TETRAETHYLAMMONIUM BINDING TO THE OUTER MOUTH OF THE KcsA POTASSIUM CHANNEL: IMPLICATIONS FOR ION PERMEATION

REFERENCES

• Hille B. Ionic Channels of Excitable Membranes. Sinauer Associates. 1992
   Google Scholar
• Conley E. C., Brammar W. J. The Ion Channel Factsbook. Academic Press, Great Britain 1999
   Google Scholar
• MacKinnon R., Yellen G. Mutations Affecting TEA Blockade and Ion Permeation in Voltage-Activated K+ Channels. Science 1990; 250: 276–279
   PubMed Web of Science ®Google Scholar
• Heginbotham L., MacKinnon R. The Aromatic Binding Site for Tetraethylammonium Ion on Potassium Channels. Neuron 1992; 8: 483–491
   PubMed Web of Science ®Google Scholar
• Pascual J. M., Shieh C.-C., Kirsch G. E., Brown A. M. Multiple Residues Specify External Tetraethylammonium Blockade in Voltage-Gated Potassium Channels. Biophys. J. 1995; 69: 428–434
   PubMed Web of Science ®Google Scholar
• Molina A., Castellano A. G., Lopez-Barneo J. Pore Mutations in Shaker K+ Channels Distinguish Between the Sites of Tetraethylammonium Blockade and C-Type Inactivation. J. Physiol. 1997; 499: 361–367
   Google Scholar
• Bretschneider F., Wrisch A., Lehmann-Horn F., Grissmer S. External Tetraethylammonium as a Molecular Caliper for Sensing the Shape of the Outer Vestibule of Potassium Channels. Biophys. J. 1999; 76: 2351–2360
   PubMed Web of Science ®Google Scholar
• Blaustein R. O., Cole P. A., Williams C., Miller C. Tethered Blockers as Molecular “Tape Measures” for a Voltage-Gated K+ Channel. Nat. Struct. Biol. 2000; 7: 309–311
   PubMedGoogle Scholar
• Thompson J., Begenisich T. Interaction Between Quaternary Ammonium Ions in the Pore of Potassium Channels. Evidence Against an Electrostatic Repulsion Mechanism. J. Gen. Physiol. 2000; 115: 769–782
   PubMed Web of Science ®Google Scholar
• Thompson J., Begenisich T. Affinity and Location of an Internal K(+) Ion Binding Site in Shaker K Channels. J. Gen. Physiol. 2001; 117: 373–384
   PubMed Web of Science ®Google Scholar
• Doyle D. A., Cabral J. M., Pfuetzner R. A., Kuo A., Gulbis J. M., Cohen S. L., Chait B. T., MacKinnon R. The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity. Science 1998; 280: 69–77
   PubMed Web of Science ®Google Scholar
• MacKinnon R., Cohen S. L., Kuo A., Lee A., Chait B. T. Structural Conservation in Prokaryotic and Eukaryotic Potassium Channels. Science 1998; 280: 106–109
   PubMed Web of Science ®Google Scholar
• Grissmer S., Nguyen A. N., Aiyar J., Hanson D. C., Mather R. J., Gutman G. A., Karmilowicz M. J., Auperin D. D., Chandy K. G. Pharmacological Characterization of Five Cloned Voltage-Gated K+ Channels, Types Kv1.1, 1.2, 1.3, 1.5, and 3.1, Stably Expressed in Mammalian Cell Lines. Mol. Pharmacol. 1994; 45: 1227–1234
   PubMed Web of Science ®Google Scholar
• Heginbotham L., LeMasurier M., Kolmakova-Partensky L., Miller C. Single Streptomyces Lividans K(+) Channels: Functional Asymmetries and Sideness of Proton Activation. J. Gen. Physiol. 1999; 114: 551–560
   PubMed Web of Science ®Google Scholar
• Meuser D., Splitt H., Wagner R., Schrempf H. Exploring the Open Pore of the Potassium Channel from Streptomyces Lividans. FEBS Lett. 1999; 462: 447–452
   PubMed Web of Science ®Google Scholar
• Meuser D., Splitt H., Wagner R., Schrempf H. Mutations Stabilizing an Open Conformation within the External Region of the Permeation Pathway of the Potassium Channel KcsA. Eur. Biophys. J. 2001; 30: 385–391
   PubMed Web of Science ®Google Scholar
• Cornell W. D., Cieplack P., Bayly C. I., Gould I. R., Merz K. M., Ferguson D. M., Spellmeyer D. C., Fox T., Caldwell J. W., Kollman P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995; 117: 5179–5197
   Web of Science ®Google Scholar
• Luzhkov V. B. and Aqvist, J. Mechanisms of Tetraethylammonium Ion Block in the KcsA Potassium Channel. FEBS Lett. 2001; 495: 191–196
   Google Scholar
