Molecular recognition properties of FN3 monobodies that bind the Src SH3 domain

Chem Biol. 2004 Jun;11(6):835-44. doi: 10.1016/j.chembiol.2004.04.009.


We have constructed a phage-displayed library based on the human fibronectin tenth type III domain (FN3) scaffold by randomizing residues in its FG and BC loops. Screening against the SH3 domain of human c-Src yielded six different clones. Five of these contained proline-rich sequences in their FG loop that resembled class I (i.e., +xxPxxP) peptide ligands for the Src SH3 domain. The sixth clone lacked the proline-rich sequence and showed particularly high binding specificity to the Src SH3 domain among various SH3 domains tested. Competitive binding, loop replacement, and NMR perturbation experiments were conducted to analyze the recognition properties of selected binders. The strongest binder was able to pull down full-length c-Src from murine fibroblast cell extracts, further demonstrating the potential of this scaffold for use as an antibody mimetic.

Publication types

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

MeSH terms

  • Animals
  • Binding Sites
  • Binding, Competitive
  • CSK Tyrosine-Protein Kinase
  • Clone Cells
  • Fibronectins / chemistry
  • Humans
  • Ligands
  • Mice
  • Models, Molecular
  • Molecular Mimicry / physiology
  • Peptide Library
  • Peptides / chemical synthesis
  • Peptides / chemistry*
  • Peptides / metabolism
  • Phosphotransferases / chemistry*
  • Phosphotransferases / metabolism
  • Proline / chemistry
  • Protein Structure, Tertiary
  • Protein-Tyrosine Kinases
  • Proto-Oncogene Proteins / chemistry*
  • Proto-Oncogene Proteins / metabolism
  • src Homology Domains / physiology*
  • src-Family Kinases


  • Fibronectins
  • Ligands
  • Peptide Library
  • Peptides
  • Proto-Oncogene Proteins
  • Proline
  • Phosphotransferases
  • Protein-Tyrosine Kinases
  • CSK Tyrosine-Protein Kinase
  • src-Family Kinases
  • CSK protein, human