A De Novo Designed Coiled-Coil Peptide with a Reversible pH-Induced Oligomerization Switch

Abstract

Protein conformational switches have many useful applications but are difficult to design rationally. Here we demonstrate how the isoenergetic energy landscape of higher-order coiled coils can enable the formation of an oligomerization switch by insertion of a single destabilizing element into an otherwise stable computationally designed scaffold. We describe a de novo designed peptide that was discovered to switch between a parallel symmetric pentamer at pH 8 and a trimer of antiparallel dimers at pH 6. The transition between pentamer and hexamer is caused by changes in the protonation states of glutamatic acid residues with highly upshifted pKa values in both oligomer forms. The drastic conformational change coupled with the narrow pH range makes the peptide sequence an attractive candidate for introduction of pH sensing into other proteins. The results highlight the remarkable ability of simple-α helices to self-assemble into a vast range of structural states.

Navigating the structural landscape ofde novoα–helical bundles

“…This presents exciting prospects for developing sequences to switch gross structural state in response to facile perturbations. 70,[93][94][95][96][97] Coiled-coil peptides that show multiple-defined states have been described by others. Lizatović et al design a pH-responsive sequence that switches between a pentameric bundle and parallel hexameric bundle.…”

“…Lizatović et al design a pH-responsive sequence that switches between a pentameric bundle and parallel hexameric bundle. 93 Grigoryan et al present the design of carbon-nanotube solubilizing peptides, which wrap around the surface of the nanotubes. In isolation, one of these peptides forms a tetramer, and another forms a dimer/hexamer mixture.…”

Computational design of a protein family that adopts two well-defined and structurally divergent de novo folds

“…There are many examples of de novo designed amino acid sequences that fold to a single designed target structure (Huang et al, 2016;Lu et al, 2018) , but designing new amino acid sequences capable of adopting divergent structural conformations is challenging since the free energy difference between the two states must be small enough that a few amino acid changes can shift the global energy minimum from one state to the other, and both states must be stable relative to the unfolded state. Redesigns of natural protein backbones have yielded large conformational changes for systems such as the Zn antennafinger, Zinc-binding/Coiled coil (ZiCo), and designed peptide Sw2, that involve changes in oligomerization state from a homotrimeric 3-helix bundle to a monomeric zinc-finger fold (Ambroggio and Kuhlman, 2006;Cerasoli et al, 2005;Hori and Sugiura, 2004) , and the pHios de novo design also involves a change in oligomerization state (pentamer to hexamer; (Lizatović et al, 2016) ). In other cases, the engineered proteins have two well-defined states that are quite similar, for example the dynamic switching of DANCER proteins primarily involves a single tryptophan residue (Davey et al, 2017) , and the Rocker channel has two symmetrically related states that are structurally identical (Joh et al, 2017) .…”

Protein function prediction in genomes: Critical assessment of coiled-coil predictions based on protein structure data

“…Coiled-coil structures are claimed to be better understood than those of any other fold 7,8 and are increasingly used as building blocks in the emerging fields of synthetic biology and de novo protein design 9,10 . The most advanced -2 -design case so far is likely a coiled-coil that can switch between pentameric and hexameric states upon pH-change 11 . While writing up amino acid sequences forming coiled-coils with dedicated oligomeric state is possible now, the complementary approach to detect coiled-coil regions in amino acid sequences is likely to be resolved as well given the biochemical understanding of this structural motif.…”