Revealing the Architecture of a K ⁺ Channel Pore Through Mutant Cycles with a Peptide Inhibitor

TLDR

Thermodynamic mutant cycles provide a formalism for studying energetic coupling between amino acids on the interaction surface in a protein–protein complex. This method is directly applicable to sodium, calcium, and other ion channels where inhibitor or modulatory proteins bind with high affinity. The authors applied thermodynamic mutant cycles to the Shaker potassium channel and a high‑affinity scorpion‑toxin inhibitor, using pairwise interaction assignments to map the spatial arrangement of channel amino acids relative to the inhibitor structure. The analysis constrained the Shaker channel pore‑forming region, locating its amino‑terminal border 12–15 Å from the central axis.

Abstract

Thermodynamic mutant cycles provide a formalism for studying energetic coupling between amino acids on the interaction surface in a protein-protein complex. This approach was applied to the Shaker potassium channel and to a high-affinity peptide inhibitor (scorpion toxin) that binds to its pore entryway. The assignment of pairwise interactions defined the spatial arrangement of channel amino acids with respect to the known inhibitor structure. A strong constraint was placed on the Shaker channel pore-forming region by requiring its amino-terminal border to be 12 to 15 angstroms from the central axis. This method is directly applicable to sodium, calcium, and other ion channels where inhibitor or modulatory proteins bind with high affinity.