Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 6, 2014, Pages 2128-2133

  Kim, Ilsoo ^a   Warshel, Arieh ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Coarse grained model; Potassium ion channel; Voltage sensin

Indexed keywords

COARSE-GRAINED MODEL; POTASSIUM ION CHANNEL; VOLTAGE SENSING;

ELECTRODES; ION CHANNEL GATING; KV1.2 POTASSIUM CHANNEL; MODELS, BIOLOGICAL; MODELS, MOLECULAR;

EID: 84893823516     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1324014111     Document Type: Article

References (39)

1. Catterall WA (2010) Ion channel voltage sensors: Structure, function, and pathophysiology. Neuron 67(6):915-928.
2. Bezanilla F (2008) How membrane proteins sense voltage. Nat Rev Mol Cell Biol 9(4): 323-332.
3. Jiang Y, et al. (2003) X-ray structure of a voltage-dependent K+ channel. Nature 423(6935):33-41.
4. Long SB, Campbell EB, Mackinnon R (2005) Crystal structure of a mammalian voltagedependent Shaker family K+ channel. Science 309(5736):897-903.
5. Tao X, Lee A, Limapichat W, Dougherty DA, MacKinnon R (2010) A gating charge transfer center in voltage sensors. Science 328(5974):67-73.
6. Payandeh J, Scheuer T, Zheng N, Catterall WA (2011) The crystal structure of a voltage-gated sodium channel. Nature 475(7356):353-358.
7. Lecar H, Larsson HP, Grabe M (2003) Electrostatic model of S4 motion in voltagegated ion channels. Biophys J 85(5):2854-2864.
8. Dryga A, Chakrabarty S, Vicatos S, Warshel A (2012) Realistic simulation of the activation of voltage-gated ion channels. Proc Natl Acad Sci USA 109(9):3335-3340.
9. Pathak MM, et al. (2007) Closing in on the resting state of the Shaker K+ channel. Neuron 56(1):124-140.
10. Henrion U, et al. (2012) Tracking a complete voltage-sensor cycle with metal-ion bridges. Proc Natl Acad Sci USA 109(22):8552-8557.
11. Khalili-Araghi F, et al. (2010) Calculation of the gating charge for the Kv1.2 voltageactivated potassium channel. Biophys J 98(10):2189-2198.
12. Delemotte L, Tarek M, Klein ML, Amaral C, Treptow W (2011) Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations. Proc Natl Acad Sci USA 108(15):6109-6114.
13. Jensen MO, et al. (2012) Mechanism of voltage gating in potassium channels. Science 336(6078):229-233.
14. Hille B (2001) Ion Channels of Excitable Membranes (Sinauer, Sunderland, MA), Vol 507.
15. Jiang Y, Ruta V, Chen J, Lee A, MacKinnon R (2003) The principle of gating charge movement in a voltage-dependent K+ channel. Nature 423(6935):42-48.
16. Long SB, Campbell EB, Mackinnon R (2005) Voltage sensor of Kv1.2: Structural basis of electromechanical coupling. Science 309(5736):903-908.
17. Armstrong CM, Bezanilla F (1973) Currents related to movement of the gating particles of the sodium channels. Nature 242(5398):459-461.
18. Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117(4):500-544.
19. Schoppa NE, McCormack K, Tanouye MA, Sigworth FJ (1992) The size of gating charge in wild-type and mutant Shaker potassium channels. Science 255(5052):1712-1715.
20. Aggarwal SK, MacKinnon R (1996) Contribution of the S4 segment to gating charge in the Shaker K+ channel. Neuron 16(6):1169-1177.
21. Seoh SA, Sigg D, Papazian DM, Bezanilla F (1996) Voltage-sensing residues in the S2 and S4 segments of the Shaker K+ channel. Neuron 16(6):1159-1167.
22. Vargas E, et al. (2012) An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations. J Gen Physiol 140(6): 587-594.
23. Jogini V, Roux B (2007) Dynamics of the Kv1.2 voltage-gated K+ channel in a membrane environment. Biophys J 93(9):3070-3082.
24. Messer BM, et al. (2010) Multiscale simulations of protein landscapes: Using coarsegrained models as reference potentials to full explicit models. Proteins 78(5): 1212-1227.
25. Dryga A, Chakrabarty S, Vicatos S, Warshel A (2012) Coarse grained model for exploring voltage dependent ion channels. Biochim Biophys Acta 1818(2):303-317.
26. Catterall WA (1986) Voltage-dependent gating of sodium channels: Correlating structure and function. Trends Neurosci 9:7-10.
27. Rychkova A, Warshel A (2013) Exploring the nature of the translocon-assisted protein insertion. Proc Natl Acad Sci USA 110(2):495-500.
28. Zagotta WN, Hoshi T, Dittman J, Aldrich RW (1994) Shaker potassium channel gating. II: Transitions in the activation pathway. J Gen Physiol 103(2):279-319.
29. Schoppa NE, Sigworth FJ (1998) Activation of shaker potassium channels. I. Characterization of voltage-dependent transitions. J Gen Physiol 111(2):271-294.
30. Sigg D, Qian H, Bezanilla F (1999) Kramers' diffusion theory applied to gating kinetics of voltage-dependent ion channels. Biophys J 76(2):782-803.
31. Chowdhury S, Chanda B (2013) Free-energy relationships in ion channels activated by voltage and ligand. J Gen Physiol 141(1):11-28.
32. Schwaiger CS, et al. (2012) The free energy barrier for arginine gating charge translation is altered by mutations in the voltage sensor domain. PLoS One 7(10): e45880.
33. Sigg D, Bezanilla F, Stefani E (2003) Fast gating in the Shaker K+ channel and the energy landscape of activation. Proc Natl Acad Sci USA 100(13):7611-7615.
34. Bezanilla F, Perozo E, Stefani E (1994) Gating of Shaker K+ channels: II. The components of gating currents and a model of channel activation. Biophys J 66(4): 1011-1021.
35. Xu Y, Ramu Y, Shin HG, Yamakaze J, Lu Z (2013) Energetic role of the paddle motif in voltage gating of Shaker K+ channels. Nat Struct Mol Biol 20(5):574-581.
36. Dryga A, Warshel A (2010) Renormalizing SMD: The renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules. J Phys Chem B 114(39):12720-12728.
37. Mukherjee S, Warshel A (2011) Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase. Proc Natl Acad Sci USA 108(51): 20550-20555.
38. Islas LD, Sigworth FJ (1999) Voltage sensitivity and gating charge in Shaker and Shab family potassium channels. J Gen Physiol 114(5):723-742.
39. Colquhoun D, Hawkes A (1995) A Q-matrix cookbook. How to write only one program to calculate the single-channel and macroscopic predictions for any kinetic mechanism. Single-Channel Recording, eds Sakmann B, Neher E (Plenum, New York), pp 589-633.