Computational design of a symmetric homodimer using β-strand assembly

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20562-7. doi: 10.1073/pnas.1115124108. Epub 2011 Dec 5.

Abstract

Computational design of novel protein-protein interfaces is a test of our understanding of protein interactions and has the potential to allow modification of cellular physiology. Methods for designing high-affinity interactions that adopt a predetermined binding mode have proved elusive, suggesting the need for new strategies that simplify the design process. A solvent-exposed backbone on a β-strand is thought of as "sticky" and β-strand pairing stabilizes many naturally occurring protein complexes. Here, we computationally redesign a monomeric protein to form a symmetric homodimer by pairing exposed β-strands to form an intermolecular β-sheet. A crystal structure of the designed complex closely matches the computational model (rmsd = 1.0 Å). This work demonstrates that β-strand pairing can be used to computationally design new interactions with high accuracy.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Crystallography, X-Ray / methods
  • DNA / chemistry
  • Dimerization
  • Escherichia coli / metabolism
  • Light
  • Molecular Conformation
  • Protein Conformation
  • Protein Engineering / methods
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Scattering, Radiation
  • Software
  • Solvents
  • Surface Properties
  • Thermodynamics
  • Ultracentrifugation

Substances

  • Proteins
  • Solvents
  • DNA

Associated data

  • PDB/3ZY7