Measuring the stability of partly folded proteins using TMAO

Standard methods for measuring free energy of protein unfolding by chemical denaturation require complete folding at low concentrations of denaturant so that a native baseline can be observed. Alternatively, proteins that are completely unfolded in the absence of denaturant can be folded by addition of the osmolyte trimethylamine N‐oxide (TMAO), and the unfolding free energy can then be calculated through analysis of the refolding transition. However, neither chemical denaturation nor osmolyte‐induced refolding alone is sufficient to yield accurate thermodynamic unfolding parameters for partly folded proteins, because neither method produces both native and denatured baselines in a single transition. Here we combine urea denaturation and TMAO stabilization as a means to bring about baseline‐resolved structural transitions in partly folded proteins. For Barnase and the Notch ankyrin domain, which both show two‐state equilibrium unfolding, we found that ΔG° for unfolding depends linearly on TMAO concentration, and that the sensitivity of ΔG° to urea (the m‐value) is TMAO independent. This second observation confirms that urea and TMAO exert independent effects on stability over the range of cosolvent concentrations required to bring about baseline‐resolved structural transitions. Thermodynamic parameters calculated using a global fit that assumes additive, linear dependence of ΔG° on each cosolvent are similar to those obtained by standard urea‐induced unfolding in the absence of TMAO. Finally, we demonstrate the applicability of this method to measurement of the free energy of unfolding of a partly folded protein, a fragment of the full‐length Notch ankyrin domain.