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K+/Na+ Selectivity in K Channels and Valinomycin: Over-coordination Versus Cavity-size constraints

Varma, Sameer, Sabo, Dubravko, Rempe, Susan B.·2008·Journal of Molecular Biology
DOI 10.1016/j.jmb.2007.11.059
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Research works printed but not linked: 54

  1. Page, 2006, Role of Na+ and K+ in enzyme function, Physiol. Rev., 86, 1049, 10.1152/physrev.00008.2006 · DOI
  2. Draper, 1998, RNA shows its metal, Nature Struct. Biol., 5, 927, 10.1038/2901 · DOI
  3. Pauling, 1948, Nature of forces between large molecules of biological interest, Nature, 161, 707, 10.1038/161707a0 · DOI
  4. Bezanilla, 1972, Negative conductance caused by entry of sodium and cesium ions into the potassium channels of squid axons, J. Gen. Physiol., 60, 588, 10.1085/jgp.60.5.588 · DOI
  5. Aqvist, 1992, Ion-selective properties of a small ionophore in methanol studied by free energy perturbation simulations, J. Phys. Chem., 96, 10019, 10.1021/j100203a079 · DOI
  6. Doyle, 1998, The structure of the potassium channel: molecular basis of K+ conduction and selectivity, Science, 280, 69, 10.1126/science.280.5360.69 · DOI
  7. Miller, 2001, See potassium run, Nature, 414, 23, 10.1038/35102126 · DOI
  8. Zhou, 2001, Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution, Nature, 414, 43, 10.1038/35102009 · DOI
  9. Gouaux, 2005, Principles of selective ion transport in channels and pumps, Science, 310, 1461, 10.1126/science.1113666 · DOI
  10. Ohtomo, 1980, Bull. Chem. Soc. Jpn., 53, 1789, 10.1246/bcsj.53.1789 · DOI
  11. Tongraar, 1998, Born-Oppenheimer ab initio QM/MM dynamics simulations of Na+ and K+ in water: from structure making to structure breaking effects, J. Phys. Chem. A, 102, 10340, 10.1021/jp982270y · DOI
  12. Neilson, 2001, Neutron and X-ray scattering studies of hydration in aqueous solutions, Phil. Trans. Roy. Soc. ser. A, 359, 1575, 10.1098/rsta.2001.0866 · DOI
  13. Soper, 2006, Ion solvation and water structure in potassium halide aqueous solutions, Biophys. Chem., 124, 180, 10.1016/j.bpc.2006.04.009 · DOI
  14. Ramaniah, 1999, Ab initio molecular-dynamics simulation of K+ solvation in water, J. Chem. Phys., 111, 1587, 10.1063/1.479418 · DOI
  15. Rempe, 2004, Inner shell definition and absolute hydration free energy of K+(aq) on the basis of quasi-chemical theory and ab initio molecular dynamics, Phys. Chem. Chem. Phys., 6, 1966, 10.1039/B313756B · DOI
  16. Varma, 2006, Coordination numbers of alkali metal ions in aqueous solutions, Biophys. Chem., 124, 192, 10.1016/j.bpc.2006.07.002 · DOI
  17. Varma, 2007, Tuning ion coordination architectures to enable selective partitioning, Biophys. J., 93, 1093, 10.1529/biophysj.107.107482 · DOI
  18. Guidoni, 1999, Potassium and sodium binding in the outer mouth of the K, Biochemistry, 38, 8599, 10.1021/bi990540c · DOI
  19. Berneche, 2000, Molecular dynamics of the KcsA K+ channel in a bilayer membrane, Biophys. J., 78, 2900, 10.1016/S0006-3495(00)76831-7 · DOI
  20. Shrivastava, 2002, K+ versus Na+ ions in a K channel selectivity filter: a simulation study, Biophys. J., 83, 633, 10.1016/S0006-3495(02)75197-7 · DOI
  21. Noskov, 2004, Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands, Nature, 431, 830, 10.1038/nature02943 · DOI
  22. Jordan, 2007, New and notable: tuning a potassium channel – the caress of the surroundings, Biophys. J., 93, 1091, 10.1529/biophysj.107.110205 · DOI
  23. Aqvist, 2000, Ion permeation mechanism of the potassium channel, Nature, 404, 881, 10.1038/35009114 · DOI
  24. Berneche, 2001, Energetics of ion conduction through the K+ channel, Nature, 414, 73, 10.1038/35102067 · DOI
  25. Bichet, 2004, Evolving potassium channels by means of yeast selection reveals structural elements important for selectivity, Proc. Natl Acad. Sci. USA, 101, 4441, 10.1073/pnas.0401195101 · DOI
  26. Bichet, 2006, Electrostatic interactions in the channel cavity as an important determinant of potassium channel selectivity, Proc. Natl Acad. Sci. USA, 103, 14355, 10.1073/pnas.0606660103 · DOI
  27. Shi, 2006, Atomic structure of a Na+- and K+-conducting channel, Nature, 440, 570, 10.1038/nature04508 · DOI
  28. Bostick, 2007, Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state, Proc. Natl Acad. Sci. USA, 104, 9260, 10.1073/pnas.0700554104 · DOI
