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The peptides related to inactivation of sodium channels were synthesized by the solid-phase method for the purpose of proposing a more precise concept than so far obtained for the inactivation and to determine the main factors that control inactivation. The three-dimensional structures of the peptides were determined using 1H-NMR spectroscopy. It was newly discovered that hydrogen bonding was formed between the amide proton of Ile in the IFM (IFM1488-1490) motif of the III-IV linker and the hydroxyl oxygen atom of the side chain of Thr located adjacent to the IFM motif. This hydrogen bonding characterizes the structure around the IFM motif. By calculating the solvent-accessible surface area of the peptide corresponding to the III-IV linker, it was found that a hydrophobic cluster was formed. The hydrophobic cluster stabilizes the structure of the IFM motif. Moreover, the solvent-accessible surface area of the IFM motif correlated with the sustained currents of the incompletely inactivated sodium channels. The free energy of stabilization by hydrophobic interactions (delta G, -3.9 kcal mol-1), which is calculated from the solvent-accessible surface area for the IFM motif (195 A2), was in good agreement with that calculated for the equilibrium between the open and the inactivated states of the sodium channels (-4.1 kcal mol-1). The structure of the III-IV linker peptide in a phosphate buffer also formed a hydrophobic cluster, as well as in SDS micelles, although no hydrogen bonding was formed. This distinction results in the following conformational change in the IFM motif: in SDS micelles, the side chains of Ile and Phe in the IFM motif were directed to the hydrophobic cluster, whereas those in a phosphate buffer were directed opposite to the cluster and solvent exposed. The secondary structures of IIIS4-S5 and IVS4-S5, which are considered to form a receptor site, assumed alpha-helical conformations around the N-terminal half of the sequences. The residue A1329 in MPD3, which is considered to interact with F1489 of the IFM motif, was found to locate within the alpha-helix. A hydrophobic cluster was formed on one side of the helix of MP-D4, which also plays an important role in the inactivation. A new concept for the process of fast inactivation is presented. In response to the voltage-dependent activation and the movement of the S4 segments, the two hydrophobic clusters due to the IVS4-S5 and the III-IV linker interact with each other. This interaction increases the hydrophobicity around the IFM motif. The increased hydrophobicity causes the conformational switching of the IF1488-1489 residues to allow F1489 to interact with A1329 of IIIS4-S5 and/or with N1662 in IVS4-S5. As a consequence of this process, the inactivation gate closes.

Structures of Peptides Related to the Inactivation Gate on Sodium Channels