Conformation of the Combining Site of Immunoglobulins

Amzel, L.

Abstract

The specificity and the affinity of antibodies are determined by the conformation of six short stretches of sequences usually called the complementarity determining residues (CDR's). The total number of amino acids contained in the CDR's is not very large and therefore, using the known three-dimensional structures of the antigen binding fragments (Fab's) of several immunoglobulins, attempts have been made at modelling the conformation of the combining site of different immunoglobulin molecules. In this study, we propose to implement and evaluate procedures that will extend through the use of energy minimization methods the initial studies on the prediction of the conformation of the binding sites of immunoglobulins. The procedures will include protocols and parameters that will be optimized to produce the correct coordinates of a known structure based on others. At least one structure will be left out of the data based used during this development stage. The success of the procedures will be assessed by their ability to produce correct coordinates for the binding site of the structure that was never included in the data base. If the methods are successful, they will be used initially to further the studies on the binding characteristics of the mouse phosphoryl choline binding proteins (myeloma and hybridoma). The ability to model the conformation of the binding site of immunoglobulins based on sequence data represents an important step towards understanding antibody specificity. In addition, the same methods and procedures could be used to compute the structures of homologous proteins based on a known structure. This would include proteins in evolutionarily related species, mutated proteins, specifically modified proteins and other cases of molecules of similar sequence.