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PIP2-Binding Site in Kir Channels: Definition by Multiscale Biomolecular Simulations†

By Phillip J. Stansfeld, Richard Hopkinson, Frances M. Ashcroft and Mark S. P. Sansom
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Publisher: American Chemical Society
OAI identifier: oai:pubmedcentral.nih.gov:2895862
Provided by: PubMed Central

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Citations

  1. (2001). A coarse grain model for phospholipid simulations.
  2. (1984). A consistent empirical potential for water-protein interactions.
  3. (2005). A multiscale coarse-graining method for biomolecular systems.
  4. (1999). Activation of inwardly rectifying K þ channels by distinct PtdIns(4,5)P-2 interactions.
  5. (2005). Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly.
  6. (2002). Alterations in conserved Kir channel-PIP2 interactions underlie channelopathies.
  7. (2009). Aminoglycoside Association Pathways with the 30S Ribosomal Subunit.
  8. (1997). Anionic phospholipids activate ATP-sensitive potassium channels.
  9. (2006). AnionicphospholipidsinteractionswiththepotassiumchannelKcsA: Simulation studies.
  10. (2005). ATP sensitivity of ATP-sensitive K þ channels: Role of the γ-phosphate group of ATP and the R50 residue of mouse Kir6.2.
  11. (2006). ATPsensitive K þ channels: Regulation of bursting by the sulphonylurea receptor, PIP2 and regions of Kir6.2.
  12. (2008). Binding of anionic lipids to at least three nonannular sites on the potassium channel KcsA is required for channel opening.
  13. (2004). Coarse grain models and the computer simulation of soft materials.
  14. (2009). Coarse-grained MD simulations and protein-protein interactions: The cohesin-dockerin system.
  15. (2008). Coarse-grained MD simulations of membrane protein-bilayer self-assembly.
  16. (2007). Coarse-grained molecular dynamics simulations of membrane proteins and peptides.
  17. (2008). Coarse-Graining of Condensed Phase and Biomolecular Systems ,
  18. (1993). Comparative protein modeling by satisfaction of spatial restraints.
  19. (2009). Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel.
  20. (2005). Conformational dynamics of M2 helices in KirBac channels: Helix flexibility in relation to gating via molecular dynamics simulations.
  21. (2007). Control of inward rectifier K channel activity by lipid tethering of cytoplasmic domains.
  22. (2007). Crystal structure of a Kir3.1-prokaryotic Kir channel chimera.
  23. (2003). Crystal structure of the potassium channel KirBac1.1 in the closed state.
  24. Cukras,C.A.,Jeliazkova,I.,andNichols,C.G.(2002)Structuraland functional determinants of conserved lipid interaction domains of inward rectifying Kir6.2 channels.
  25. (1998). Direct activation of inward rectifier potassium channels by PIP2 and its stabilization by Gβγ.
  26. (2005). Electrostatics of the intracellular vestibule of K þ channels.
  27. (2008). Embedded cholesterol in the nicotinic acetylcholine receptor.
  28. (2004). Functional characterization of a prokaryotic Kir channel.
  29. (2005). GROMACS: Fast, flexible, and free.
  30. (2008). Helix-helix interactions in membrane proteins: Coarse grained simulations of glycophorin helix dimerization.
  31. (2007). High-resolution structure of the open
  32. (2007). How does a voltage-sensor interact with a lipid bilayer? Simulations of a potassium channel domain.
  33. (2007). Identification of the PIP2-binding site on Kir6.2 by molecular modelling and functional analysis.
  34. (1997). Inward rectifier potassium channels.
  35. (1999). Inwardly rectifying potassium channels.
  36. (2009). Ion channel gates: Comparative analysis of energy barriers.
  37. (2009). KirBac1.1: It’s an inward rectifying potassium channel.
  38. (1997). LINCS: A linear constraint solver for molecular simulations.
  39. (2008). Lipids and membrane protein structures.
  40. Marrink,S.J.,deVries,A.H.,andMark,A.E.(2004)Coarsegrained model for semiquantitative lipid simulations.
  41. (2008). Mechanosensitive membrane channels in action.
  42. (2009). Molecular dynamics simulations of PIP2 and PIP3 in lipid bilayers: Determination of ring orientation, and the effects of surface roughness on a Poisson-Boltzmann description.
  43. (1984). Molecular dynamics with coupling to an external bath.
  44. (2008). motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations.
  45. (2007). Multiscale modeling of biomolecular systems: In serial and in parallel.
  46. (2006). New roles for a key glycine and its neighboring residue in potassium channel gating.
  47. P.(2007)Moleculardynamicssimulationsofinwardlyrectifying(Kir) potassium channels: A comparative study.
  48. (2003). Phosphatidylinositol 4,5-bisphosphate (PIP2) modulation of ATP and pH sensitivity in Kir channels. A tale of an active and a silent PIP2 site in the N terminus.
  49. (2007). Phosphoinositide-mediated gating of inwardly rectifying K þ channels. Pfluegers Arch.
  50. (1999). Phosphoinositides decrease ATP sensitivity of the cardiac ATP-sensitive K þ channel. A molecular probe for the mechanism of ATP-sensitive inhibition.
  51. (2006). Phospholipids and the origin of cationic gating charges in voltage sensors.
  52. (2007). Pleckstrin homology (PH) domains and phosphoinositides.
  53. (1981). Polymorphic transitions in single-crystals: A new molecular-dynamics method.
  54. Rotkiewicz,P.,andSkolnick,J.(2008)Fastprocedureforreconstruction of full-atom protein models from reduced representations.
  55. (2005). sites for modulating gating and rectification.
  56. (2002). Structural basis of inward rectification:CytoplasmicporeoftheGprotein-gatedinwardrectifier GIRK1 at 1.8 A ˚ resolution.
  57. (2000). StructuraldeterminantsofPIP2regulationofinwardrectifierK(ATP) channels.
  58. (1999). The GROMOS biomolecular simulation program package.
  59. (1995). The inward rectifier potassium channel family.
  60. (2008). The MARTINI coarse grained force field: Extension to proteins.
  61. (2007). The MARTINI forcefield: Coarse grained model for biomolecular simulations.
  62. (2002). The open pore conformation of potassium channels.
  63. (2002). The PyMOL Molecular Graphics System , DeLano Scientific,
  64. (2002). The role of NH2-terminal positive charges in the activity of inward rectifier K-ATP channels.
  65. (2003). The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res.
  66. (1996). VMD: Visual Molecular Dynamics.