Application of electrospray ionization mass spectrometry to study the hydrophobic interaction between the ε and θ subunits of DNA polymerase III

The interactions between the N-terminal domain of the ε (ε186) and θ subunits of DNA polymerase III of Escherichia coli were investigated using electrospray ionization mass spectrometry. The ε186–θ complex was stable in 9 M ammonium actetate (pH 8), suggesting that hydrophobic interactions have a predominant contribution to the stability of the complex. Addition of primary alkanols to ε186–θ in 0.1 M ammonium acetate (pH 8), led to dissociation of the complex, as observed in the mass spectrometer. The concentrations of methanol, ethanol, and 1-propanol required to dissociate 50% of the complex were 8.9 M, 4.8 M, and 1.7 M, respectively. Closer scrutiny of the effect of alkanols on ε186, θ, and ε186–θ showed that ε186 formed soluble aggregates prior to precipitation, and that the association of ε186 with θ stabilized ε186. In-source collision-induced dissociation experiments and other results suggested that the ε186–θ complex dissociated in the mass spectrometer, and that the stability (with respect to dissociation) of the complex in vacuo was dependent on the solution from which it was sampled