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Modeling the pore structure of voltage-gated sodium channels in closed, open, and fast-inactivated conformation reveals details of site 1 toxin and local anesthetic binding

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Abstract

In this work molecular modeling was applied to generate homology models of the pore region of the Na v 1.2 and Na v 1.8 isoforms of human voltage-gated sodium channels. The models represent the channels in the resting, open, and fast-inactivated states. The transmembrane portions of the channels were based on the equivalent domains of the closed and open conformation potassium channels KcsA and MthK, respectively. The critical selectivity loops were modeled using a structural template identified by a novel 3D-search technique and subsequently merged with the transmembrane portions. The resulting draft models were used to study the differences of tetrodotoxin binding to the tetrodotoxin-sensitive Na v 1.2 (EC50: 0.012 μM) and -insensitive Na v 1.8 (EC50: 60 μM) isoforms, respectively. Furthermore, we investigated binding of the local anesthetic tetracaine to Na v 1.8 (EC50: 12.5 μM) in resting, conducting, and fast-inactivated state. In accordance with experimental mutagenesis studies, computational docking of tetrodotoxin and tetracaine provided (1) a description of site 1 toxin and local anesthetic binding sites in voltage-gated sodium channels. (2) A rationale for site 1 toxin-sensitivity versus -insensitivity in atomic detail involving interactions of the Na v 1.2 residues F385-I and W943-II. (3) A working hypothesis of interactions between Na v 1.8 in different conformational states and the local anesthetic tetracaine.

Tetracaine in complex with Nav1.8 in fast-inactivated form. The ligand is represented in CPK and colored by atom type. Ribbons and amino acids are colored by domain: yellow = domain I, blue = domain II, green = domain III, red = domain IV, pink = inactivation gate. Main interaction partners are shown in CPK. a) Tetracaine bound to the inner vestibule. View along the membrane plane. b) Same view as in a but limited to main interaction partners only. The polar head group of tetracaine interacts with the DEKA-motif residues, its hydrophobic tail with the hydrophobic and mainly aromatic residues of S6-IV and the inactivation gate

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Acknowledgements

HS thanks the Swiss Institute of Bioinformatics for support of this work. He also thanks GlaxoSmithKline for generous travel grants and a modified version of SPDBV.

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Authors and Affiliations

  1. SBC Lab AG, Seebüelstrasse 26, 8185, Winkel, Switzerland

    Holger Scheib

  2. Department of Structural Biology and Bioinformatics, University of Geneva, 1, rue Michel-Servet, 1211, Geneva 4, Switzerland

    Holger Scheib

  3. Swiss Institute of Bioinformatics, Centre Médicale Universitaire, 1, rue Michel-Servet, 1211, Geneva 4, Switzerland

    Holger Scheib

  4. GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, SG1 2NY, Stevenage, Hertfordshire, UK

    Iain McLay, Jeff J. Clare, Tim J. Dale & Simon N. Tate

  5. GlaxoSmithKline, Five Moore Drive, Research Triangle Park, NC, 27709, USA

    Nicolas Guex

  6. GlaxoSmithKline New Frontiers Science Park (North), Third Avenue, Harlow, Essex, CM19 5AW, UK

    Frank E. Blaney

  7. sienabiotech SpA, via Fiorentina 1, 53100, Siena, Italy

    Graeme M. Robertson

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  1. Holger Scheib
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  2. Iain McLay
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Correspondence to Holger Scheib.

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Scheib, H., McLay, I., Guex, N. et al. Modeling the pore structure of voltage-gated sodium channels in closed, open, and fast-inactivated conformation reveals details of site 1 toxin and local anesthetic binding. J Mol Model 12, 813–822 (2006). https://doi.org/10.1007/s00894-005-0066-y

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  • DOI: https://doi.org/10.1007/s00894-005-0066-y

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