TY - JOUR T1 - Architecture and the Pore Block of Eukaryotic Voltage-Gated Sodium Channels in View of the NavAb Bacterial Sodium Channel Structure JF - Molecular Pharmacology JO - Mol Pharmacol DO - 10.1124/mol.112.078212 SP - mol.112.078212 AU - Denis B Tikhonov AU - Boris S Zhorov Y1 - 2012/04/13 UR - http://molpharm.aspetjournals.org/content/early/2012/04/13/mol.112.078212.abstract N2 - The x-ray structure of bacterial sodium channel NavAb provides a new template to study sodium and calcium channels. Unlike potassium channels, NavAb contains P2 helices in the outer-pore region. Since the sequence similarity between eukaryotic and prokaryotic sodium channels in this region is poor, the structural similarity is unclear. We analyzed it by using experimental data on tetrodotoxin block of sodium channels. Key tetrodotoxin-binding residues are outer carboxylates in repeats I, II, and IV three positions downstream from the selectivity-filter residues. In a NavAb-based model of Nav1 channels derived from the sequence alignment without insertions/deletions, the outer carboxylates did not face the pore and therefore did not interact with tetrodotoxin. A hypotheses that evolutionary appearance of Nav1 channels involved point deletions in an ancestral channel between the selectivity-filter and the outer carboxylates allowed building a NavAb-based model with tetrodotoxin-channel contacts similar to those proposed before. This hypothesis also allowed reproducing in Nav1 the folding-stabilizing contacts between long-side-chain residues in P1 and P2, which are seen in NavAb. The NavAb-based inner-pore model of Nav1 preserved major features of our previous KcsA-based models, including the access pathway for ligands through the III/IV repeat interface and their interaction with specific residues. Thus, structural properties of eukaryotic voltage-gated sodium channels, which are implied by functional data, were reproduced in the NavAb-based models built using the unaltered template structure, but adjusted sequence alignment. Noteworthy, sequences of eukaryotic calcium channels align with NavAb without insertions/deletions suggesting that NavAb is a promising basis for modeling calcium channels. ER -