Interactions between a voltage sensor and a toxin via multiscale simulations

Biophysical Journal

Volumn 98, Issue 8, 2010, Pages 1558-1565

  Wee, Chze Ling ^a,b   Gavaghan, David ^b   Sansom, Mark S P ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77951612656     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.12.4321     Document Type: Article

References (57)

1. 1. Swartz, K. J. 2007. Tarantula toxins interacting with voltage sensors in potassium channels. Toxicon. 49:213-230. (Pubitemid 46148995)
2. Alabi, A. A., M. I. Bahamonde, ..., K. J. Swartz. 2007. Portability of paddle motif function and pharmacology in voltage sensors. Nature. 450:370-375.
3. 3. Ruta, V., and R. MacKinnon. 2004. Localization of the voltage-sensor toxin, receptor on KvAP. Biochemistry. 43:10071-10079. (Pubitemid 39030898)
4. Jung, H. J., J. Y. Lee, ..., J. I. Kim. 2005. Solution structure and lipid membrane partitioning of VSTx1, an inhibitor of the KvAP potassium channel. Biochemistry. 44:6015-6023.
5. Lee, S. Y., and R. MacKinnon. 2004. A membrane-access mechanism of ion channel inhibition by voltage sensor toxins from spider venom. Nature. 430:232-235.
6. Phillips, L. R., M. Milescu, ..., K. J. Swartz. 2005. Voltage-sensor activation with a tarantula toxin, as cargo. Nature. 436:857-860.
7. 7. Milescu, M., J. Vobecky, ..., K. J. Swartz. 2007. Tarantula toxins interact with voltage sensors within lipid membranes. J. Gen. Physiol. 130:497-511. (Pubitemid 350036736)
8. + channel gating and voltage sensor toxin sensitivity depend on the mechanical state of the lipid membrane. Proc. Natl. Acad. Sci. USA. 105:19276-19281.
9. 9. Swartz, K. J. 2004. Towards a structural view of gating in potassium channels. Nat. Rev. Neurosci. 5:905-916. (Pubitemid 39593354)
10. + channel. Nature. 423:42-48.
11. 11. Ruta, V., J. Chen, and R. MacKinnon. 2005. Calibrated measurement of gating-charge arginine displacement in the KvAP voltage-dependent K+ channel. Cell. 123:463-475. (Pubitemid 41546676)
12. Swartz, K. J. 2008. Sensing voltage across lipid membranes. Nature. 456:891-897.
13. Wang, J. M., S. H. Roh, ..., K. J. Swartz. 2004. Molecular surface of tarantula toxins interacting with voltage sensors in K(v) channels. J. Gen. Physiol. 123:455-467.
14. 14. Murata, Y., H. Iwasaki, ..., Y. Okamura. 2005. Phosphoinositide phosphatase activity coupled to an intrinsic voltage sensor. Nature. 435:1239-1243. (Pubitemid 40943089)
15. Ramsey, I. S., M. M. Moran, ..., D. E. Clapham. 2006. A voltage-gated proton-selective channel, lacking the pore domain. Nature. 440: 1213-1216.
16. Sasaki, M., M. Takagi, and Y. Okamura. 2006. A voltage sensordomain protein is a voltage-gated proton channel. Science. 312: 589-592.
17. 17. Sands, Z. A., and M. S. P. Sansom. 2007. How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain. Structure. 15:235-244. (Pubitemid 46209817)
18. Krepkiy, D., M. Mihailescu, ..., K. J. Swartz. 2009. Structure and hydration of membranes embedded with voltage-sensing domains. Nature. 462:473-479.
19. 19. Bemporad, D., C. L. Wee, ..., M. S. P. Sansom. 2006. VSTx1, a modifier of Kv channel gating, localizes to the interfacial region, of lipid bilayers. Biochemistry. 45:11844-11855. (Pubitemid 44497812)
20. v channel gatingmodifier toxin. Biophys. J. 95:3816-3826.
21. Swartz, K. J., and R. MacKinnon. 1995. An inhibitor of the Kv2.1 potassium channel isolated from the venom of a Chilean tarantula. Neuron. 15:941-949.
22. + channel gate modifier hanatoxin and lipid bilayer membranes analyzed by molecular dynamics simulation. Eur. Biophys. J. 35:373-381.
23. Bond, P. J., C. L. Wee, and M. S. P. Sansom. 2008. Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. Biochemistry. 47:11321-11331.
24. Marrink, S. J., A. H. de Vries, and A. E. Mark. 2004. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B. 108:750-760.
25. Monticelli, L., S. K. Kandasamy, ..., S. J. Marrink. 2008. The MARTINI coarse grained force field: extension to proteins. J. Chem. Theory Comput. 4:819-834.
26. Shih, A. Y., A. Arkhipov, ..., K. Schulten. 2006. Coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B. 110:3674-3684.
27. 27. Shelley, J. C., M. Y. Shelley, ..., M. L. Klein. 2001. A coarse grain model for phospholipid simulations. J. Phys. Chem. B. 105:4464-4470. (Pubitemid 35381588)
