An improved experimental system for determining small folding entropy changes resulting from proline to alanine substitutions

Changes in protein stability can be achieved by making substitutions that increase or decrease the available conformations of the unfolded protein without altering the conformational freedom of the folded protein. Matthews and coworkers ( 1987 ) proposed that proline to alanine (P → A) substitution would achieve this type of entropic destabilization. By comparing the Ramachandran area associated with alanine and proline residues, Matthews et al. estimated the unfolding entropy change resulting from P → A substitution to be 4.8 cal mol−1 K−1. Although such an entropy difference would produce a substantial free energy change, accurately resolving such free energy changes into entropic and enthalpic components has been difficult. Here, we attempt to quantify the unfolding entropy change produced by P → A substitution by amplifying the effect through multiple substitutions, and by decreasing the uncertainty in determining the unfolding entropy. Variants of a repeat protein, the Drosophila Notch ankyrin domain, were constructed with a varying number of P → A substitutions at structurally conserved positions. Unfolding entropy values of the variants were determined from free energy measurements taken over a common temperature range using chemical denaturation. Our findings confirm the prediction that increasing the number of proline residues present in similar local environments increases the unfolding entropy. The average value of this increase in unfolding entropy is 7.7 ± 4.2 cal mol−1 K−1, which is within error of the value estimated by Matthews et al. ( 1987 ).