Molecular features of an alcohol binding site in a neuronal potassium channel

Biochemistry. 2003 Sep 30;42(38):11243-52. doi: 10.1021/bi034738f.


Aliphatic alcohols (1-alkanols) selectively inhibit the neuronal Shaw2 K(+) channel at an internal binding site. This inhibition is conferred by a sequence of 13 residues that constitutes the S4-S5 loop in the pore-forming subunit. Here, we combined functional and structural approaches to gain insights into the molecular basis of this interaction. To infer the forces that are involved, we employed a fast concentration-clamp method (10-90% exchange time = 800 micros) to examine the kinetics of the interaction of three members of the homologous series of 1-alkanols (ethanol, 1-butanol, and 1-hexanol) with Shaw2 K(+) channels in Xenopus oocyte inside-out patches. As expected for a second-order mechanism involving a receptor site, only the observed association rate constants were linearly dependent on the 1-alkanol concentration. While the alkyl chain length modestly influenced the dissociation rate constants (decreasing only approximately 2-fold between ethanol and 1-hexanol), the second-order association rate constants increased e-fold per carbon atom. Thus, hydrophobic interactions govern the probability of productive collisions at the 1-alkanol binding site, and short-range polar interactions help to stabilize the complex. We also examined the relationship between the energetics of 1-alkanol binding and the structural properties of the S4-S5 loop. Circular dichroism spectroscopy applied to peptides corresponding to the S4-S5 loop of various K(+) channels revealed a correlation between the apparent binding affinity of the 1-alkanol binding site and the alpha-helical propensity of the S4-S5 loop. The data suggest that amphiphilic interactions at the Shaw2 1-alkanol binding site depend on specific structural constraints in the pore-forming subunit of the channel.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alcohols / chemistry
  • Alcohols / metabolism*
  • Alcohols / pharmacology
  • Animals
  • Binding Sites
  • Circular Dichroism
  • Drosophila Proteins*
  • Kinetics
  • Mutagenesis, Site-Directed
  • Neurons / metabolism*
  • Oocytes
  • Patch-Clamp Techniques / methods
  • Potassium Channels / chemistry*
  • Potassium Channels / genetics
  • Potassium Channels / metabolism*
  • Protein Structure, Secondary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Shaw Potassium Channels
  • Thermodynamics
  • Xenopus


  • Alcohols
  • Drosophila Proteins
  • Potassium Channels
  • Recombinant Proteins
  • Shaw Potassium Channels
  • Shaw protein, Drosophila