The specificity of cross-reactivity: promiscuous antibody binding involves specific hydrogen bonds rather than nonspecific hydrophobic stickiness

Protein Sci. 2003 Oct;12(10):2183-93. doi: 10.1110/ps.03172703.


Proteins are renowned for their specificity of function. There is, however, accumulating evidence that many proteins, from enzymes to antibodies, are functionally promiscuous. Promiscuity is of considerable physiological importance. In the immune system, cross-reactive or multispecific antibodies are implicated in autoimmune and allergy conditions. In most cases, however, the mechanism behind promiscuity and the relationship between specific and promiscuous activities are unknown. Are the two contradictory? Or can a protein exhibit several unrelated activities each of which is highly specific? To address these questions, we studied a multispecific IgE antibody (SPE7) elicited against a 2,4-dinitrophenyl hapten (DNP). SPE7 is able to distinguish between closely related derivatives such as NP (nitrophenol) and DNP, yet it can also bind a number of unrelated ligands. We find that, like DNP, the cross-reactants are themselves bound specifically-close derivatives of these cross-reactants show very low or no binding to SPE7. It has been suggested that cross-reactivity is simply due to "hydrophobic stickiness", nonspecific interactions between hydrophobic ligands and binding sites. However, partitioning experiments reveal that affinity for SPE7 is unrelated to ligand hydrophobicity. These data, combined with crystal structures of SPE7 in complex with four different ligands, demonstrate that each cross-reactant is bound specifically, forming different hydrogen bonds dependant upon its particular chemistry and the availability of complementary antibody residues. SPE7 is highly homologous to the germline antinitrophenol (NP) antibody B1-8. By comparing the sequences and binding patterns of SPE7 and B1-8, we address the relationship between affinity maturation, specificity, and cross-reactivity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Anthracenes / chemistry
  • Anthraquinones / chemistry
  • Anthraquinones / immunology
  • Antibody Affinity / immunology
  • Antibody Specificity / immunology
  • Base Sequence
  • Binding, Competitive / immunology
  • Cloning, Molecular
  • Cross Reactions / immunology*
  • Crystallography, X-Ray
  • Dinitrophenols / chemistry
  • Dinitrophenols / immunology
  • Enzyme-Linked Immunosorbent Assay / methods
  • Haptens / chemistry
  • Haptens / immunology
  • Hydrogen Bonding*
  • Hydrophobic and Hydrophilic Interactions*
  • Immunoglobulin E / chemistry
  • Immunoglobulin E / immunology
  • Immunoglobulin Fab Fragments / genetics
  • Immunoglobulin Fab Fragments / immunology
  • Immunoglobulin Variable Region / genetics
  • Immunoglobulin Variable Region / immunology
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • Nitrophenols / chemistry
  • Nitrophenols / immunology
  • Recombinant Proteins / genetics
  • Recombinant Proteins / immunology
  • Schiff Bases / chemistry
  • Sequence Analysis, DNA
  • Sequence Homology, Amino Acid


  • Anthracenes
  • Anthraquinones
  • Dinitrophenols
  • Haptens
  • Immunoglobulin Fab Fragments
  • Immunoglobulin Variable Region
  • Nitrophenols
  • Recombinant Proteins
  • Schiff Bases
  • Immunoglobulin E
  • alizarin