Conformational flexibility in the binding surface of the potassium channel blocker ShK

Inbal Sher, Department of Chemistry, Bar Ilan University, Ramat Gan, Israel
Shih Chieh Chang, Department of Medicinal Chemistry, Monash University, Parkville, Australia
Ying Li, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, USA
Sandeep Chhabra, Department of Medicinal Chemistry, Monash University, Parkville, Australia
Arthur G. Palmer III, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, USA
Raymond S. Norton, Department of Medicinal Chemistry, Monash University, Parkville, Australia
Jordan H. Chill, Department of Chemistry, Bar Ilan University, Ramat Gan, Israel

ShK is a 35-residue peptide that binds with high affinity to human voltage-gated potassium channels through a conserved K-Y dyad. Here we employ NMR measurements of backbone amide ¹⁵N spin relaxation rates to investigate motions of the ShK backbone. Although ShK is rigid on the ps-ns timescale, increased linewidths observed for eleven backbone amide ¹⁵N resonances identify chemical or conformational exchange contributions to spin relaxation. Relaxation dispersion profiles indicate that exchange between major and minor conformers occurs on the sub-millisecond timescale. Affected residues are mostly clustered around the central helix-kink-helix structure and the critical K22-Y23 motif. We suggest that the less structured minor conformer increases the exposure of Y23, known to contribute to binding affinity and selectivity, thereby facilitating its interaction with potassium channels. These findings have potential implications for the design of new channel blockers based on ShK.