Systematic In Silico Analysis of Interhelical Electrostatic Interactions in Leucine Zippers

Leucine zippers are parallel coiled-coil dimers composed of two α-helices with a repeating heptad pattern, designated as a-g. Hydrophobic residues at the a and d positions form the dimerization core, whereas charged residues at the e and g positions generate interhelical electrostatic interactions that influence stability and specificity. Oppositely charged e-g pairs are generally considered stabilizing, whereas like-charged pairs are expected to be destabilizing. However, their collective effects across an extended leucine zipper interface have not been systematically evaluated. Here, we designed a 40-residue homodimeric leucine zipper containing 10 e-g interaction positions. Ten e-g positions were independently assigned to one of three states-neutral, salt-bridge-forming, or repulsive-yielding 59,049 models. Each model was then analyzed with FoldX to calculate the interaction energy and component energy terms. Increasing the number of salt bridges progressively improved the interaction energy, with an average stabilization of 1.68 kcal/mol relative to neutral pairs. Unexpectedly, repulsive pairs were also modestly favorable relative to neutral pairs, improving interaction energy by 0.48 kcal/mol. Energy decomposition showed that favorable solvation and van der Waals contributions outweighed the electrostatic penalty. These effects were position-dependent, indicating that leucine zipper stability reflects a balance of electrostatics, solvation, packing, and positional context.