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Protein Engineering, Vol. 14, No. 1, 67-74, January 2001
© 2001 Oxford University Press

A central core structure in an antibody variable domain determines antigen specificity

Pernilla Jirholt1, Leif Strandberg2, Bo Jansson2, Elias Krambovitis3, Eskil Söderlind2, Carl A.K. Borrebaeck1, Roland Carlsson2, Lena Danielsson2 and Mats Ohlin1,4

1 Department of Immunotechnology, Lund University, S-220 07 Lund, 2 BioInvent Therapeutic AB, S-223 70 Lund, Sweden and 3 Department of Applied Biochemistry and Immunology, Institute of Molecular Biology and Biotechnology, GR-711 10 Heraklion, Greece

Antibody binding sites provide an adaptable surface capable of interacting with essentially any molecular target. Using CDR shuffling, residues important for the assembly of mucin-1 specific paratopes were defined by random recombination of the complementarity determining regions derived from a set of mucin-1 specific clones, previously selected from an antibody fragment library. It was found that positions 33 and 50 in the heavy chain and 32, 34, 90, 91 and 96 in the light chain were conserved in many of the clones. These particular residues seem to be located centrally in the binding site as indicated by a structure model analysis. The importance of several of these conserved residues was supported by their presence in a mouse monoclonal antibody with a known structure and the same epitope specificity. Several of these corresponding residues in the mouse monoclonal antibody are known to interact with the antigen. In conclusion, critical residues important for maintaining a human antigen-specific binding site during the process of in vitro antibody evolution were defined. Furthermore, an explanation for the observed restricted germline gene usage in certain antibody responses against protein epitopes is provided.


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