Electrostatic interactions in the GCN4 leucine zipper: Substantial contributions arise from intramolecular interactions enhanced on binding

The GCN4 leucine zipper is a peptide homodimer that has been the subject of a number of experimental and theoretical investigations into the determina nts of affinity and specificity. Here, we utilize this model system to inve stigate electrostatic effects in protein binding using continuum calculatio ns. A particularly novel feature of the computations made here is that they provide an interaction-by-interaction breakdown of the electrostatic contr ibutions to the free energy of docking that includes changes in the interac tion of each functional group with solvent and changes in interactions betw een all pairs of functional groups on binding. The results show that (1) el ectrostatic effects disfavor binding by roughly 15 kcal/mol due to desolvat ion effects that are incompletely compensated in the bound state, (2) while no groups strongly stabilize binding, the groups that are most destabilizi ng are charged and polar side chains at the interface that have been implic ated in determining binding specificity, and (3) attractive intramolecular interactions (e.g., backbone hydrogen bonds) that are enhanced on binding d ue to reduced solvent screening in the bound state contribute significantly to affinity and are likely to be a general effect in other complexes. A co mparison is made between the results obtained in an electrostatic analysis carried out calculationally and simulated results corresponding to idealize d data from a scanning mutagenesis experiment. It is shown that scanning ex periments provide incomplete information on interactions and, if overinterp reted, tend to overestimate the energetic effect of individual side chains that make attractive interactions. Finally, a comparison is made between th e results available from a continuum electrostatic model and from a simpler surface-area dependent solvation model. In this case, although the simpler model neglects certain interactions, on average it performs rather well.