[2a]

Initial y-axis is fraction unfolded and final y-axis is ΔG. 
i.        \(\frac{\left[U\right]}{\left[T\right]-\left[U\right]}=K_{eq}=\exp\left(\frac{-\Delta G}{RT}\right)\)
ii.        \(\ln\left(\frac{\left[U\right]}{\left[T\right]-\left[U\right]}\right)=\frac{-\Delta G}{RT}\)
iii.     \(-RT\cdot\ln\left(\frac{\left[U\right]}{\left[T\right]-\left[U\right]}\right)=\Delta G\)
iv.         \(RT\cdot\ln\left(\frac{1}{F}-1\right)=\Delta G\)
where F = fraction unfolded and [T] = total Barnase protein.

[2b]

If the protein does not undergo conformational relaxation, meaning the protein does not undergo any major global conformational changes with varying mutations or mutations that may change local conformations do not propagate change through the entire protein, then the results of Kellis et al. would be plausible because the changes in free energy can be attributed to the mutational differences. If the protein does undergo conformational relaxation and minor changes could result in changes in secondary and/or tertiary structure, the change in urea would be smaller because the mutant would be more stable and thus ΔΔG would be smaller, but it would be incorporating free energy changes not directly involved with mutation site. Doubt could arise around the results of Kellis et al. because free energy change from the mutation site could be affected by other energy changes between distal domains.
To determine whether or not this is occurring, one could test protein heat capacity (calorimetry), ligand binding at specific residues (e.g. lysine residues), and mass spectrometry of isotope-labeling (residue reactivity over time), all of which could indicate major conformational changes.
Protein site mutations most likely to propagate global conformational change would be disruptive or non-conservative changes (e.g. A to K or E to R).

[3]

\(\left[B\right]_{ss}\ =\ 0.3\ \mu M;\ \left[L\right]_{ss}=0.8\ \mu M;\ \left[C\right]_{ss}\ =\ 6.5\ \mu M;\ k_{on}=3E6\ \frac{1}{M\cdot s}\)
Complex formation: \(k_{on}\left[B\right]_{ss}\left[L\right]_{ss}\ =\ 0.72\ \frac{\mu M}{s}\)_
Complex dissociation: \(k_{off}\left[C\right]_{ss}\ =\ 0.72\ \frac{\mu M}{s}\)
Equilibrium dissociation constant: \(K_d=\frac{\left[B\right]_{ss}\left[L\right]_{ss}}{\left[C\right]_{ss}}=0.037\ \mu M\)
Rate of dissociation: \(k_{off}=K_d\cdot K_{on}\ =\ 0.11\ \frac{1}{s}\)