Structural resolution of switchable states of a de novo peptide assembly

De novo protein design is advancing rapidly. However, most designs are for single states. Here we report a de novo designed peptide that forms multiple alpha -helical-bundle states that are accessible and interconvertible under the same conditions. Usually in such designs amphipathic alpha helices associate to form compact structures with consolidated hydrophobic cores. However, recent rational and computational designs have delivered open alpha -helical barrels with functionalisable cavities. By placing glycine judiciously in the helical interfaces of an alpha -helical barrel, we obtain both open and compact states in a single protein crystal. Molecular dynamics simulations indicate a free-energy landscape with multiple and interconverting states. Together, these findings suggest a frustrated system in which steric interactions that maintain the open barrel and the hydrophobic effect that drives complete collapse are traded-off. Indeed, addition of a hydrophobic co-solvent that can bind within the barrel affects the switch between the states both in silico and experimentally. So far most of the de novo designed proteins are for single states only. Here, the authors present the de novo design and crystal structure determination of a coiled-coil peptide that assembles into multiple, distinct conformational states under the same conditions and further characterise its properties with biophysical experiments, NMR and MD simulations.

Automated summary

De novo protein design has been rapidly evolving, with recent advancements allowing for the creation of peptide structures that can exist in multiple alpha-helical-bundle states under the same conditions. This design demonstrates a frustrated system with interconverting states, influenced by steric interactions and the hydrophobic effect. Further studies using biophysical experiments, NMR, and MD simulations have characterized the unique properties of this peptide.