title: Modeling study of antibody combining sites to (alpha 1-6)dextrans. Predictions of the conformational contribution of VL-CDR3 and J kappa segments to groove-type combining sites.
abstract: The shuffling of the V kappa-Ox1 light chain joined to J kappa 4 of J kappa 5 instead of J kappa 2 reduced or abolished antigen binding of three groove-type anti-(alpha 1-6)dextran monoclonal antibodies, raising questions as to the structural roles of J kappa in antibody combining sites. The J kappa 4 light chain used contains Pro95A at the V kappa-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 combining sites, the models with length variation in the VL-CDR3 loop by only 1 residue altered the shape of the combining site dramatically; whereas those with replacement of J kappa or having amino acid substitutions in VL-CDR3 affect the combining site less extensively. A distinct loop configuration of VL-CDR3 appears in models having either a Pro, Gly, or Ala insertion at position 95A. These results indicate that the length of VL-CDR3 is crucial for its loop conformation and may, therefore, have played a major role in abolishing dextran binding activity of the J kappa 4 variants. The potential of V kappa-Ox1 genes in generating conformational diversity in the loop of VL-CDR3 and its influence in forming different combining sites are discussed.
authors.affiliation: Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, New York 10032.
authors.forename: D
authors.initials: D
authors.lastname: Wang
authors.forename: J M
authors.initials: JM
authors.lastname: Hubbard
authors.forename: E A
authors.initials: EA
authors.lastname: Kabat
mesh_terms: D000595:Amino Acid Sequence; D000906:Antibodies / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D000911:Antibodies, Monoclonal / Q000737:chemistry / Q000378:metabolism; D001483:Base Sequence; D001666:Binding Sites, Antibody; D017252:CD3 Complex / Q000737:chemistry / Q000378:metabolism*; D003196:Computer Graphics; D003911:Dextrans / Q000378:metabolism*; D007143:Immunoglobulin Heavy Chains / Q000737:chemistry / Q000378:metabolism; D007133:Immunoglobulin Joining Region / Q000737:chemistry / Q000378:metabolism; D007147:Immunoglobulin Light Chains / Q000737:chemistry / Q000378:metabolism; D007135:Immunoglobulin Variable Region / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D000906:Antibodies; D000911:Antibodies, Monoclonal; D017252:CD3 Complex; D003911:Dextrans; D007143:Immunoglobulin Heavy Chains; D007133:Immunoglobulin Joining Region; D007147:Immunoglobulin Light Chains; D007135:Immunoglobulin Variable Region; C041999:alpha-1,6-dextran