A de novo designed protein protein interface

Protein Sci. 2007 Dec;16(12):2770-4. doi: 10.1110/ps.073125207.

Abstract

As an approach to both explore the physical/chemical parameters that drive molecular self-assembly and to generate novel protein oligomers, we have developed a procedure to generate protein dimers from monomeric proteins using computational protein docking and amino acid sequence design. A fast Fourier transform-based docking algorithm was used to generate a model for a dimeric version of the 56-amino-acid beta1 domain of streptococcal protein G. Computational amino acid sequence design of 24 residues at the dimer interface resulted in a heterodimer comprised of 12-fold and eightfold variants of the wild-type protein. The designed proteins were expressed, purified, and characterized using analytical ultracentrifugation and heteronuclear NMR techniques. Although the measured dissociation constant was modest ( approximately 300 microM), 2D-[(1)H,(15)N]-HSQC NMR spectra of one of the designed proteins in the absence and presence of its binding partner showed clear evidence of specific dimer formation.

Publication types

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

MeSH terms

  • Algorithms
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / isolation & purification
  • Computational Biology
  • Computer Simulation
  • Dimerization
  • Fourier Analysis
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Conformation
  • Protein Engineering*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary

Substances

  • Bacterial Proteins
  • IgG Fc-binding protein, Streptococcus