Diverse binding site structures revealed in homology models of polyreactive immunoglobulins

We describe here computer-assisted homology models of the combining site structure of three polyreactive immunoglobulins. Template-based models of Fv (VL-VH) fragments were derived for the surface IgM expressed by the malignant CD5 positive B cells from three patients with chronic lymphocytic leukaemia (CLL). The conserved framework regions were constructed using crystal coordinates taken from highly homologous human variable domain structures (Pot and Hil). Complementarity determining regions (CDRs) were predicted by grafting loops, taken from known immunoglobulin structures, onto the Fv framework models. The CDR templates were chosen, where possible, to be of the same length and of high residue identity or similarity. LCDR1, 2 and 3 as well as HCDR1 and 2 for the Fv were constructed using this strategy. For HCDR3 prediction, a database containing the Cartesian coordinates of 30 of these loops was complied from unliganded antibody X-ray crystallographic structures and an HCDR3 of the same length as that of the B CLL Fv was selected as a template. In one case (Yar), the resulting HCDR3 model gave unfavourable interactions when incorporated into the Fv model. This HCDR3 was therefore modelled using an alternative strategy of construction of the loop stems, using a previously described HCDR3 conformation (Pot), followed by chain closure with a beta-turn. The template models were subjected to positional refinement using energy minimisation and molecular dynamics simulations (X-PLOR). An electrostatic surface description (GRASP) did not reveal a common structural feature within the binding sites of the three polyreactive Fv. Thus, polyreactive immunoglobulins may recognise similar and multiple antigens through a diverse array of binding site structures.