Molecular modeling of combining sites

Modeling of the CDRs of antibodies of unknown three-dimensional structure was attempted in several laboratories, using different energy minimization and computer graphics approaches. The proposed models were subsequently compared with the determined crystallographic structures. The apparent occurrence of 'canonical structures' for most of the CDRs allowed successful approximation of the folding of the main polypeptide chain for the unknown antibodies. Establishing the orientation of side-chains is generally beyond the reach of these procedures, although in several cases they were correctly predicted. The biggest problems for modeling are posed by 1) the less predictable structure of the CDR3 of VH; 2) the relative positioning of VH and V, ; 3) the difficulty in placing solvent molecules which could be tightly bound to the combining site or its surroundings and thus contribute to its conformational stability; and 4) predicting possible conformational change that may take place upon antigen binding. Modeling attempts have been partially successful in determining the conformation of some of the CDRs compared with those observed in the crystal structures of the complexes with antigen. Thus they suggest agreement with the experimental observation that there is no major conformational change in going from the uncomplexed to the complexed anti-body-combining site.

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