Ion channels of glutamate receptors: structural modeling

References

• Andersen TF, Tikhonov DB, Bolcho U, Bolshakov K, Nelson JK, Pluteanu F, Mellor IR, Egebjerg J, Stromgaard K. Uncompetitive antagonism of AMPA receptors: mechanistic insights from studies of polyamine toxin derivatives. J Med Chem 2006; 49: 5414–5423
   Google Scholar
• Antonov SM, Johnson JW. Voltage-dependent interaction of open-channel blocking molecules with gating of NMDA receptors in rat cortical neurons. J Physiol 1996; 493: 425–445
   Google Scholar
• Beck C, Wollmuth LP, Seeburg PH, Sakmann B, Kuner T. NMDAR channel segments forming the extracellular vestibule inferred from the accessibility of substituted cysteines. Neuron 1999; 22: 559–570
   Google Scholar
• Bennett JA, Dingledine R. Topology profile for a glutamate receptor: three transmembrane domains and a channel-lining reentrant membrane loop. Neuron 1995; 24: 373–384
   Google Scholar
• Benveniste M, Mayer ML. Trapping of glutamate and glycine during open channel block of rat hippocampal neuron NMDA receptors by 9-aminoacridine. J Physiol 1995; 483: 367–384
   Google Scholar
• Berneche S, Roux B. A gate in the selectivity filter of potassium channels. Structure 2005; 13: 591–600
   PubMed Web of Science ®Google Scholar
• Blanpied TA, Boeckman FA, Aizenman E, Johnson JW. Trapping channel block of NMDA-activated responses by amantadine and memantine. J Neurophysiol 1997; 77: 309–323
   PubMed Web of Science ®Google Scholar
• Blanpied TA, Clarke RJ, Johnson JW. Amantadine inhibits NMDA receptors by accelerating channel closure during channel block. J Neurosci 2005; 25: 3312–3322
   PubMed Web of Science ®Google Scholar
• Bolshakov KV, Tikhonov DB, Gmiro VE, Magazanik LG. Different arrangement of hydrophobic and nucleophilic components of channel binding sites in N-methyl-D-aspartate and AMPA receptors of rat brain is revealed by channel blockade. Neurosci Lett 2000; 291: 101–104
   Google Scholar
• Bolshakov KV, Gmiro VE, Tikhonov DB, Magazanik LG. Determinants of trapping block of N-methyl-d-aspartate receptor channels. J Neurochem 2003; 87: 56–65
   PubMed Web of Science ®Google Scholar
• Bolshakov KV, Kim KH, Potapjeva NN, Gmiro VE, Tikhonov DB, Usherwood PN, Mellor IR, Magazanik LG. Design of antagonists for NMDA and AMPA receptors. Neuropharmacology 2005; 49: 144–155
   Google Scholar
• Bruhova I, Zhorov BS. KvAP-based model of the pore region of Shaker potassium channel is consistent with cadmium- and ligand-binding experiments. Biophys J 2005; 89: 1020–1029
   Google Scholar
• Burnashev N, Villarroel A, Sakmann B. Dimensions and ion selectivity of recombinant AMPA and kainate receptor channels and their dependence on Q/R site residues. J Physiol 1996; 496: 165–173
   PubMed Web of Science ®Google Scholar
• Chen GQ, Cui C, Mayer ML, Gouaux E. Functional characterization of a potassium-selective prokaryotic glutamate receptor. Nature 1999; 402: 817–821
   Web of Science ®Google Scholar
• del Camino D, Holmgren M, Liu Y, Yellen G. Blocker protection in the pore of a voltage-gated K+ channel and its structural implications. Nature 2000; 403: 321–325
   PubMed Web of Science ®Google Scholar
• Dilmore JG, Johnson JW. Open channel block and alteration of N-methyl-D- aspartic acid receptor gating by an analog of phencyclidine. Biophys J 1998; 75: 1801–1816
   Google Scholar
• Dingledine R, Borges K, Bowie D, Traynelis SF. The glutamate receptor ion channels. Pharmacol Rev 1999; 51: 7–61
   PubMed Web of Science ®Google Scholar
• Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, 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
• Jiang Y, Lee A, Chen J, Cadene M, Chait BT, MacKinnon R. The open pore conformation of potassium channels. Nature 2002; 417: 523–526
   PubMed Web of Science ®Google Scholar
• Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, MacKinnon R. X-ray structure of a voltage-dependent K+ channel. Nature 2003; 423: 33–41
   PubMed Web of Science ®Google Scholar
