Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

Takamitsu Hattori, Darson Lai, Irina S. Dementieva, Sherwin P. Montaño, Kohei Kurosawa, Yupeng Zheng, Louesa R. Akin, Kalina M. ͆wist-Rosowska, Adrian T. Grzybowski, Akiko Koide, Krzysztof Krajewski, Brian D. Strahl, Neil L. Kelleher, Alexander J. Ruthenburg, Shohei Koide*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

25 Scopus citations


Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. This "antigen clasping" produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen- binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody-antigen recognition and suggests a strategy for developing extremely specific antibodies.

Original languageEnglish (US)
Pages (from-to)2092-2097
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number8
StatePublished - Feb 23 2016


  • Antibody engineering
  • Antibody validation
  • Data reproducibility
  • Epigenetics
  • Protein-protein interaction

ASJC Scopus subject areas

  • General


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