Solution structures of the inactivation gate particle peptides of rat brain type‐IIA and human heart sodium channels in SDS micelles

The Ile-Phe-Met (IFM) motif located in the Ill-IV linker of voltage-gated sodium channels has been identified as a major component of the fast inactivation gate. If Gln was substituted for Phe, the role in the gate was disrupted completely. If Ile was replaced by Gln inactivation became slightly incomplete and if the Thr, which is adjacent to the IFM motif (-IFMT-), was replaced by Met, inactivation became much more incomplete than in the I/Q mutation, but not as vigorous as in the F/Q mutation. Previously, we studied the structures of the inactivation gate-related peptide (K1480-K1496 in rat brain type-IIA, MP-3A) and its F1489/Q substituted one (MP-4A) in SDS micelles and found that the conformational change of the IFM hydrophobic cluster due to the F/Q substitution may be a reason for disrupting the gate. In this study, in order to obtain supporting evidence for this view and also to further knowledge of the effect of I/Q and T/M mutations on the structure of the IFM cluster, we studied the structures of 11488Q [MP(rb)-3QFMT] and T1491M [MP(rb)-31FMM] substituted peptides. The fragment peptide K1477-K1493 [MP(hh)-3A] and its T1488M substituted peptide [MP(hh)-3IFMM] in the human heart sodium channel were also studied. It was found that the backbone structures around the IMF motif of MP-3A, MP(hh)-3A and MP(rb)-3QFMT resemble one another in such a manner that the residues Ile(Gln) and Thr are brought so close together that they form a unique type of lid to occlude the pore. In contrast, the residues between Ile and M1491 of MP(rb)-3IFMM or M1488 of MP(hh)-3IFMM were fairly far apart from each other. We conclude that Thr plays an important role in forming a structure of the IFM hydrophobic cluster for inactivation.