• Jones KS, VanDongen HM, VanDongen AM. The NMDA receptor M3 segment is a conserved transduction element coupling ligand binding to channel opening. J Neurosci 2002; 22: 2044–2053
   Google Scholar
• Kashiwagi K, Masuko T, Nguyen CD, Kuno T, Tanaka I, Igarashi K, Williams K. Channel blockers acting at N-methyl-D-aspartate receptors: differential effects of mutations in the vestibule and ion channel pore. Mol Pharmacol 2002; 61: 533–545
   Web of Science ®Google Scholar
• Kohda K, Wang Y, Yuzaki M. Mutation of a glutamate receptor motif reveals its role in gating and delta2 receptor channel properties. Nat Neurosci 2000; 3: 315–322
   PubMedGoogle Scholar
• Kroemer RT, Koutsilieri E, Hecht P, Liedl KR, Riederer P, Kornhuber J. Quantitative analysis of the structural requirements for blockade of the N-methyl-D-aspartate receptor at the phencyclidine binding site. J Med Chem 1998; 41: 393–400
   PubMed Web of Science ®Google Scholar
• Kuner T, Wollmuth LP, Karlin A, Seeburg PH, Sakmann B. Structure of the NMDA receptor channel M2 segment inferred from the accessibility of substituted cysteines. Neuron 1996; 17: 343–352
   PubMed Web of Science ®Google Scholar
• Kuner T, Beck C, Sakmann B, Seeburg PH. Channel-lining residues of the AMPA receptor M2 segment: structural environment of the Q/R site and identification of the selectivity filter. J Neurosci 2001; 21: 4162–4172
   PubMed Web of Science ®Google Scholar
• Kuner T, Seeburg PH, Guy HR. A common architecture for K+ channels and ionotropic glutamate receptors?. Trends Neurosci 2003; 26: 27–32
   Google Scholar
• Kuo A, Gulbis JM, Antcliff JF, Rahman T, Lowe ED, Zimmer J, Cuthbertson J, Ashcroft FM, Ezaki T, Doyle DA. Crystal structure of the potassium channel KirBac1.1 in the closed state. Science 2003; 300: 1922–1926
   PubMed Web of Science ®Google Scholar
• Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999; 35: 133–152
   PubMed Web of Science ®Google Scholar
• Lenaeus MJ, Vamvouka M, Focia PJ, Gross A. Structural basis of TEA blockade in a model potassium channel. Nat Struct Biol 2005; 12: 454–459
   Google Scholar
• Li Z, Scheraga HA. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 1987; 84: 6611–6615
   PubMed Web of Science ®Google Scholar
• Lipkind GM, Fozzard HA. KcsA crystal structure as framework for a molecular model of the Na(+) channel pore. Biochemistry 2000; 39: 8161–8170
   PubMed Web of Science ®Google Scholar
• Lipkind GM, Fozzard HA. Modeling of the outer vestibule and selectivity filter of the L-type Ca2 +  channel. Biochemistry 2001; 40: 6786–6794
   PubMed Web of Science ®Google Scholar
• Lipkind GM, Fozzard HA. Molecular modeling of interactions of dihydropyridines and phenylalkylamines with the inner pore of the L-type Ca2 +  channel. Mol Pharmacol 2003; 63: 499–511
   PubMed Web of Science ®Google Scholar
• Lipkind GM, Fozzard HA. Molecular modeling of local anesthetic drug binding by voltage-gated sodium channels. Mol Pharmacol 2005; 68: 1611–1622
   PubMed Web of Science ®Google Scholar
• Long SB, Campbell EB, Mackinnon R. Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. Science 2005; 309: 897–903
   PubMed Web of Science ®Google Scholar
• MacDonald JF, Bartlett MC, Mody I, Pahapill P, Reynolds JN, Salter MW, Schneiderman JH, Pennefather PS. Actions of ketamine, phencyclidine and MK-801 on NMDA receptor currents in cultured mouse hippocampal neurones. J Physiol 1991; 432: 483–508
   Google Scholar
• Magazanik LG, Buldakova SL, Samoilova MV, Gmiro VE, Mellor IR, Usherwood PN. Block of open channels of recombinant AMPA receptors and native AMPA/kainate receptors by adamantane derivatives. J Physiol 1997; 505: 655–663
   Google Scholar
• Mealing GA, Paris J, Lou A, Edwards A, Hou ST, MacManus JP, Hakim AM, Morley P. Structural modifications to an N-methyl-D-aspartate receptor antagonist result in large differences in trapping block. J Neurochem 2001; 78: 316–324
   Google Scholar
• O'Reilly AO, Khambay BP, Williamson MS, Field LM, Wallace BA, Davies TG. 2006. Modelling insecticide binding sites at the voltage-gated sodium channel. Biochem J 396:255–263.