28. 28. Izvekov, S., and G. A. Voth. 2005. A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B. 109:2469-2473. (Pubitemid 40304419)
29. Voth, G. A. 2008. Coarse-Graining of Condensed Phase and Biomolecular Systems. CRC Press, Boca Raton, FL. 456 p.
30. Scott, K. A., P. J. Bond, ..., M. S. P. Sansom. 2008. Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure. 16:621-630.
31. 31. Bond, P. J., J. Holyoake, ..., M. S. Sansom. 2007. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J. Struct. Biol. 157:593-605. (Pubitemid 46304257)
32. 32. Periole, X., T. Huber, ..., T. P. Sakmar. 2007. G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. J. Am. Chem. Soc 129:10.126-10132. (Pubitemid 47312953)
33. 33. Reynwar, B. J., G. Iilya, ..., M. Deserno. 2007. Aggregation and vesiculation of membrane proteins by curvature-mediated interactions. Nature. 447:461-464. (Pubitemid 46816743)
34. Hall, B. A., and M. S. P. Sansom. 2009. Coarse-grained MD simulations and protein-protein, interactions: the cohesin-dockerin system, J. Chem. Theory Comput. 5:2465-2471.
35. Periole, X., M. Cavalli, ..., M. A. Ceruso. 2009. Combining an elastic network with, a coarse-grained molecular force field: structure, dynamics, and intermolecular recognition. J. Chem. Theory Comput. 5:2531-2543.
36. 36. Ayton, G. S., W. G. Noid, and G. A. Voth. 2007. Multiscale modeling of biomolecular systems: in serial and in parallel. Curr. Opin. Struct. Biol. 17:192-198. (Pubitemid 46584804)
37. 37. Bond, P. J., and M. S. P. Sansom. 2007. Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations. Proc. Natl. Acad. Sci. USA. 104:2631-2636. (Pubitemid 46327931)
38. + channel, and its dependence on the lipid membrane. Proc. Natl. Acad. Sci, USA, 102:15441-15446.
39. Bond, P. J., and M. S. P. Sansom. 2006. Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 128:2697-2704.
40. +channel. Nature. 423:33-41.
41. 41. Krznaric, D., and C. Levcopoulos. 1998. Fast algorithms for complete linkage clustering. Discrete Comput. Geom. 19:131-145. (Pubitemid 128021270)
42. 42. Rotkiewicz, P., and J. Skolnick. 2008. Fast procedure for reconstruction of full-atom protein, models from reduced representations. J. Comput. Chem, 29:1460-1465. (Pubitemid 351757769)
43. 43. Sali, A., and T. L. Blundell. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:779-815. (Pubitemid 24007801)
44. van Gunsteran, W. F., P. Kruger, ..., I. G. Tironi. 1996. Biomolecular Simulation: The GROMOS96 Manual and User Guide. Biomos & Hochschulverlag AG an der ETH Zurich, Groningen/Zurich.
45. 45. Berger, O., O. Edholm, and F. Jähnig. 1997. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys. J. 72:2002-2013. (Pubitemid 27184429)
46. Marrink, S. J., O. Berger,...,F. Jähnig. 1998. Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations. Biophys. J. 74:931-943.
47. Hermans, J., H. J. C. Berendsen, ..., J. P. M. Postma. 1984. A consistent empirical potential for water-protein interactions. Biopolymers. 23:1513-1518.
48. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald-an N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
49. 49. Hess, B., H. Bekker, ..., J. G. E. M. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18:1463-1472. (Pubitemid 127637344)
50. Miyamoto, S., and P. A. Kollman. 1992. Settle-an analytical version of the Shake and Rattle algorithm for rigid water models. J. Comput. Chem. 13:952-962.
51. Berendsen, H. J. C., J. P. M. Postma, ..., J. R. Haak. 1984. Molecular dynamics with coupling to an external bath, J. Chem. Phys. 81:3684- 3690.
52. Wee, C. L., D. Bemporad, Z. A. Sands, D. Gavaghan, and M. S. P. Sansom. 2007. SGTx1, a Kv channel gating-modifier toxin, binds to the .interfacial region of lipid bilayers. Biophys. J. 92:L07-L09.
53. Alabi, A. A., and K. J. Swartz. 2007. VSTx1 stabilizes a closed state in K(v)2.1-K(v)AP paddle chimeras. Biophys. J. S:471A.
54. Milescu, M., F. Bosmans, ..., K. J. Swartz. 2009. Interactions between lipids and voltage sensor paddles detected with tarantula toxins. Nat. Struct. Mol. Biol. 16:1080-1085.
55. 55. Schmidt, D., Q. X. Jiang, and R. MacKinnon. 2006. Phospholipids and the origin of cationic gating charges in voltage sensors. Nature. 444:775-779. (Pubitemid 44949608)
56. +) channel KvAP in DPhPC and POPE:POPG decane lipid bilayers. J. Mol. Biol. 390:902-912.
57. + channel in a lipid membrane-like environment. Nature. 450:376-382.