arXiv2017
Leucine zippers are alpha helical monomers dimerized to a coiled coil structure. Various scenarios for dimerization span interaction of unstructured monomers that form alpha helices in the process of dimerization to preformed alpha helical monomers dimerizing.Another suggested possibility, a trigger sequence hypothesis (M. O. Steinmetz et al., Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 7062-7067), is that a C terminal (CT) part of each monomer is a trigger sequence that is dimerized and, subsequently, the remainder N terminal (NT) part of each monomer (that is partially ordered) zips together to form the coiled coil. In this work, methods are developed to computationally explore the trigger sequence hypothesis based on an extension of a previously introduced (R. I. Cukier, J. Chem. Phys. 2011, 134, 045104) Hamiltonian Temperature Replica Exchange Method Mean Square (HTREM_MS) procedure, which scales the Hamiltonian in both potential and kinetic energies, to enhance sampling generically, along with additional restraints to enhance sampling in desired regions of conformational space. The method is applied to a 31-residue truncation of the 33-residue leucine zipper (GCN4-p1) of the yeast transcriptional activator GCN4. Using a variety of HTREM_MS simulations, we find that the NT of one monomer of the dimer becomes disordered when the NT parts of the monomers are separated. In contrast, when the CT parts of the monomers are separated, both monomers remain alpha helical. These simulations suggest that the CT does act as a trigger sequence and are consistent with a disordered NT. We also investigate whether the disordered NT can be induced to re-form the dimerized leucine zipper. It does, but with some lack of recovery of alpha helical hydrogen bonding structure in the NT.