De novo predictions of the quaternary structure of leucine zippers and other coiled coils

Abstract

Coiled coils possess a quaternary structure comprised of the side-by-side arrangement of a-helices. Due their inherent structural simplicity, they are ideal model systems for both theoretical and experimental studies. Among the coiled coils are the leucine zippers, which play an important role in the activation of DNA transcription. In contrast to the large amount of available experimental data, an overview of which is
presented, there are very few theoretical studies. To address this need, the status of existing theoretical approaches to predict coiled coil quaternary structure is described. Furthermore, to treat the conformational equilibria inherent in these systems, an extension of entropy sampling Monte Carlo simulations is developed that can treat multimers. Here, the approach is applied to GCN4 leucine zippers in the context of a reduced protein model. Not only is the native conformation successfully predicted, but the model also reproduces the experimentally observed helix content in the denatured state and the observed two-state thermodynamic behavior. Such two-state behavior arises from the dissociation of highly helical dimeric chains to form monomers of low, isolated chain helix content.