Modeling the Outer Pore of Sodium and Calcium Channels

Abstract

In the absence of x-ray structures of sodium and calcium channels, their homology models based on x-ray structures of potassium channels are used to design and rationalize experiments. A challenge is to model the outer-pore region that folds differently from potassium channels. Here we report a model of the outer-pore region of NaV1.4, which is based on a large body of experimental data, including specific contacts of toxins with individual channel residues. The model inherits from our previous model the general disposition of the P-helices, the selectivity-filter residues, and the outer carboxylates, but provides a novel view on the role of other highly conserved residues in the outer pore. In the absence of secondary-structure elements, structural stability of the outer pore should be supported by specific contacts. We propose a network of such contacts including intra- and inter-domain H-bonds, knob-into-the-hole contacts, and hydrophobic interactions. Glycine residues downstream the selectivity filter are proposed to participate in knob-into-hole contacts with P-helices and S6s. These contacts explain known tetrodotoxin resistance of snakes adapted to toxic prey due to NaV1.4 mutation Ile/Val in the P-helix of repeat 4. Polar residues in P-helices, which are five positions upstream from the selectivity-filter residues, form H-bonds with the ascending-limb backbones. The exceptionally conserved tryptophans are engaged in inter-repeat H-bonds to form a ring whose π-electrons would facilitate the passage of ions from the outer carboxylates to the selectivity filter. The outer-pore model of CaV1.2 derived from the NaV1.4 model is also stabilized by the ring of exceptionally conservative tryptophans and H-bonds between P-helices and ascending limbs. In this model a highly conserved aspartate downstream the selectivity-filter glutamate in repeat II facilitates passage of calcium ions moving to the selectivity-filter ring through the tryptophan ring. Supported by CIHR.