The Measure of Interior Disorder in a Folded Protein and Its Contribution to Stability

To investigate whether any parameter other than packing density determines the quality of packing in a folded protein, the contribution of van der Waals interactions between hydrophobic core residues to protein stability at fixed packing density is investigated experimentally in this study. To this end, we employed a novel sequence variation scheme called “residue shuffling”, defined as permutation of guest residues at equivalent host sites in a symmetric sequence frame. By comparing the stability of the analogues generated by permutation of hydrophobic core residues in a synthetic two-stranded R-helical coiled-coil scaffold, we conclude that the number of permissible rotamers, based on the avoidance of steric clashes, is another packing parameter. Rotamer number measures the degree of disorder in the hydrophobic core of a folded protein and complements packing density in evaluating packing free energy by gauging packing entropy, the dynamical aspect of packing.