What are the internal motions of an ion channel protein when it “gates” between closed and open-channel conformations? In 2005, Zhou, Pearson, and Auerbach (ZPA) (Biophys. J. 89:3680–3685) showed that Φ, a parameter derived from the forward and backward rate constants of a chemical reaction, may in some cases provide temporal information about the moving parts of a protein. This “primer” is intended for ion channel biologists and others who seek an intuitive understanding of how rate constants might reflect the relative timing of the internal motions of proteins. Here, I will focus on the method of Φ-value analysis and, specifically, the basis for the temporal interpretation of Φ.
The gating isomerization of an ion channel is a chemical reaction in which the reactant (C for closed) is separated from the product (O for open) by a potential energy barrier. Ion channels are...