  29. Valiyaveetil, 2006, Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation, Science, 314, 1004, 10.1126/science.1133415 · DOI
  30. Shealy, 2003, Sequence-function analysis of the K+-selective family of ion channels using a comprehensive alignment and the KcsA channel structure, Biophys. J., 84, 2929, 10.1016/S0006-3495(03)70020-4 · DOI
  31. Noskov, 2007, Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels, J. Gen. Physiol., 129, 135, 10.1085/jgp.200609633 · DOI
  32. Asthagiri, 2006, Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity, J. Chem. Phys., 125, 24701, 10.1063/1.2205853 · DOI
  33. Shemyakin, 1969, Cyclodepsipeptides as chemical tools for studying ionic transport through membranes, J. Membr. Biol., 1, 402, 10.1007/BF01869790 · DOI
  34. Lauger, 1972, Carrier-mediated ion transport: electrical relaxation experiments give insight into the kinetics of ion transport through artificial lipid membrane, Science, 178, 24, 10.1126/science.178.4056.24 · DOI
  35. Rose, 1974, Stability of sodium and potassium complexes of valinomycin, Biochim. Biophys. Acta, 372, 426, 10.1016/0304-4165(74)90204-9 · DOI
  36. Grell, 1975, Membranes, vol. 3
  37. Eisenman, 1991, Free energies underlying ion binding and transport in protein channels: free energy perturbation simulations of ion binding and selectivity for valinomycin, J. Chem. Soc. Faraday Trans., 87, 2099, 10.1039/ft9918702099 · DOI
  38. Widom, 1982, Potential-distribution theory and the statistical mechanics of fluids, J. Phys. Chem., 86, 869, 10.1021/j100395a005 · DOI
  39. Pratt, 1998, Quasi-chemical theories of associated liquids, Mol. Phys., 95, 909
  40. Lee, 1988, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B, 37, 785, 10.1103/PhysRevB.37.785 · DOI · Paper page
  41. Becke, 1993, Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys., 98, 5648, 10.1063/1.464913 · DOI · Paper page
  42. Wang, 2004, A study of the conformations of valinomycin in solution phase, Biopolymers, 75, 85, 10.1002/bip.20103 · DOI
  43. Eisenman, 1969, The effects of the macrotetralide actin antibiotics on the equilibrium extraction of alkali metal salts into organic solvent, J. Membr. Biol., 1, 294, 10.1007/BF01869787 · DOI
  44. Wyttenbach, 1999, Host/guest conformations of biological systems: valinomycin/alkali ions, Intr. J. Mass Spec., 193, 143, 10.1016/S1387-3806(99)00113-X · DOI
  45. Baker, 2001, Electrostatics of nanosystems: application to microtubules and the ribosome, Proc. Natl Acad. Sci. USA, 98, 10037, 10.1073/pnas.181342398 · DOI
  46. Marcus, 1983, Thermodynamic functions of transfer of single ions from water to nonaqueous and mixed solvents. Part 1 - Gibbs free energies of transfer to nonaqueous solvents, Pure and Appl. Chem., 55, 977, 10.1351/pac198355060977 · DOI
  47. Ivanov, 1975, Conformational states and biological activity of cyclic peptides, Tetra. Rep., 31, 2177, 10.1016/0040-4020(75)80216-X · DOI
  48. Daggett, 1992, Molecular dynamics simulations of helix denaturation, J. Mol. Biol., 223, 1121, 10.1016/0022-2836(92)90264-K · DOI
  49. Avbelj, 2000, Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities, Proc. Natl Acad. Sci. USA, 97, 10786, 10.1073/pnas.200343197 · DOI
  50. Garcia, 2002, α-Helical stabilization by side-chain shielding of backbone hydrogen bonds, Proc. Natl Acad. Sci. USA, 99, 2782, 10.1073/pnas.042496899 · DOI
  51. Varma, 2007, The cPLA2 C2α domain in solution: structure and dynamics of its Ca2+-activated and cation-free states, Biophys. J., 92, 956, 10.1529/biophysj.106.091850 · DOI
  52. Feinstein, 1971, The detection of ionophorous antibiotic-cation complexes in water with fluorescent probes, Proc. Natl Acad. Sci. USA, 68, 2037, 10.1073/pnas.68.9.2037 · DOI
  53. Noskov, 2006, Ion selectivity in potassium channels, Biophys. Chem., 124, 279, 10.1016/j.bpc.2006.05.033 · DOI
  54. Bayley, 2004, Functional engineered channels and pores, Mol. Membr. Biol., 21, 209, 10.1080/09687680410001716853 · DOI

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Metadata

Authors
Varma, S., Sabo, D., & Rempe, S. B.
Venue
Journal of Molecular Biology
Publisher
Elsevier BV
Published
2008-02
Volume
376
Issue
1
Pages
13-22
ISSN
0022-2836
DOI
10.1016/j.jmb.2007.11.059
Cited by
150
References
0
Language
en
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)

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