Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel

Journal of Physical Chemistry B

Volumn 111, Issue 5, 2007, Pages 1090-1098

  Kutteh, Ramzi ^a   Vandenberg, Jamie I ^b,c   Kuyucak, Serdar ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b VICTOR CHANG CARDIAC RESEARCH INSTITUTE   (Australia)

^c UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CARDIOLOGY; CHANNEL FLOW; COMPUTER SIMULATION; ELECTROSTATICS; GENES; MOLECULAR DYNAMICS; POTENTIAL ENERGY;

CONTINUUM ELECTROSTATICS; FAST INACTIVATION; GENETIC MUTATIONS; POTASSIUM CHANNEL;

PROTEINS;

EID: 33847064660     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp066294d     Document Type: Article

References (52)

1. Kr potassium channel. Cell 1995, 81, 299-307.
2. Smith, P. L.; Baukrowitz, T.; Yellen, G. The inward rectification mechanism of the HERG cardiac potassium channel. Nature 1996, 379, 833-836.
3. Kr channel. J. Gen. Physiol. 1996, 107, 611-619.
4. Kr: The HERG channel. J. Mol. Cell. Cardiol. 2001, 33, 835-849.
5. Curran, M. E.; Splawski, I.; Timothy, K. W.; Vincent, G. M.; Green, E. D.; Keating, M. T. A molecular basis for cardiac arrhythmia: HERG mutations cause long QT syndrome. Cell 1995, 80, 795-803.
6. Brugada, R.; Hong, K.; Dumaine, R.; Cordeiro, J.; Gaita, F.; Borggrefe, M.; Menendez, T. M.; Brugada, J.; Pollevick, G. D.; Wolpert, C.; Burashnikov, E.; Matsuo, K.; Wu, Y. S.; Guerchicoff, A.; Bianchi, F.; Giustetto, C.; Schimpf, R.; Brugada, P.; Antzelevitch, C. Sudden death associated with short-QT syndrome linked to mutations in HERG. Circulation 2004, 109, 30-35.
7. + channels: Friend and foe. Trends Pharmacol. Sci. 2001, 22, 240-246.
8. + channel. A model for bad behavior. J. Med. Chem. 2003, 46, 2017-2022.
9. Yellen, G. The moving parts of voltage-gated ion channels. Q. Rev. Biophys. 1998, 31, 239-95.
10. +channel: Progress in understanding the molecular basis of its unusual gating kinetics. Eur. Biophys. J. 2004, 33, 89-97.
11. Piper, D. R.; Varghese, A.; Sanguinetti, M. C.; Tristani-Firouzi, M. Gating currents associated with intra-membrane charge displacement in HERG potassium channels. Proc. Nat. Acad. Sci. U.S.A. 2003, 100, 10534-10539.
12. Smith, P. L.; Yellen, G. Fast and slow voltage sensor movements in HERG potassium channels. J. Gen. Physiol. 2002, 119, 275-293.
13. + channels. Circ. Res. 1998, 82, 386-395.
14. Herzberg, I. M.; Trudeau, M. C.; Robertson, G. A. Transfer of rapid inactivation and sensitivity to the class III antiarrhythmic drug E-4031 from HERG to M-eag channels. J. Physiol. 1998, 511, 3-14.
15. Schonherr, R.; Heinemann, S. H. Molecular determinants for activation andinactivation of HERG, a human inward rectifier potassium channel. J. Physiol. 1996, 493, 635-642.
16. Liu, J.; Zhang, M.; Jiang, M.; Tseng, G. N. Structural and functional role of theextracellular S5-P linker in the HERG potassium channel. J. Gen. Physiol. 2002, 120, 723-737.
17. + channel S5-P extracellular linker: Role of anamphipathic α-helix in C-type inactivation. J. Biol. Chem. 2003, 278, 42136-42148.
18. Trudeau, M.; Warmke, J.; Ganetzky, B.; Robertson, G. HERG, a human inward rectifier in the voltage-gated potassium channel family. Science 1995, 269, 92-95.
19. Jiang, M.; Zhang, M.; Maslennikov, I. V.; Liu, J.; Wu, D. M.; Korolkova, Y. V.; Arseniev, A. S.; Grishin, E. V.; Tseng, G. N. Dynamic conformational changes of extracellular S5-P linkers in the hERG channel. J. Physiol. 2005, 569, 75-89.
20. + conduction and selectivity. Science 1998, 280, 69-77.
21. + channel-Fab complex at 2.0 Å resolution. Nature 2001, 414, 43-48.
22. Jiang, Y.; Lee, A.; Chen, J.; Cadane, M.; Chait, B. T.; MacKinnon, R. Crystal structure and mechanism of a calcium-gated potassium channel. Nature 2002, 417, 515-522.
23. + channel. Nature 2003, 423, 33-41.
24. Mitcheson, J. S.; Chen, J.; Lin, M.; Culberson, C.; Sanguinetti, M. C. A structural basis for drug-induced long QT syndrome. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 12329-12333
25. + channel: Application to ligand binding. Bioorg. Med. Chem. Lett. 2005, 15, 1737-1741.