• Crouzy S., Berneche S., Roux B. Extracellular Blockade of K(+) Channels by TEA: Results from Molecular Dynamics Simulations of the KcsA Channel. J. Gen. Physiol 2001; 118: 207–218
   PubMed Web of Science ®Google Scholar
• Zhou Y., Morais-Cabral J. H., Kaufman A., MacKinnon R. Chemistry of Ion Coordination and Hydration Revealed by a K+ Channel–Fab Complex at 2.0 A Resolution. Nature 2001; 414: 43–48
   PubMed Web of Science ®Google Scholar
• Guidoni L., Torre V., Carloni P. Water and Potassium Dynamics Inside the KcsA K+ Channel. FEBS Lett. 2000; 477: 37–42
   PubMed Web of Science ®Google Scholar
• Luzhkov V. B., Aqvist J. A Computational Study of Ion Binding and Protonation States in the KcsA Potassium Channel. Biochim. Biophys. Acta 2000; 1481: 360–370
   PubMed Web of Science ®Google Scholar
• Ranatunga K. M., Shrivastava I. H., Smith G. R., Sansom M. S. Side-Chain Ionization States in a Potassium Channel. Biophys. J. 2001; 80: 1210–1219
   PubMed Web of Science ®Google Scholar
• Berneche S., Roux B. The Ionization State and the Conformation of Glu-71 in the KcsA K(+) Channel. Biophys. J. 2002; 82: 772–780
   PubMed Web of Science ®Google Scholar
• Morris G. M., Goodsell D. S., Halliday R. S., Huey R., Hart W. E., Belew R. K., Olson A. J. Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function. J. Comp. Chem. 1998; 19: 1639–1662
   Web of Science ®Google Scholar
• Bayly C., Cieplack P., Cornell W., Kollman P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints Deriving Atomic Charges: The RESP Model. J. Phys. Chem. 1993; 97: 10269–10280
   Web of Science ®Google Scholar
• Frisch M. J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Zakrzewski V. G., Montgomery J. A., Jr., Stratmann R. E., Burant J. C., Dapprich S., Millam J. M., Daniels A. D., Kudin K. N., Strain M. C., Farkas O., Tomasi J., Barone V., Cossi M., Cammi R., Menucci B., Pomelli C., Adamo C., Clifford S., Ochterski J., Petersson G. A., Ayala P. Y., Cui Q., Morokuma K., Malick D. K., Rabuck A. D., Raghavachari K., Foresman J. B., Cioslowski J., Ortiz J. V., Baboul A. G., Stefanov B. B., Liu G., Liashenko A., Piskorz P., Komaromi I., Gomperts R., Martin R. L., Fox D. J., Keith T., Al-Laham M. A., Peng C. Y., Nanayakkara A., Gonzalez C., Challacombe M., Gill P.M. W., Johnson B. G., Chen W., Wong M. W., Andres J. L., Head-Gordon M., Replogle E. S., Pople J. A. Gaussian 98 (Revision A.9). Gaussian, Inc., Pittsburgh, PA 1998
   Google Scholar
• Zhong Q., Moore P. B., Newns D. M., Klein M. L. Molecular Dynamics Study of the LS3 Voltage-Gated Ion Channel. FEBS Lett. 1998; 427: 267–270
   PubMed Web of Science ®Google Scholar
• Moore P. B., Zhong Q., Husslein T., Klein M. L. Simulation of the HIV-1 Vpu Transmembrane Domain as a Pentameric Bundle. FEBS Lett. 1998; 431: 143–148
   PubMed Web of Science ®Google Scholar
• Zhong Q., Husslein T., Moore P. B., Newns D. M., Pattnaik P., Klein M. L. The M2 Channel of Influenza A Virus: A Molecular Dynamics Study. FEBS Lett. 1998; 434: 265–271
   PubMed Web of Science ®Google Scholar
• Guidoni L., Torre V., Carloni P. Potassium and Sodium Binding to the Outer Mouth of the K+ Channel. Biochemistry 1999; 38: 8599–8604
   PubMed Web of Science ®Google Scholar
• Guidoni L., Torre V., Carloni P. Potassium Permeation Through the Selectivity Filter of the KcsA Channel: A Density Functional Study, Submitted 2001
   Google Scholar
• Case D. A., Pearlman D. A., Caldwell J. W., Cheatham III T. E., Ross W. S., Simmerling C. L., Darden T. A., Merz K. M., Stanton R. V., Cheng A. L., Vincent J. J., Crowley M., Tsui V., Radmer R., Duan Y., Pitera J., Massova I., Seibel G. L., Singh U. C., Weiner P., Kollman P. A. Amber 6. University of California, San Francisco 1999
   Google Scholar
• Kaminski G., Duffy E. M., Matsui T., Jorgensen W. L. Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model. J. Phys. Chem. 1994; 98: 13077–13082
   Web of Science ®Google Scholar
• Aqvist J. Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations. J. Phys. Chem. 1990; 94: 8021–8024
