The third-dimensional structure of the complex between an Fv antibody fragment and an analogue of the main immunogenic region of the acetylcholine receptor: A combined two-dimensional NMR, homology, and molecular modeling approach

Binding of autoantibodies to the acetylcholine receptor (AChR) plays a majo r role in the autoimmune disease Myasthenia gravis (MG). In this paper, we propose a structure model of a putative immunocomplex that gives rise to th e reduction of functional AChR molecules during the course of MG. The model complex consists of the [G(70), Nle(76)] decapeptide analogue of the main immunogenic region (MIR), representing the major antigenic epitope of AChR, and the single chain Fv fragment of monoclonal antibody 198, a potent MG a utoantibody. The structure of the complexed decapeptide antigen [G(70), Nle (76)]MIR was determined using two-dimensional nmr, whereas the antibody str ucture was derived by means of homology modeling. The final complex was con structed using calculational docking and molecular dynamics. We termed this approach "directed modeling," since the known peptide structure directs th e prestructured antibody binding site to its final conformation. The indepe ndently derived structures of the peptide antigen and antibody binding site already showed a high degree of surface complementarity after the initial docking calculation, during which the peptide was conformationally restrain ed The docking routine was a soft algorithm. applying a combination of Mont e Carlo simulation and energy minimization, The observed shape complementar ity in the docking process suggested that the structure assessments already led to anti-idiotypic conformations of peptide antigen and antibody fragme nt. Refinement of the complex by dynamic simulation yielded improved surfac e adaptation by small rearrangements within antibody and antigen. The compl ex presented herein was analyzed in terms of antibody-antigen interactions, properties of contacting surfaces, and segmental mobility. The structural requirements for AChR complexation by autoantibodies were explored and comp ared with experimental data from alanine scans of the MIR peptides. The ana lysis revealed that the N-terminal loop of the peptide structure, which is indispensable for antibody recognition, aligns three hydrophobic groups in a favorable arrangement leading to the burial of 40% of the peptide surface in the binding cleft upon complexation. These data should be valuable in t he rational design of an Fv mutant with much improved affinity for the MIR and AChR to be used in therapeutic approaches in MG. (C) 2000 John Wiley & Sons, Inc.