De novo design of bioactive protein switches

Nature. 2019 Aug;572(7768):205-210. doi: 10.1038/s41586-019-1432-8. Epub 2019 Jul 24.

Abstract

Allosteric regulation of protein function is widespread in biology, but is challenging for de novo protein design as it requires the explicit design of multiple states with comparable free energies. Here we explore the possibility of designing switchable protein systems de novo, through the modulation of competing inter- and intramolecular interactions. We design a static, five-helix 'cage' with a single interface that can interact either intramolecularly with a terminal 'latch' helix or intermolecularly with a peptide 'key'. Encoded on the latch are functional motifs for binding, degradation or nuclear export that function only when the key displaces the latch from the cage. We describe orthogonal cage-key systems that function in vitro, in yeast and in mammalian cells with up to 40-fold activation of function by key. The ability to design switchable protein functions that are controlled by induced conformational change is a milestone for de novo protein design, and opens up new avenues for synthetic biology and cell engineering.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Allosteric Regulation*
  • Bcl-2-Like Protein 11 / metabolism
  • Cell Nucleus / metabolism
  • Cell Survival
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression Regulation
  • HEK293 Cells
  • Humans
  • Protein Binding
  • Protein Engineering / methods*
  • Protein Transport
  • Proteins / chemical synthesis*
  • Proteins / chemistry*
  • Proteins / metabolism
  • Proteolysis
  • Proto-Oncogene Proteins c-bcl-2 / metabolism
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Synthetic Biology

Substances

  • BCL2 protein, human
  • Bcl-2-Like Protein 11
  • Proteins
  • Proto-Oncogene Proteins c-bcl-2