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Proceedings of the 31 st European Peptide SymposiumMichal Lebl, Morten Meldal, Knud J. Jensen, Thomas Hoeg-Jensen (Editors)European Peptide Society, 2010Molecular Modeling of the Interactions Between μ-ConotoxinSmIIIA and the Pore of Voltage-Gated Sodium ChannelSubtypes Na V 1.2 and Na V 1.4Pawel Gruszczynski 1,2,3 , Doju Yoshikami 3 , Rajmund Kazmierkiewicz 1 ,Min-Min Zhang 3 , Baldomero M. Olivera 3 , Grzegorz Bulaj 4 , andThomas E. Cheatham 41 Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University ofGdansk, Gdansk, 80-822, Poland; 2 Faculty of Chemistry, University of Gdansk, Gdansk,80-952, Poland; 3 Departments of Biology; 4 Medicinal Chemistry, University of Utah,Salt Lake City, 84112, UT, U.S.A.Introductionµ-Conotoxin SmIIIA is a conopeptide derived from the venom of a marine snail Conusstercusmuscarum. This peptide was initially found to preferentially and irreversibly blockTTX-resistant sodium currents in amphibian dorsal root ganglion neurons [1]. Thecombination of NMR and biochemical studies suggested that the last two intercystine loopswere critical for the peptide’s ability to block TTX-resistant sodium channels [2]. Recentexperiments show that SmIIIA targets mammalian sodium channels, including twosubtypes Na V 1.2 (neuronal subtype) and Na V 1.4 (skeletal muscle subtype) (Zhang, M.M.,et al. manuscript in preparation). The block of these two subtypes by SmIIIA issignificantly more potent, as compared to that for other two similar μ-conotoxins, namelySIIIA and KIIIA. Since all three peptides, SmIIIA, SIIIA and KIIIA share structuralsimilarities of the last two intercystine, the functional differences provided an opportunityand rationale to explore how SmIIIA may interact with both isoforms of sodium channels.No modeling studies have been reported to-date on the molecular interactions betweenµ-conotoxins and neuronal subtypes of sodium channels.The molecular structures of sodium channels, including Na V 1.2 and Na V 1.4, are stillunknown, although several structural models have been proposed [3,4-9]. To characterizemolecular interactions between SmIIIA and sodium channels, we employed a model ofNa V 1.4 proposed by Lipkind and Fozzard [6] as a template to build a new model of Na V 1.2using homology modeling method. Previously published studies on the docking skeletalmuscle specific μ-conotoxin GIIIA into Na V 1.4 facilitated our efforts to evaluatetoxin-channel complexes. Specific docking models were chosen based on knowninteractions of GIIIA [3,9-14], energy and clustering. Surprisingly, our molecular modelingand docking results suggest multiple binding modes of µ-conotoxin SmIIIA with Na V 1.2and Na V 1.4. Our work provides a hypothesis that diverse modes of the molecularinteractions between µ-conotoxins and the pore of the sodium channels subtypes may bepresent.Results and DiscussionWe present a series of structural binding models of µ-conotoxin SmIIIA into two channelsubtypes Na V 1.2 and Na V 1.4. We also show three different types of binding modes forGIIIA docked to Nav1.4 channel. It is postulated that there are more than one binding modefor both of the conopeptides, but some of them are more preferred than the other. Ourmodels might be useful to explain some difficult-to-interpret experimental data on theinteractions between GIIIA and Nav1.4 and ravel that there is more than one binding modelof the GIIIA with Na V 1.4, similarly to what we observed for the interactions betweenSmIIIA and each of the channels subtypes, Na V 1.2 and Na V 1.4.There is no available experimental data, where mutant analysis was employed forexploring interactions between SmIIIA and both Na V 1.2 and Na V 1.4 sodium channels.Therefore our work provides a basis for such mutational studies. Here, we propose theresidues that can be mutated in the SmIIIA µ-conotoxin to verify our models. Within eachof our models, we find Arg13 as the key residue that block the sodium channel filter.We hypothesize, that our results can be transferred to other µ-conotoxins. Forexample, in KIIIA Ala-walk experiment [15] shown that substitution of the key-residue318