Method for predicting the state of association of discretized protein models. Application to leucine zippers

A method that employs a transfer matrix treatment combined with Monte Carlo sampling has been used to calculate the configurational free energies of folded and unfolded states of lattice models of proteins. The method is successfully applied to study the monomer-dimer equilibria in various coiled coils. For the short coiled coils, GCN4 leucine zipper, and its fragments, Fos and Jun, very good agreement is found with experiment. Experimentally, some subdomains of the GCN4 leucine zipper form stable dimeric structures, suggesting the regions of differential stability in the parent structure. Our calculations suggest that the stabilities of the subdomains are in general different from the values expected simply from the stability of the corresponding fragment in the wild type molecule. Furthermore, parts of the fragments structurally rearrange in some regions with respect to their corresponding wild type positions. Our results suggest for an Asn in the dimerization interface at least a pair of hydrophobic interacting helical turns at each side is required to stabilize the stable coiled coil. Finally, the specificity of heterodimer formation in the Fos-Jun system comes from the relative instability of Fos homodimers, resulting from unfavorable intra- and interhelical interactions in the interfacial coiled coil region.