Hamiltonian replica exchange method studies of a leucine zipper dimer

A melting curve (stability versus temperature) of a leucine zipper dimer was obtained with the use of explicit solvent molecular dynamics (MD). Leucine zippers form stable dimers in solution at physiological temperatures by formation of coiled coil alpha helical structures, using a characteristic heptadic repeating unit. We simulated a 31-residue truncation of the 33 residue parallel two-stranded leucine zipper (GCN4-p1) of the yeast transcriptional activator GCN4 that has four such repeats. The dimer remains bound using conventional MD sampling at the lowest temperature used, while mainly breaking apart at the highest temperature used. However, to obtain a melting curve, the sampling efficiency must be improved, especially at the lower temperatures. Configurational sampling was enhanced with the introduction of a Hamiltonian replica exchange method (HREM), which will be referred to as HTREM, which scales the Hamiltonian in both potential and kinetic energies. The potential scaling is carried out only for the protein-protein and protein-solvent interactions and the kinetic scaling only for the protein degrees of freedom. By limiting the number of scaled degrees of freedom, a smaller number of systems can be used relative to temperature REM where all degrees of freedom are scaled. The HTREM does enhance the sampling especially at the lower temperatures and a melting curve is constructed. A mutant leucine zipper is also simulated where five glutamates are protonated and five lysines are deprotonated in order to investigate the role that electrostatic interactions and salt bridges play in dimer stability. The mutant is considerably less stable than the wild type based on the melting curves. The connection between dimer stability, monomer alpha helix unwinding, and salt bridge presence is investigated. Among the possible salt bridges of GCN4-p1, those found in experiments are also found in the simulation at the lowest simulation temperature, and the corresponding salt bridge fractions at higher temperature are much lower. A difference between the N terminal and C terminal halves of the monomers regarding their alpha helix stability is found, with the N terminal less stable than the C terminal parts, in accord with biophysical analyses of two monomeric 16-residue peptides derived from GCN4-p1.