   Web of Science ®Google Scholar
• Jorgensen W. L., Chandrasekhar J., Madura J. D. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983; 79: 926–935
   Web of Science ®Google Scholar
• Chen B., Martin M. G., Siepmann J. I. Thermodynamic Properties of the Williams, OPLS-AA, and MMFF94 All-Atom Foce Fields for Normal Alkanes. J. Phys. Chem. B 1998; 102: 2578–2586
   Web of Science ®Google Scholar
• Essman U., Perera L., Berkowitz M. L., Darden T., Lee H., Pedersen L. G. A Smooth Particle Mesh Ewald Method. J. Chem. Phys. B 1995; 103: 8577–8593
   Web of Science ®Google Scholar
• Berendsen H.J. C., Postma J.P. M., van Gunsteren W. F., Di Nola A., Haak J. R. Molecular Dynamics with Coupling to an External Bath. J. Chem. Phys. 1984; 81: 3684–3690
   Web of Science ®Google Scholar
• Ryckaert J.-P., Ciccotti G., Berendsen H.J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of N-Alkanes. J. Comp. Phys. 1977; 23: 327–341
   Web of Science ®Google Scholar
• McLachlan A. D. Gene Duplications in the Structural Evolution of Chymotrypsin. J. Mol. Biol. 1979; 128: 49–79
   PubMed Web of Science ®Google Scholar
• Allen M. P., Tildesley D. J. Computer Simulation of Liquids. Oxford University Press, New York 1987
   Google Scholar
• Lee S. H., Rasaia J. C. Molecular Dynamics Simulation of Ion Mobility 2. Alkali Metal and Halide Ions Using the SPC/E Model for Water at 25°C. J. Phys. Chem. 1996; 100: 1420–1425
   Web of Science ®Google Scholar
• Honig B., Nicholls A. Classical Electrostatic in Biology and Chemistry. Science 1995; 268: 1144–1149
   PubMed Web of Science ®Google Scholar
• Gilson M. K., Sharp K. A., Honig B. H. Calculating the Electrostatic Potential of Molecules in Solution: Method and Error Assessment. J. Comp. Chem. 1987; 9: 327–335
   Web of Science ®Google Scholar
• Brand H. V., Curtiss L. A., Iton L. E., Trouw F. R., Brun T. O. Theoretical and Inelastic Neutron-Scattering Studies of Tetraethilammonium Cation as Molecular Sieve Template. J. Phys. Chem. 1994; 98: 1293–1301
   Web of Science ®Google Scholar
• Aqvist J., Luzhkov V. Ion Permeation Mechanism of the Potassium Channel. Nature 2000; 404: 881–884
   PubMed Web of Science ®Google Scholar
• Ma J. C., Dougherty D. A. The Cation-π Interaction. Chem. Rev. 1997; 97: 1303–1324
   PubMed Web of Science ®Google Scholar
• Sulpizi M., Carloni P. Cation-pi Versus OH-π Interactions in Proteins: A Density Functional Study. J. Phys. Chem. 2000; 104: 10087–10091
   Web of Science ®Google Scholar
• Berneche S., Roux B. Molecular Dynamics of the KcsA K(+) Channel in a Bilayer Membrane. Biophys. J 2000; 78: 2900–2917
   PubMed Web of Science ®Google Scholar
• MacKinnon R. Biophysical Society 45th Annual Meeting, Boston, MA, 2001
   Google Scholar
• Ikeda S. R., Korn S. J. Influence of Permeating Ions on Potassium Channel Block by External Tetraethylammonium. J. Physiol 1995; 486: 267–272
   PubMed Web of Science ®Google Scholar
• Immke D., Wood M., Kiss L., Korn S. J. Potassium-Dependent Changes in the Conformation of the Kv2.1 Potassium Channel Pore. J. Gen. Physiol 1999; 113: 819–836
   PubMed Web of Science ®Google Scholar
• Van Gunsteren W. F., Berendsen H.J. C. Groningen Molecular Simulation (GROMOS) Library Manual, B. V. Biomos, 1987
   Google Scholar
• MacKerell A. D., Jr., Bashford D., Bellot M., Dunbrack R. L., Evanseck J. D., Field M. J., Fischer S., Gao J., Guo H., Joseph-McCarthy D., Ha S., Kuchnir L., Kuczera K., Lau F.T. K., Mattos C., Michnick S., Ngo T., Nguyen D. T., Prodhom B., Reiher W. E., Roux B., Schlenkrich M., Smith J., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Karplus M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem.B 1998; 102: 3586–3616
   PubMed Web of Science ®Google Scholar
• Roux B., MacKinnon R. The Cavity and Pore Helices in the KcsA K+ Channel: Electrostatic Stabilization of Monovalent Cations. Science 1999; 285: 100–102
   PubMed Web of Science ®Google Scholar