Molecular dynamics simulation of the cytosolic mouth in Kcv-type potassium channels

Biochemistry

Volumn 46, Issue 16, 2007, Pages 4826-4839

  Tayefeh, Sascha ^a   Kloss, Thomas ^a   Thiel, Gerhard ^a   Hertel, Brigitte ^a   Moroni, Anna ^b   Kast, Stefan M ^a  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

KCV-TYPE POTASSIUM CHANNELS; LOCAL SEQUENCE MOTIFS; POISSON-BOLTZMANN; STRUCTURAL AVERAGING;

COMPUTER SIMULATION; INTEGRAL EQUATIONS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; POTASSIUM; SIMULATED ANNEALING;

CELL CULTURE;

ALANINE; POTASSIUM CHANNEL; POTASSIUM CHANNEL KCV; POTASSIUM ION; PROLINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHANNEL GATING; CONTROLLED STUDY; DELETION MUTANT; ENERGY TRANSFER; HUMAN; HUMAN CELL; HYDROPHILICITY; MOLECULAR DYNAMICS; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; POTASSIUM CHANNELS; POTASSIUM CHANNELS, INWARDLY RECTIFYING; SEQUENCE ALIGNMENT; THERMODYNAMICS; VIRAL PROTEINS;

EID: 34247485862     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi602468r     Document Type: Article

References (74)

