and related peptaibols: Model ion channels. Eur. Biophys. J. 22:105-124.
43. Sansom, M. S. 1993b. Structure and function of channel-forming peptaibols. Q. Rev. Biophys. 26:365-421.
44. Sansom, M. S. P., I. D. Kerr, J. Breed, and R. Sankararamakrishnan. 1996. Water in channel-like cavities: Structure and dynamics. Biophys. J. 70:693-702.
45. Sansom, M. S. P., and H. Weinstein. 2000. Hinges, swivels and switches: The role of prolines in signalling via transmembrane alpha-helices. Trends Pharmacol. Sci. 21:445-451.
46. Shrivastava, I. H., and M. S. P. Sansom. 2000. Simulations of ion permeation through a potassium channel: Molecular dynamics of KcsA in a phospholipid bilayer. Biophys. J. 78:557-570.
47. Sigworth, F. J. 1985. Open channel noise: 1. Noise in acetylcholine-receptor currents suggests conformational fluctuations. Biophys. J. 47:709-720.
48. Smart, O. S., J. Breed, G. R. Smith, and M. S. P. Sansom. 1997. A novel method for structure-based prediction of ion channel conductance properties. Biophys. J. 72:1109-1126.
49. Smart, O. S., G. M. P. Coates, M. S. P. Sansom, G. M. Alder, and C. L. Bashford. 1998. Structure-based prediction of the conductance properties of ion channels. Faraday Discuss. 111:185-199.
50. Smart, O. S., J. M. Goodfellow, and B. A. Wallace. 1993. The pore dimensions of gramicidin A. Biophys. J. 65:2455-2460.
51. Smart, O. S., J. G. Neduvelil, X. Wang, B. A. Wallace, and M. S. P. Sansom. 1996. HOLE: A program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14:354-360.
52. Tieleman, D. P., and H. J. C. Berendsen. 1998. A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys. J. 74:276-2801.
53. Tieleman, D. P., H. J. C. Berendsen, and M. S. P. Sansom. 1999a. An alamethicin channel in a lipid bilayer: Molecular dynamics simulations. Biophys. J. 76:1757-1769.
54. Tieleman, D. P., H. J. C. Berendsen, and M. S. P. Sansom. 2001a. Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water interfaces. Biophys. J. 80:331-346.
55. Tieleman, D. P., J. Breed, H. J. C. Berendsen, and M. S. P. Sansom. 1998. Alamethicin channels in a membrane: Molecular dynamics simulations. Faraday Disc. 111:209-223.
56. Tieleman, D. P., S. J. Marrink, and H. J. C. Berendsen. 1997. A computer perspective of membranes: Molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta. 1331:235-270.
57. Tieleman, D. P., and M. S. P. Sansom. 2001. Molecular dynamics simulations of antimicrobial peptides: From membrane binding to transmembrane channels. Int. J. Quant. Chem. 83:166-179.
58. Tieleman, D. P., M. S. P. Sansom, and H. J. C. Berendsen. 1999b. Alamethicin helices in a bilayer and in solution: Molecular dynamics simulations. Biophys. J. 76:40-49.
59. Tieleman, D. P., I. H. Shrivastava, M. B. Ulmschneider. and M. S. P. Sansom. 2001b. Proline-induced hinges in trans-membrane helices: Possible roles in ion-channel gating. Proteins Struct. Funct. Genet. 44:63-72.
60. Tieleman, D. P., G. R. Smith, P. C. Biggin, and M. S. P. Sansom. 2001c. Simulation approaches to ion channel structure-function relationships. Q. Rev. Biophys. 34:473-561.
61. Tobias. D. J., K. C. Tu, and M. L. Klein. 1997. Atomic-scale molecular dynamics simulations of lipid membranes. Curr. Opin. Colloid Interface Sci. 2:15-26.
62. Unwin, N. 1995. Acetylcholine receptor channel imaged in the open state. Nature. 373:37-43.
63. Vodyanoy, I., S. M. Bezrukov, and V. A. Parsegian. 1993. Probing alamethicin channels with water-soluble polymers: Size-modulated osmotic action. Biophys. J. 65:23-27.
64. Wang, W., O. Donini, C. M. Reyes, and P. A. Kollman. 2001. Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu. Rev. Biophys. Biomol. Struct. 30:211-243.
65. Warshel, A., and A. Papazyan. 1998. Electrostatic effects in macromolecules: Fundamental concepts and practical modeling. Curr. Opin. Struct. Biol. 8:211-217.
66. Weber, W., P. H. Hunenberger, and J. A. McCammon. 2000. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation. J. Phys. Chem. B. 104:3668-3675.
67. White, S. H., and W. C. Wimley. 1999. Membrane protein folding and stability: Physical principles. Annu. Rev. Biophys. Biomed. 28:319-365.
68. Woolley, G. A., P. C. Biggin, A. Schultz, L. Lien, D. C. J. Jaikaran, J. Breed, K. Crowhurst, and M. S. P. Sansom. 1997. Intrinsic rectification of ion flux in alamethicin channels: Studies with an alamethicin dimer. Biophys. J. 73:770-778.
69. Woolley, G. A., and B. A. Wallace. 1992. Model ion channels: Gramicidin and alamethicin. J. Membr. Biol. 129:109-136.
70. Yeh, I. C., and M. L. Berkowitz. 1999. Ewald summation for systems with slab geometry. J. Chem. Phys. 111:3155-3162.
71. You, S. C., S. Y. Peng, L. Lien, J. Breed, M. S. P. Sansom, and G. A. Woolley. 1996. Engineering stabilized ion channels: Covalent dimers of alamethicin. Biochemistry. 35:6225-6232.