Computational Study of Mammalian Sodium Channels

Abstract

Mammalian sodium (NaV) channels are membrane proteins with potential therapeutic applications. Lack of crystal structures is the main bottleneck for studying these channels. Constructing a model of NaV channels using computational methods is an alternative way to study NaV channels and would be valuable in structure-based drug design. I constructed a homology model for NaV1.4 based on the crystal structure of bacterial counterparts. The extensive functional data for the binding of µ–conotoxin GIIIA to NaV1.4 were used to validate the model. The predictions of the binding were in good agreement with mutagenesis data. The standard binding free energy of GIIIA was also calculated from its potential of mean force (PMF) and was consistent with the experimental value. I then used the validated model to study binding of other µ-conotoxins, including KIIIA, PIIIA, and BuIIIB. The results indicated that there is a common motif for binding of µ–conotoxins to NaV1 which is useful in understanding experimental results and designing new analogues. The NaV1.4 model was also used to study the ion permeation. Linking of the residues at the selectivity filter (DEKA) with residues in the neighbouring domain was found to be important for keeping the permeation pathway open. The results revealed that there was a Na+ ion binding site inside the DEKA locus, and 1-2 Na+ ions could occupy the vestibule near the EEDD ring. These sites are separated by a low free energy barrier, suggesting inward conduction occurs when a Na+ ion in the vestibule goes over the free energy barrier and pushes the Na+ ion in the filter to the intracellular cavity, consistent with the classical knock-on mechanism. The model also provides a good description of the observed Na+/K+ selectivity. In summary, the validated model of NaV1.4 provides a reasonable platform for future studies of mammalian NaV channels and design selective analogues with therapeutic applications.