Both the variable and constant domains of immunoglobulins fold into a compact three-dimensional structure composed exclusively of β sheets (see Figure 23-13b). A typical Ig domain contains two β sheets (one with three strands and one with four strands) held together like a sandwich by a disulfide bond. The residues that point inward are mostly hydrophobic and help stabilize this sandwich structure. The residues exposed to the aqueous environment show a greater frequency of polar and charged side chains. The spacing of the cysteine residues that make up the disulfide bond and a small number of strongly conserved residues characterize this evolutionarily ancient structural motif, termed the immunoglobulin fold. The basic immunoglobulin fold is also found in numerous eukaryotic proteins that are not directly involved in antigen-specific recognition, including the Ig superfamily of cell-adhesion molecules, or IgCAMs (see Chapter 20).

The region on an antigen that makes contact with the corresponding antibody is called an epitope. A protein antigen usually contains multiple epitopes, which are often exposed loops or surfaces on the protein and are thus accessible to antibody molecules. Each homogeneous antibody preparation derived from a clonal population of B cells recognizes a single molecularly defined epitope on the corresponding antigen.

In order to solve the structure of an antibody complexed to its cognate epitope on an antigen, it is important to have a source of homogeneous immunoglobulin and of antigen in pure form (see Chapter 3). As we have seen, homogeneous immunoglobulins can be obtained from B-cell tumors, but in that case, the antigen for which the antibody is specific is usually not known. The breakthrough essential for generating homogeneous antibody preparations suitable for structural analysis was the development of techniques to obtain antibodies from hybridomas by use of a special selection medium (see Chapter 4, pages 135–136). The creation of immortalized cell lines that produce antibodies of defined specificity, called monoclonal antibodies, has yielded essential tools for the cell biologist: monoclonal antibodies are widely used not only for the specific detection of macromolecules, but also for detection and quantitation of drugs, drug metabolites, and even signaling molecules such as cAMP. Monoclonal antibodies can detect proteins and their modifications (phosphorylation, nitrosylation, methylation, acetylation, etc.) as well as complex carbohydrates, (glyco)lipids, and nucleic acids and their modifications, and they have therefore found widespread use in the laboratory as well as for diagnostic and therapeutic purposes.

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We now have detailed insights into the structure of a large number of monoclonal antibodies, each in a complex with the antigen for which it is specific. There are no hard-and-fast rules that describe these interactions, other than the usual rules of molecular complementarity of proteins with other (macro)molecules (see Chapter 3). The CDRs make the most important contributions to the antigen-antibody interface. The CDR3 of the V_H region of the Ig heavy chain plays a particularly prominent role, as does the CDR3 of the V_L region of the Ig light chain.