1. Plugge, B., Gazzarrini, S., Nelson, M., Cerana, R., Van Etten, J. L., Derst, C., DiFrancesco, D., Moroni, A., and Thiel, G. (2000) A potassium channel protein encoded by chlorella virus PBCV-1, Science 287, 1641-1644.
2. Gazzarrini, S., Severino, M., Lombardi, M., Morandi, M., DiFrancesco, D., Van Etten, J. L., Thiel, G., and Moroni, A. (2003) The viral potassium channel Kcv: structural and functional features, FEBS Lett. 552, 12-16.
3. Kang, M., Graves, M., Mehmel, M., Moroni, A., Gazzarrini, S., Thiel, G., Gurnon, J. R., and Van Etten, J. L. (2004) Genetic diversity in chlorella viruses flanking Kcv, a gene that encodes a potassium ion channel protein, Virology 326, 150-159.
4. + channels, Science 258, 1152-1155.
5. Kuo, A., Gulbis, J. M., Antcliff, J. F., Rahman, T., Lowe, E. D., Zimmer, J., Cuthbertson, J., Ashcroft, F. M., Ezaki, T., and Doyle, D. A. (2003) Crystal structure of the potassium channel KirBac1.1 in the closed state, Science 300, 1922-1926.
6. Gazzarrini, S., Kang, M., Van Etten, J. L., Tayefeh, S., Kast, S. M., DiFrancesco, D., Thiel, G., and Moroni, A. (2004) Long-distance interactions within the potassium channel pore are revealed by molecular diversity of viral proteins, J. Biol. Chem. 279, 28443-28449.
7. Doyle, D. A. (2004) Structural changes during ion channel gating, Trends Neurosci. 27, 298-302.
8. Doyle, D. A. (2004) Structural themes in ion channels, Eur. Biophys. J. 33, 175-179.
9. +-channel activation gating, Science 285, 73-78.
10. Beckstein, O., Biggin, P. C., Bond, P., Bright, J. N., Domene, C., Grottesi, A., Holyoake, J., and Sansom, M. S. P. (2003) Ion channel gating: insights via molecular simulations, FEBS Lett. 555, 85-90.
11. Grottesi, A., Domene, C., Hall, B., and Sansom, M. S. P. (2005) Conformational dynamics of M2 helices in KirBac channels: Helix flexibility in relation to gating via molecular dynamics simulations, Biochemistry 44, 14586-14594.
12. Kuo, A., Domene, C., Johnson, L. N., Doyle, D. A., and Vénien-Bryan, C. (2005) Two different conformational states of the KirBac3.1 potassium channel revealed by electron crystallography, Structure 13, 1463-1472.
13. Robertson, J. L., and Roux, B. (2005) One channel: open and closed, Structure 13, 1398-1400.
14. + channels, Annu. Rev. Biophys. Biomol. Struct. 34, 153-171.
15. Bichet, D., Lin, Y., Ibarra, C. A., Huang, C. S., Yi, B. A., Jan, Y. N., and Jan, L. Y. (2004) Evolving potassium channels by means of yeast selection reveals structural elements important for selectivity, Proc. Natl. Acad. Sci. U.S.A. 101, 4441-4446.
16. + channel: Simulation studies of KirBac1.1, Biophys. J. 87, 256-267.
17. VanDongen, A. M. J. (2004) K channel gating by an affinity switching selectivity filter, Proc. Natl. Acad. Sci. U.S.A. 101, 3248-3252.
18. Corsero-Morales, J. F., Cuello, L. G., Zhao, Y., Jogini, V., Cortes, D. M., Roux, B., and Perozo, E. (2006) Molecular determinants of gating at the potassium-channel selectivity filter, Nat. Struct. Mol. Biol. 13, 311-318.
19. Shrivastava, I. H., and Bahar, I. (2006) Common mechanism of pore opening shared by five different potassium channels, Biophys. J. 90, 3929-3940.
20. + channel Kcv, J. Membr. Biol. 210, 1-9.
21. Moroni, A., Viscomi, C., Sangiorgio, V., Pagliuca, C., Meckel, T., Horvath, F., Gazzarrini, S., Valbuzzi, P., Van Etten, J. L., DiFrancesco, D., and Thiel, G. (2002) The short N-terminus is required for functional expression of the virus-encoded miniature K(+) channel Kcv, FEBS Lett. 530, 65-69.
22. +-Kanal Kcv: Funktionelle Rolle des N-Terminus bei der Regulation von Kanalaktivität, Ph.D. Thesis, Technische Universität Darmstadt, Darmstadt, Germany.
23. Sansom, M. S. P., Shrivastava, I. H., Bright, J. N., Tate, J., Capener, C. E., and Biggin, P. C. (2002) Potassium channels: structures, models, simulations, Biochim. Biophys. Acta 1565, 294-307.
24. Woolf, T. B., and Roux, B. (1994) Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer, Proc. Natl. Acad. Sci. U.S.A. 91, 11631-11635.
25. Woolf, T. B., and Roux, B. (1996) Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer, Proteins: Struct., Funct., Genet. 24, 92-114.
26. Berneche, S., and Roux, B. (2000) Molecular dynamics of the KcsA K(+) channel in a bilayer membrane, Biophys. J. 78, 2900-2917.
27. Allen, T. W., Kuyucak, S., and Chung, S. H. (1999) Molecular dynamics study of the KcsA potassium channel, Biophys. J. 77, 2502-2516.
28. Roux, B., Allen, T., Bernèche, S., and Im, W. (2004) Theoretical and computational models of biological ion channels, Q. Rev. Biophys. 37, 15-103.
29. Capener, C. E., Shrivastava, I. H., Ranatunga, K. M., Forrest, L. R., Smith, G. R., and Sansom, M. S. P. (2000) Homology modeling and molecular dynamic simulation studies of an inward rectifier potassium channel, Biophys. J. 78, 2929-2942.
30. Capener, C. E., Kim, H. J., Arinaminpathy, Y., and Sansom, M. S. P. (2002) Ion channels: structural bioinformatics and modelling, Hum. Mol. Genet. 11, 2425-2433.
31. Haider, S., Grottesi, A., Hall, B. A., Ashcroft, F. M., and Sansom, M. S. P. (2005) Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating, Biophys. J. 88, 3310-3320.
32. Yu, K., Fu, W., Liu, H., Luo, X., Chen, K. X., Ding, J., Shen, J., and Jiang, H. (2004) Computational simulations of interactions of scorpion toxins with the voltage-gated potassium ion channel, Biophys. J. 86, 3542-3555.
33. Roux, B., Berneche, S., and Im, W. (2000) Ion channels, permeation, and electrostatics: insight into the function of KcsA, Biochemistry 39, 13295-13306.
34. Beglov, D., and Roux, B. (1997) An integral equation to describe the solvation of polar molecules in liquid water, J. Phys. Chem. B 101, 7821-7826.
