A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins

Characterization of the unfolded state is essential for understanding the protein folding problem. in the unfolded state, a protein molecule samples vastly different conformations. Here I present a simple theoretical method for treating residual charge-charge interactions in the unfolded state. The method is based on modeling an unfolded protein as a Gaussian chain. After sampling over all conformations, the electrostatic interaction energy between two charged residues (separated by / peptide bonds) is given by W = 332(6/pi)(1/2)[1 - pi(1/2)xexp (x(2))erfc(x)]/epsilond, where d = bl(1/2) + s and x = fcd/6(1/2). in unfolded barnase, the residual interactions lead to downward pK(a) shifts of approximate to 0.33 unit, in agreement with experiment. pK(a) shifts in the unfolded state significantly affect pH dependence of protein folding stability, and the predicted effects agree very well with experimental results on barnase and four other proteins. For T4 lysozyme, the charge reversal mutation K147E is found to stabilize the unfolded state even more than the folded state (1.39 vs. 0.46 kcal/mol), leading to the experimentally observed result that the mutation is net destabilizing for the folding. The Gaussian-chain model provides a quantitative characterization of the unfolded state and may prove valuable for elucidating the energetic contributions to the stability of thermophilic proteins and the energy landscape of protein folding.