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 Waa ls interactions between hydrophobic core residues to protein stability at f ixed packing density is investigated experimentally in this study. To this end, we employed a novel sequence variation scheme called "residue shufflin g", defined as permutation of guest residues at equivalent host sites in a symmetric sequence frame. By comparing the stability of the analogues gener ated by permutation of hydrophobic core residues in a synthetic two-strande d alpha-helical coiled-coil scaffold, we conclude that the number of permis sible rotamers, based on the avoidance of steric clashes, is another packin g parameter. Rotamer number measures the degree of disorder in the hydropho bic core of a folded protein and complements packing density in evaluating packing free energy by gauging packing entropy, the dynamical aspect of pac king.