26. Pearlstein, R. A.; Vaz, R. J.; Kang, J.; Chen, X.; Preobrazhenskaya, M.; Shchekotihin, A. E.; Korolev, A. M.; Lysenkova, L. N.; Miroshinkova, O. L.; Hendrix, J.; Rampe, D. Characterization of HERG potassium channel inhibition using 3D QSAR and homology modeling approaches. Bioorg. Med. Chem. Lett. 2003, 13, 1829-1835.
27. + channel using docking and molecular dynamics methods. FEBS Lett. 2005, 579, 2939-2944.
28. Farid, R.; Day, T.; Friesner, R. A.; Pearlstein, R. A. New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies. Bioorg. Med. Chem. 2006, 14, 3160-3173.
29. Tseng, G. N.; Guy, H. R. Structure-function studies of outer mouth and voltage sensor domain of HERG. Novartis Found. Symp. 2005, 266 19-43.
30. Humphrey, W.; Dalke, A.; Schulten, K. VMD-Visual molecular dynamics. J. Mol. Graphics 1996, 14, 33-38.
31. + selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations. Biochim. Biophys. Acta 2001, 1548, 194-202.
32. Weber, W.; Hunenberger, P. H.; McCammon, J. A. Molecular dynamics simulations of apolyalanine octapeptide under Ewald boundary conditions: Influence of artifical periodicity on peptide conformation. J. Phys. Chem. B 2000, 104, 3668-3675.
33. Kale, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. NAMD2: Greater scalability for parallel molecular dynamics. J. Comput. Phys. 1999, 151, 283-312.
34. MacKerell, A. D., Jr.; Bashford, D.; Bellott, R. L.; Dunbrack, R. L., Jr.; 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., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
35. Feller, S.; Zhang, Y.; Pastor, R.; Brooks, B. Constant pressure molecular dynamics: The Langevin piston method. J. Chem. Phys. 1995, 703,4613-4621.
36. Nagle, J. F.; Tristram-Nagle, S. Structure of lipid bilayers. Biochim. Biophys. Acta 2000, 1469, 159-195.
37. Beveridge, D. L.; DiCapua, F. M. Free energy via molecular simulation: Applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 1989, 18, 431-492.
38. King, P. M. Free energy via molecuar simulation: A primer. In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; van Gunsteren, W. F., Weiner, P. K., Wilkinson, A. J., Eds.; ESCOM: Leiden, The Netherlands, 1993; Vol. 2, pp 267-314.
39. Pearlman, D. A.; Kollman, P. A. Free energy perturbation calculations: Problems and pitfalls along the gilded road. In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; van Gunsteren, W. F., Weiner, P. K., Eds.; ESCOM: Leiden, The Netherlands, 1989; pp 101-119.
40. Rocchia, W.; Alexov, E.; Honig, B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions. J. Phys. Chem. B 2001, 105, 6507-6514.
41. Rocchia, W.; Sridharan, S.; Nicholls, A.; Alexov, E.; Chiabrera, A.; Honig, B. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. J. Comput. Chem. 2002, 23, 128-137.
42. Gilson, M. K.; Sharp, K. A.; Honig, B. H. Calculating the electrostatic potential of molecules in solution - Method and error assessment. J. Comput. Chem. 1988, 9, 327-335.
43. Kuyucak, S.; Andersen, O. S.; Chung, S. H. Models of permeation in ion channels. Rep. Prog. Phys. 2001, 64, 1427-1472.
44. Smart, O. S.; Goodfellow, J. M.; Wallace, B. A. The pore dimensions of gramicidin A. Biophys. J. 1993, 65, 2455-2460.
45. Bernèche, S.; Roux, B. Energetics of ion conduction through the K+ channel. Nature 2001, 414, 73-77.
46. Numaguchi, H.; Johnson, J. P.; Petersen, C. I.; Balser, J. R. A sensitive mechanism for cation modulation of potassium current. Nat. Neurosci. 2000, 3, 429-430.
47. Aqvist, J.; Luzhkov, V. Ion permeation mechanism of the potassium channel. Nature 2000, 404, 881-884.
48. + channel selectivity filter by mutant cycle-based structure analysis. Neuron 1996, 16, 131-139.
49. + channel. Biophys. J. 1998, 74, 1808-1820.
50. + channels. Neuron 1993, 11, 353-358.
51. Fan, J. S.; Jiang, M.; Dun, W.; McDonald, T. V.; Tseng, G. N. Effects of outer mouth mutations on hERG channel function: A comparison with similar mutations in the Shaker channel. Biophys. J. 1999, 76, 3128-3140.
52. + permeation and block of hERG potassium channels. J. Gen. Physiol. 2006, 128, 55-71.