Modelling antibody combining sites: a review

The combining site in an antibody is built up from six hypervariable loop regions, three from the light chain and three from the heavy chain. Three-dimensional structures have been elucidated by X-ray crystallographic studies for a variety of combining sites and for four protein-antibody complexes. Since sequence determination is relatively straightforward, whilst structure determination is often difficult and time consuming, it would be useful to be able to predict the structure of a combining site from its sequence. Knowledge of the structure would facilitate modifications of antibodies for specific aims. The structure of an antibody combining site for which only the sequence is known can be modelled on the basis of homology with a protein of known structure. The most demanding steps are modelling of the hypervariable loops and inclusion of the amino acid side chains. Final energy refinement of the model is achieved by conventional energy minimization techniques, but simulated annealing promises to be a powerful way of predicting side chain conformation. Four different groups have modelled antibody combining sites and compared their predictions with observed structures: for the main chain conformations resolutions of less than 1 A have been achieved. Future developments will increase the efficiency of the modelling procedures and permit accurate predictions of side chain conformations.