ArticleBiophysical journal2005
Modeling P-loops domain of sodium channel: homology with potassium channels and interaction with ligands.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61 citing papers in PubMed, 124 citations in OpenAlex.
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- Snakes (Colubridae: Erythrolamprus) With a Complex Toxic Diet Show Convergent yet Highly Heterogeneous Voltage-gated Sodium Channel Evolution.Genome biology and evolution · 2026Article
- Neurocardiology: translational advancements and potential.The Journal of physiology · 2025Review
- Mechanisms of dihydropyridine agonists and antagonists in view of cryo-EM structures of calcium and sodium channels.The Journal of general physiology · 2023Article
- Evaluation of Toxicity Equivalency Factors of Tetrodotoxin Analogues with a Neuro-2a Cell-Based Assay and Application to Puffer Fish from Greece.Marine drugs · 2023Article
- Discovery of Selective Inhibitors of NaACS medicinal chemistry letters · 2022Article
- P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models.Membranes · 2022Review
- Phenylalkylamines in calcium channels: computational analysis of experimental structures.Journal of computer-aided molecular design · 2020Article
- Discovery of a selective, state-independent inhibitor of NaScientific reports · 2020Article
- Bases of Bacterial Sodium Channel Selectivity Among Organic Cations.Scientific reports · 2019Article
- Large-effect mutations generate trade-off between predatory and locomotor ability during arms race coevolution with deadly prey.Evolution letters · 2018Article
- Predicting Structural Details of the Sodium Channel Pore Basing on Animal Toxin Studies.Frontiers in pharmacology · 2018Review
- Differential binding of tetrodotoxin and its derivatives to voltage-sensitive sodium channel subtypes (NaBritish journal of pharmacology · 2017Article
- Guanidinium Toxins and Their Interactions with Voltage-Gated Sodium Ion Channels.Marine drugs · 2017Review
- Synthesis, pharmacological evaluation and molecular docking of pyranopyrazole-linked 1,4-dihydropyridines as potent positive inotropes.Molecular diversity · 2017Article
- Mutant cycle analysis with modified saxitoxins reveals specific interactions critical to attaining high-affinity inhibition of hNaV1.7.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Analysis of inter-residue contacts reveals folding stabilizers in P-loops of potassium, sodium, and TRPV channels.European biophysics journal : EBJ · 2016Article
- Characterization of the honeybee AmNaV1 channel and tools to assess the toxicity of insecticides.Scientific reports · 2015Article
- Determinants of Cation Permeation and Drug Sensitivity in Predicted Transmembrane Helix 9 and Adjoining Exofacial Re-entrant Loop 5 of Na+/H+ Exchanger NHE1.The Journal of biological chemistry · 2015Article
- Predicting a double mutant in the twilight zone of low homology modeling for the skeletal muscle voltage-gated sodium channel subunit beta-1 (Nav1.4 β1).Computational and structural biotechnology journal · 2015Article
1 more citing papers are in PubMed but not listed here.
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2 authors at 1 institution in 1 country.
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Abstract
A large body of experimental data on Na+ channels is available, but the interpretation of these data in structural terms is difficult in the absence of a high-resolution structure. Essentially different electrophysiological and pharmacological properties of Na+ and K+ channels and poor identity of their sequences obstruct homology modeling of Na+ channels. In this work, we built the P-loops model of the Na+ channel, in which the pore helices are arranged exactly as in the MthK bacterial K+ channel. The conformation of the selectivity-filter region, which includes residues in positions -2 through +4 from the DEKA locus, was shaped around rigid molecules of saxitoxin and tetrodotoxin that are known to form multiple contacts with this region. Intensive Monte Carlo minimization that started from the MthK-like conformation produced practically identical saxitoxin- and tetrodotoxin-based models. The latter was tested to explain a wide range of experimental data that were not used at the model building stage. The docking of tetrodotoxin analogs unambiguously predicted their optimal orientation and the interaction energy that correlates with the experimental activity. The docking of mu-conotoxin produced a binding model consistent with experimentally known toxin-channel contacts. Monte Carlo-minimized energy profiles of tetramethylammonium pulled through the selectivity-filter region explain the paradoxical experimental data that this organic cation permeates via the DEAA but not the AAAA mutant of the DEKA locus. The model is also consistent with earlier proposed concepts on the Na+ channel selectivity as well as Ca2+ selectivity of the EEEE mutant of the DEKA locus. Thus, the model integrates available experimental data on the Na+ channel P-loops domain, and suggests that it is more similar to K+ channels than was believed before.
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