Modulation of Coiled-Coil Dimer Stability through Surface Residues while Preserving Pairing Specificity

Igor Drobnak, Helena Gradišar, Ajasja Ljubetič, Estera Merljak, Roman Jerala

The coiled-coil dimer is a widespread protein structural motif and due to its designability represents an attractive building block for assembling modular nanostructures. The specificity of coiled-coil dimer pairing is mainly based on the hydro-phobic and electrostatic interactions between residues at positions a and d, and e and g of the heptad repeat, respectively. Binding affinity, on the other hand, can also be affected by surface residues that face away from the dimerization interface. Here we show how design of the local helical propensity of interacting peptides can be used to tune the stabilities of coiled-coil dimers over a wide range. By designing intramolecular charge pairs, regions of high local helical propensity can be engineered to form trigger sequences and dimer stability is adjusted without changing the peptide length or any of the directly interacting residues. This general principle is demonstrated by a change in thermal stability by more than 30 °C as a result of only two mutations outside the binding interface. The same approach was successfully used to modulate the stabilities in an orthogonal set of coiled-coils without affecting their binding preferences. The stability effects of local helical propensity and peptide charge are well described by a simple linear model, which should help improve current coiled-coil stability prediction algorithms. Our findings enable tuning the stabilities of coiled-coil-based building modules match a diverse range of applications in synthetic biology and nanomaterials.