Molecular Modeling of KCNQ Channel Structure

Chemical structures and electrostatic surface potentials (range, −0.1 to 0.1) were plotted using Jmol, an open-source Java viewer for chemical structures in 3D: http://jmol.org/. For docking, the X. laevis KCNQ1 cryoEM structure^{42 (link)} was first altered to incorporate KCNQ3/KCNQ5 residues known to be important for retigabine and ML-213 binding, and their immediate neighbors, followed by energy minimization using the GROMOS 43B1 force field⁴³ , in DeepView^{44 (link)}. Thus, X. laevis KCNQ1 amino acid sequence LITTLYIGF was converted to LITAWYIGF, the underlined W being W265 in human KCNQ3/KCNQ5 and the italicized residues being the immediate neighbors in KCNQ3/KCNQ5. In addition, X. laevis KCNQ1 sequence WWGVVTVTTIGYGD was converted to WWGLITLATIGYGD, the underlined L being Leu314 in human KCNQ3/KCNQ5 and the italicized residues being the immediate neighbors in KCNQ5 and/or KCNQ3. Surrounding non-mutated sequences are shown to illustrate the otherwise high sequence identity in these stretches. Unguided docking of GABA, retigabine, and ML-213, to predict native binding sites, was performed using SwissDock^{45 (link)} with CHARMM forcefields^{46 (link)}. Phylogenetic analysis was performed using BLAST searching^{47 (link)} of predicted or known protein sequences from multiple genomes (where available) from each clade; KCNQ5 sequences for representative organisms from each clade are shown. Genomes were accessed using the US National Center for Biotechnology Information (NCBI), Joint Genome Institute (JGI), Kyoto Encyclopedia of Genes and Genomes (KEGG), UCSC Genome Browser Gateway, and the Elephant Shark Genome Project. Species names for the exemplars shown in Fig. 1a are as follows: Human, Homo sapiens; Frog, Xenopus tropicalis; Carp, Cyprinus carpio; Shark, Callorhincus milii; Lamprey, Petromyzon marinus; Acorn worm, Sacclogossus kowalevskii; Bat star, Patiria miniata; Snail, Biomphalaria glabrata; Fly, Musca domestica; Leech, Helobdella robusta; Tapeworm, Hymenolepsis microstoma; Nematode, Caenorhabditis elegans; Hydrozoa, Hydra vulgaris; Anthozoa, Nematostella vectensis.