An Open State Model of the Navab Channel Explored by Rosetta and Molecular Dynamics Simulation

Voltage-gated sodium (Nav) channels play a pivotal role in propagating electrical signals in excitable cells and key targets for development of novel therapeutics. Despite recent progress in determining x-ray structures of bacterial Nav channels in closed, inactivated, and partially open states, we are still missing a stable open state structure of a Nav channel that will be useful to study ion conduction, channel gating and drug - channel interactions. We used Rosetta molecular modeling software to build the full-length open state model of the bacterial NavAb channel. The fully activated state of the NavAb voltage sensor domain (VSD) was modeled using the crystal structure of NavRh channel VSD as a template. The initial open state of NavAb pore was modeled using the crystal structure of NavMs with partially open pore. Rebuilding the interacting regions of NavAb (S3, S4, S5, S6, and S4-S5 linker) using Rosetta loop modeling and relax approaches was essential to generate stable NavAb open state model. Output models were evaluated using RosettaMembrane energy function and Rosetta clustering approach. The top Rosetta models represented different alternative open states of the NavAb channel. We have conducted a set of molecular dynamics (MD) simulations on the NavAb channel open state model using the Anton supercomputer to examine its stability. The simulations revealed that the NavAb channel open state model reproducibly sustained a fully hydrated open pore that conducted sodium ions under an applied membrane potential for periods of hundreds of nanoseconds. These results suggest that our structural modeling approach could be useful for modeling multiple states of other ion channels and for rational design of novel therapeutics targeting ion channels.