MODELING STUDY OF ANTIBODY COMBINING SITES TO (ALPHA-1-6)DEXTRANS - PREDICTIONS OF THE CONFORMATIONAL CONTRIBUTION OF V(L)-CDR3 AND J-KAPPASEGMENTS TO GROOVE-TYPE COMBINING SITES

The shuffling of the V(kappa)-Ox1 light chain joined to J(kappa)4 or J (kappa)5 instead of J(kappa)2 reduced or abolished antigen binding of three groove-type anti-(alpha1-6)dextran monoclonal antibodies, raisin g questions as to the structural roles of J(kappa) in antibody combini ng sites. The J(kappa)4 light chain used contains Pro95A at the V(kapp a)-Ox1-J(kappa)4 junction, as well as a Phe to Ile substitution at the beginning of this J(kappa)4 segment. To predict whether the defect in antigen binding is a consequence of the J(kappa) replacement, the Pro insertion or the Phe to Ile substitution, model-building studies were performed. As shown by the surface representation of antibody combini ng sites, the models with length variation in the V(L)-CDR3 loop by on ly 1 residue altered the shape of the combining site dramatically; whe reas those with replacement of J. or having amino acid substitutions i n V(L)-CDR3 affect the combining site less extensively. A distinct loo p configuration of V(L)-CDR3 appears in models having either a Pro, Gl y, or Ala insertion at position 95A. These results indicate that the l ength of V(L)-CDR3 is crucial for its loop conformation and may, there fore, have played a major role in abolishing dextran binding activity of the J(kappa)4 variants. The potential of V(kappa)-Ox1 genes in gene rating conformational diversity in the loop of V(L)-CDR3 and its influ ence in forming different combining sites are discussed.