Structural resolution of switchable states of a de novo peptide assembly

Nat Commun. 2021 Mar 9;12(1):1530. doi: 10.1038/s41467-021-21851-8.

Abstract

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 α-helical-bundle states that are accessible and interconvertible under the same conditions. Usually in such designs amphipathic α helices associate to form compact structures with consolidated hydrophobic cores. However, recent rational and computational designs have delivered open α-helical barrels with functionalisable cavities. By placing glycine judiciously in the helical interfaces of an α-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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • Hydrophobic and Hydrophilic Interactions
  • Molecular Dynamics Simulation
  • Peptides / chemistry*
  • Protein Conformation
  • Protein Conformation, alpha-Helical
  • Protein Engineering
  • Proteins / chemistry
  • Solvents

Substances

  • Peptides
  • Proteins
  • Solvents