   PubMed Web of Science ®Google Scholar
• Panchenko VA, Glasser CR, Mayer ML. Structural similarities between glutamate receptor channels and K(+) channels examined by scanning mutagenesis. J Gen Physiol 2001; 117: 345–360
   Google Scholar
• Qian A, Johnson JW. Channel gating of NMDA receptors. Physiol Behav 2002; 77: 577–582
   Google Scholar
• Rosenmund C, Stern-Bach Y, Stevens CF. The tetrameric structure of a glutamate receptor channel. Science 1998; 280: 1596–1599
   PubMed Web of Science ®Google Scholar
• Sobolevsky AI, Koshelev SG, Khodorov BI. Probing of NMDA channels with fast blockers. J Neurosci 1999; 19: 10611–10626
   Google Scholar
• Sobolevsky AI, Beck C, Wollmuth LP. Molecular rearrangements of the extracellular vestibule in NMDAR channels during gating. Neuron 2002a; 33: 75–85
   Google Scholar
• Sobolevsky AI, Rooney L, Wollmuth LP. Staggering of subunits in NMDAR channels. Biophys J 2002b; 83: 3304–3314
   Google Scholar
• Sobolevsky AI, Yelshansky MV, Wollmuth LP. Different gating mechanisms in glutamate receptor and K+ channels. J Neurosci 2003; 23: 7559–7568
   Google Scholar
• Sobolevsky AI, Yelshansky MV, Wollmuth LP. State-dependent changes in the electrostatic potential in the pore of a GluR channel. Biophys J 2005; 88: 235–242
   Google Scholar
• Tikhonov DB, Zhorov BS, Magazanik LG. Intersegment hydrogen bonds as possible structural determinants of the N/Q/R site in glutamate receptors. Biophys J 1999; 77: 1914–1926
   Google Scholar
• Tikhonov DB, Mellor JR, Usherwood PN, Magazanik LG. Modeling of the pore domain of the GLUR1 channel: homology with K(+) channel and binding of channel blockers. Biophys J 2002; 82: 1884–1893
   Google Scholar
• Tikhonov DB, Zhorov BS. Sodium channel activators: model of binding inside the pore and a possible mechanism of action. FEBS Lett 2005a; 579: 4207–4212
   Web of Science ®Google Scholar
• Tikhonov DB, Zhorov BS. Modeling P-loops domain of sodium channel: homology with potassium channels and interaction with ligands. Biophys J 2005b; 88: 184–197
   PubMed Web of Science ®Google Scholar
• Villarroel A, Burnashev N, Sakmann B. Dimensions of the narrow portion of a recombinant NMDA receptor channel. Biophys J 1995; 68: 866–875
   Google Scholar
• Vorobjev VS, Sharonova IN. Tetrahydroaminoacridine blocks and prolongs NMDA receptor-mediated responses in a voltage-dependent manner. Eur J Pharmacol 1994; 253: 1–8
   Google Scholar
• Webster SM, del Camino D, Dekker JP, Yellen G. Intracellular gate opening in Shaker K+ channels defined by high-affinity metal bridges. Nature 2004; 428: 864–868
   Google Scholar
• Weiner SJ, Kollman PA, Case DA, Singh UC, Chio C, Alagona G, Profeta S, Weiner PK. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984; 106: 765–784
   Web of Science ®Google Scholar
• Wo ZG, Oswald RE. Transmembrane topology of two Kainate receptor submits revealed by N-glycosylation. Proc Natl Acad Sci USA 1994; 91: 7154–7158
   PubMedGoogle Scholar
• Wollmuth LP, Kuner T, Seeburg PH, Sakmann B. Differential contribution of the NR1- and NR2A-subunits to the selectivity filter of recombinant NMDA receptor channels. J Physiol 1996; 491: 779–797
   Google Scholar
• Wollmuth LP, Sobolevsky AI. Structure and gating of the glutamate receptor ion channel. Trends Neurosci 2004; 27: 321–328
   Web of Science ®Google Scholar
• Wood MW, VanDongen HM, VanDongen AM. Structural conservation of ion conduction pathways in K channels and glutamate receptors. Proc Natl Acad Sci USA 1995; 92: 4882–4886
   PubMedGoogle Scholar
• Yamaguchi S, Zhorov BS, Yoshioka K, Nagao T, Ichijo H, Adachi-Akahane S. Key roles of Phe1112 and Ser1115 in the pore-forming IIIS5-S6 linker of L-type Ca2 +  channel alpha1C subunit (CaV 1.2) in binding of dihydropyridines and action of Ca2 +  channel agonists. Mol Pharmacol 2003; 64: 235–248
   Google Scholar
• Yuan H, Erreger K, Dravid SM, Traynelis SF. Conserved structural and functional control of N-methyl-D-aspartate receptor gating by transmembrane domain M3. J Biol Chem 2005; 280: 29708–29716
   Web of Science ®Google Scholar
• Zhorov BS, Folkman EV, Ananthanarayanan VS. Homology model of dihydropyridine receptor: implications for L-type Ca(2 + ) channel modulation by agonists and antagonists. Arch Biochem Biophys 2001; 393: 22–41
   PubMed Web of Science ®Google Scholar
• Zhorov BS, Tikhonov DB. Potassium, sodium, calcium and glutamate-gated channels: pore architecture and ligand action. J Neurochem 2004; 88: 782–799
   PubMed Web of Science ®Google Scholar
• Zhou M, Morais-Cabral JH, Mann S, MacKinnon R. Potassium channel receptor site for the inactivation gate and quaternary amine inhibitors. Nature 2001a; 411: 657–661
   PubMed Web of Science ®Google Scholar
• Zhou Y, Morais-Cabral JH, Kaufman A, MacKinnon R. 2001b. Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution. Nature 414:43–48.
   PubMed Web of Science ®Google Scholar
• Zhou Y, MacKinnon R. 2003. The occupancy of ions in the K+ selectivity filter: charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates. J Mol Biol 333:965–975.
   PubMed Web of Science ®Google Scholar