35. Kovalenko, A., and Hirata, F. (1998) Three-dimensional density profiles of water in contact with a solute of arbitrary shape: a RISM approach, Chem. Phys. Lett. 290, 237-244.
36. + selectivity of KcsA potassium channel analyzed by reference interaction site model (RISM) integral equation theory, Chem. Phys. Lett. 365, 110-116.
37. + selectivity of KcsA potassium channel with reference interaction site model theory, Mol. Phys. 103, 191-201.
38. + conduction and selectivity, Science 280, 69-77.
39. Jiang, Y., Lee, A., Chen, J., Cadene, M., Chait, B. T., and MacKinnon, R. (2002) Crystal structure and mechanism of a calcium-gated potassium channel, Nature 417, 515-522.
40. + channel, Nature 423, 33-41.
41. + channel, Science 309, 897-903.
42. + conducting channel, Nature 23, 427-429.
43. + channel, Biophys. J. 77, 789-807.
44. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem. 4, 187-217.
45. Sali, A., and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol. 234, 779-815.
46. + channel, Biophys. J. 82, 772-780.
47. Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., and Schulten, K. (1999) NAMD2: greater scalability for parallel molecular dynamics, J. Comput. Phys. 151, 283-312.
48. MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-atom empirical potential for molecular modelling and dynamics studies of proteins, J. Phys. Chem. B 102, 3586-3616.
49. Schlenkrich, M., Brickmann, J., MacKerell, A. D., Jr., and Karplus, M. (1996) An empirical potential energy function for phospholipids: criteria for parameter optimization and applications, in Biological Membranes: A Molecular Perspective from Computa tion and Experiment (Merz, K. M., and Roux, B., Eds.) pp 31-81, Birkkauser, Boston, MA.
50. Jorgensen, W. L., Chandrasekhar, J., and Madura, J. D. (1983) Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79, 926-935.
51. Roux, B. (2006) http://thallium.bsd.uchicago.edu/RouxLab/.
52. Ryckaert, K. P., Ciccoti, G., and Berendsen, H. J. C. (1977) Numerical integration of the Cartesian equation of motions of a system with constraints: molecular dynamics of n-alkanes, J. Comput. Chem. 23, 327-341.
53. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle mesh Ewald method, J. Chem. Phys. 103, 8577-8593.
54. Tu, K., Tobias, D. J., and Klein, M. L. (1995) Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer, Bio phys. J. 69, 2558-2562.
55. Feller, S. E., Zhang, Y., Pastor, R. W., and Brooks, B. R. (1995) Constant pressure molecular dynamics simulation: the Langevin piston method, J. Chem. Phys. 103, 4613-4621.
56. Bernèche, S., Nina, M., and Roux, B. (1998) Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane, Biophys. J. 75, 1603-1618.
57. Smart, O. S., Neduvelil, J. G., Wang, X., Wallace, B. A., and Sansom, M. S. P. (1996) HOLE: a program for the analysis of the pore dimensions of ion channel structural models, J. Mol. Graphics 14, 354-360.
58. Honig, B., Sharp, K., and Yang, A. S. (1993) Macroscopic models of aqueous solutions: biological and chemical applications, J. Phys. Chem. 97, 1101-1109.
59. Weill Medical College of Cornell University, Department of Physiology and Biophysics (2005) RMSDTT: RMSD Trajectory Tool, http://physiology.med.cornell. edu/faculty/hweinstein/vmd-plugins/rmsdtt/.
60. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD - visual molecular dynamics, J. Mol. Graphics 14, 33-38.
61. + channels, J. Mol. Biol. 354, 272-288.
62. Nina, M., Beglov, D., and Roux, B. (1997) Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations, J. Phys. Chem. B 1001, 5239-5248.
63. Im, W., Beglov, D., and Roux, B. (1998) Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation, Comp. Phys. Commun. 111, 59-75.
64. Perkyns, J., and Pettitt, B. M. (1992) A site-site theory for finite concentration saline solutions J. Chem. Phys. 97, 7656-7666.
65. Kovalenko, A., and Hirata, F. (2000) Potentials of mean force of simple ions in ambient aqueous solution. I. Three-dimensional reference interaction site model approach, J. Chem. Phys. 112, 10391-10402.
66. Kovalenko, A., Ten-No, S., and Hirata, F. (1999) Solution of three-dimensional reference interaction site model and hypernetted chain equations for simple point charge water by modified method of direct inversion in iterative subspace, J. Comput. Chem. 20, 928-936.
67. Laliberté, M., and Cooper, W. E. (2004) Model for calculating the density of aqueous electrolyte solutions, J. Chem. Eng. Data 49, 1141-1151.
68. Hasted, J. B., Ritson, D. M., and Collie, C. H. (1948) Dielectric properties of aqueous ionic solutions. Parts I and II, J. Chem. Phys. 16, 1-21.
69. Kovalenko, A., and Hirata, F. (1999) Potential of mean force between two molecular ions in a polar molecular solvent: a study by the three-dimensional reference interaction site model, J. Phys. Chem. B 103, 7942-7957.
70. Brickmann, J., Goetze, T., Heiden, W., Moeckel, G., Reiling, S., Vollhardt, H., and Zachmann, C.-D. (1995) Interactive visualization of molecular scenarios with MOLCAD/SYBYL, in Data Visualisation in Molecular Science: Tools for Insight and Innovation (Bowie, J. E., Ed.) pp 83-97, Addison-Wesley, Reading, MA.
71. Grottesi, A., Domene, C., Haider, S., and Sansom, M. S. P. (2005) Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function, IEEE Trans. Nanobiosci. 4, 112-119.
72. Shrivastava, I. H., and Sansom, M. S. P. (2000) Simulations of ion permeation through a K channel: molecular dynamics of KcsA in a phosphor-lipid bilayer, Biophys. J. 78, 557-570.
73. Domene, C., Vemparala, S., Klein, M. L., Vénien-Bryan, C., and Doyle, D. A. (2006) Role of aromatic localization in the gating process of a potassium channel, Biophys. J. 90, L01-L03.
74. + channel, Biochemistry 46, 1079-1090.