Solution structure of the cytoplasmic linker between domain III-S6 and domain IV-S1 (III-IV linker) of the rat brain sodium channel in SDS micelles.

The solution structure of the 36-mer peptide MP-5A in SDS micelles was investigated by CD and (1)H-NMR spectroscopies. The MP-5A was dissected from the cytoplasmic linker (K1482-A1517) connecting domain III-segment 6 (IIIS6) and domain IV-segment 1 (IVS1; III-IV linker) of the rat brain type IIA sodium channel. The molecular energy calculations including nuclear Overhauser effect and dihedral angle restraints gave a well-converged set of the structures of MP-5A for the region between I1488 and S1506. It was found that a large hydrophobic cluster is formed by I1488-F1489-M1490 (IFM motif), Y1497-Y1498, and M1501, which may be related to the fast inactivation process of the sodium channel. The solvent-accessible surface area of the IFM motif (195 A(2)), which is known to work essentially as an inactivation gate particle to occlude the ion permeation pore, gave the free energy (DeltaG) of stabilization of -3.9 kcal mol(-1) as a result of the hydrophobic interactions with its receptor. This value agreed well with the free energy of binding (inactivation) of -4.1 kcal mol(-1) calculated for the equilibrium between the open and the inactivated states of the sodium channels. It is concluded that the fast inactivation of the sodium channel is achieved by the environmental polarity-dependent conformational switching at the IFM motif, in response to the voltage-dependent activation and the movement of the S4 segments of the sodium channel.