Paper Citing NAMD - Abstract
Mahdavi, Somayeh; Kuyucak, Serdar
Molecular Dynamics Study of Binding of mu-Conotoxin GIIIA to the Voltage-Gated Sodium Channel Na(v)1.4
PLOS ONE, 9 Art. No. e105300, AUG 18 2014
Homology models of mammalian voltage-gated sodium (Na-v) channels based on the crystal structures of the bacterial counterparts are needed to interpret the functional data on sodium channels and understand how they operate. Such models would also be invaluable in structure-based design of therapeutics for diseases involving sodium channels such as chronic pain and heart diseases. Here we construct a homology model for the pore domain of the Na(v)1.4 channel and use the functional data for the binding of mu-conotoxin GIIIA to Na(v)1.4 to validate the model. The initial poses for the Na(v)1.4-GIIIA complex are obtained using the HADDOCK protein docking program, which are then refined in molecular dynamics simulations. The binding mode for the final complex is shown to be in broad agreement with the available mutagenesis data. The standard binding free energy, determined from the potential of mean force calculations, is also in good agreement with the experimental value. Because the pore domains of Na(v)1 channels are highly homologous, the model constructed for Na(v)1.4 will provide an excellent template for other Na(v)1 channels.
