Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil

To address whether proteins fold along multiple pathways, i,i+4 bi-histidine metal binding sites are introduced into dimeric and crosslinked versions of the leucine zipper region of the growth control transcription factor, GCN4. Divalent metal ion binding enhances both the equilibrium and folding activation free energies for GCN4. The enhancement of folding rates quantifies the fraction of molecules that have the binding site in a helical geometry in the transition state. Hence, this new method, termed Psi-analysis, identifies the degree of pathway heterogeneity for a protein that folds in a two-state manner, a capability that is generally unavailable even with single molecule methods. Adjusting metal ion concentration continuously varies the stability of the bi-histidine region without additional structural perturbation to the protein. For dimeric and crosslinked versions, the accompanying changes in kinetic barrier heights at each metal ion concentration maps the folding landscape as well as establishes the importance of connectivity in pathway selection. Furthermore, this method can be generalized to other biophysical studies, where the ability to continuously tune the stability of a particular region with no extraneous structural perturbation is advantageous.