'Knobs-into-holes' engineering of antibody CH3 domains for heavy chain heterodimerization

Protein Eng. 1996 Jul;9(7):617-21. doi: 10.1093/protein/9.7.617.


'Knobs-into-holes' was originally proposed by Crick in 1952 as a model for the packing of amino acid side chains between adjacent alpha-helices. 'Knobs-into-holes' is demonstrated here as a novel and effective design strategy for engineering antibody heavy chain homodimers for heterodimerization. In this approach a 'knob' variant was first obtained by replacement of a small amino acid with a larger one in the CH3 domain of a CD4-IgG immunoadhesin: T366Y. The knob was designed to insert into a 'hole' in the CH3 domain of a humanized anti-CD3 antibody created by judicious replacement of a large residue with a smaller one: Y407T. The anti-CD3/CD4-IgG hybrid represents up to 92% of the protein A purified protein pool following co-expression of these two different heavy chains together with the anti-CD3 light chain. In contrast, only up to 57% of the anti-CD3/CD4-IgG hybrid is recovered following co-expression in which heavy chains contained wild-type CH3 domains. Thus knobs-into-holes engineering facilitates the construction of an antibody/immunoadehsin hybrid and likely other Fc-containing bifunctional therapeutics including bispecific immunoadhesins and bispecific antibodies.

MeSH terms

  • Antibodies / genetics
  • Antibodies / metabolism*
  • Antigens, CD / immunology*
  • CD3 Complex / immunology
  • CD4 Antigens / immunology
  • Dimerization
  • Genetic Variation
  • Humans
  • Immunoglobulin Fc Fragments / genetics
  • Immunoglobulin Fc Fragments / metabolism*
  • Immunoglobulin G / genetics
  • Immunoglobulin G / metabolism*
  • Immunoglobulin Heavy Chains / genetics
  • Immunoglobulin Heavy Chains / metabolism*
  • Models, Molecular
  • Protein Binding
  • Protein Engineering / methods


  • Antibodies
  • Antigens, CD
  • CD3 Complex
  • CD4 Antigens
  • Immunoglobulin Fc Fragments
  • Immunoglobulin G
  • Immunoglobulin Heavy Chains