Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten

Masayoshi Nakasako, Toshihiko Oka, Masayasu Mashumo, Hideo Takahashi, Ichio Shimada, Yoshiki Yamaguchi, Koichi Kato, Yoji Arata

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


Antigen-induced structural changes in the Fv fragment of an anti-dansyl immunoglobulin G were studied by X-ray crystallography and stopped-flow fluorescence measurement. The crystal structure of the Fv fragment complexed with dansyl-lysine was determined at a resolution of 1.85 Å. The dansyl-lysine molecule bound to a narrow cavity formed by the complementarity-determining regions H3 and H1, the N-terminal region of the VH domain and L2 of the VL domain. The structure of the binding site in the crystal structure explained well the results of the previous nuclear magnetic resonance measurements. The hapten binding caused remarkable conformational changes in H3 and its environmental structures, including the hydration structure from those observed in the unliganded state. The tip of H3 moved about 12 Å from its position in the unliganded state. In addition, because of the contacts of H3 with the VL domain at the domain interface, the conformational changes of H3 resulted in the relative rotation of the variable domains by 5° from their association observed in the unliganded state. The hydrophobic interactions at the domain interface seemed to be particularly important for the mutual rotation of the domains. The stopped-flow fluorescence measurement monitoring the interaction of the dansyl group and the binding pocket revealed that H3 was in a conformational equilibrium of three consecutive conformational states in the presence of dansyl-lysine in solution; an unliganded state preventing the access of the hapten, another unliganded state able to bind the hapten and the complex. The conformational dynamics of H3 in recognizing and binding the hapten molecule are discussed on the basis of the structural information from the present and previous studies.

Original languageEnglish
Pages (from-to)627-640
Number of pages14
JournalJournal of Molecular Biology
Issue number3
Publication statusPublished - 2005 Aug 19


  • Antigen-recognition
  • Complementarity-determining region H3
  • Domain motion
  • Fv fragment
  • X-ray crystal structure

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology


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