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
D. Wang et al., 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 Journal of biological chemistry, 268(27), 1993, pp. 20584-20589
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.