Simulations of temperature and salt concentration effects on bZIP, a basic region leucine zipper

Basic region leucine zipper (bZIP) transcription factors are dimeric proteins that recognize DNA. The monomers consist of a leucine zipper subdomain responsible for dimerization and a highly basic DNA recognition subdomain. Twelve explicit solvent molecular dynamics (MD) trajectories were run on the GCN4 bZIP transcriptional factor in the absence of DNA at three temperatures and two ion concentrations (0 mM with Cl(-) ions to neutralize the bZIP and 200 mM with additional Na(+) and Cl(-) ions) to probe the conformational ensemble that the basic region samples. In most trajectories, the basic region exhibits an alligator-jaw-like opening and closing (only one monomer moves), versus scissor-like motion, by a mainly rigid body, hinge motion centered on three "fork" residues that span the basic region to the coiled coil. In this motion, the α-helical character of the basic region monomers is mostly maintained. A broad range of distances is accessed, consistent with the absence of particular interactions for the basic region monomers. In two of the trajectories, the basic region monomers "collapse" to form a stable state. The coiled coil, leucine zipper subdomain is very stable for all of the trajectories. Ion solvation of the charged residue side chains is transient, on the scale of a few picoseconds. There is no evidence for persistent specific ion salt bridges to charged residues. For 0 mM, only certain basic region positively charged residues are substantially Cl(-) ion salt bridged. For 200 mM, in addition, some basic region negatively (positively) charged residues are salt bridged to Na(+) (Cl(-)) ions. The different ion solvation patterns at the two ion concentrations are not greatly temperature sensitive, and the conformational sampling found in the MD is remarkably unperturbed by ion concentration and/or temperature.