Design of a Single-Chain Polypeptide Tetrahedron Assembled From Coiled-Coil Segments

Nat Chem Biol. 2013 Jun;9(6):362-6. doi: 10.1038/nchembio.1248. Epub 2013 Apr 28.

Abstract

Protein structures evolved through a complex interplay of cooperative interactions, and it is still very challenging to design new protein folds de novo. Here we present a strategy to design self-assembling polypeptide nanostructured polyhedra based on modularization using orthogonal dimerizing segments. We designed and experimentally demonstrated the formation of the tetrahedron that self-assembles from a single polypeptide chain comprising 12 concatenated coiled coil-forming segments separated by flexible peptide hinges. The path of the polypeptide chain is guided by a defined order of segments that traverse each of the six edges of the tetrahedron exactly twice, forming coiled-coil dimers with their corresponding partners. The coincidence of the polypeptide termini in the same vertex is demonstrated by reconstituting a split fluorescent protein in the polypeptide with the correct tetrahedral topology. Polypeptides with a deleted or scrambled segment order fail to self-assemble correctly. This design platform provides a foundation for constructing new topological polypeptide folds based on the set of orthogonal interacting polypeptide segments.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Circular Dichroism
  • DNA / chemistry
  • Dimerization
  • Microscopy, Atomic Force
  • Microscopy, Electron, Transmission
  • Models, Molecular
  • Molecular Conformation
  • Molecular Sequence Data
  • Peptides / chemistry*
  • Plasmids / metabolism
  • Protein Binding
  • Protein Engineering / methods*

Substances

  • Peptides
  • DNA