Many of the amino acids that are common to the C and V domains are present in the core of the immunoglobulin fold and are essential for its stability. Other proteins with sequences similar to those of immunoglobulins have been found to have domains with a similar structure, called immunoglobulin-like domains (Ig-like domains). These domains are present in many proteins of the immune system, such as the KIRs expressed by NK cells described in Chapter 3. They are also frequently involved in cell–cell recognition and adhesion, and together with the immunoglobulins and the T-cell receptors, these proteins make up the extensive immunoglobulin superfamily.
4-4 The antibody molecule can readily be cleaved into functionally distinct fragments.
When fully assembled, an antibody molecule comprises three equal-sized globular portions, with its two arms joined to its trunk by a flexible stretch of polypeptide chain known as the hinge region (see Fig. 4.1b). Each arm of this Y-shaped structure is formed by the association of a light chain with the amino-terminal half of a heavy chain; the VH domain is paired with the VL domain, and the CH1 domain is paired with the CL domain. The two antigen-binding sites are formed by the paired VH and VL domains at the ends of the two arms of the Y (see Fig. 4.1b). The trunk of the Y is formed by the pairing of the carboxyterminal halves of the two heavy chains. The CH3 domains pair with each other but the CH2 domains do not interact. Carbohydrate side chains attached to the CH2 domains lie between the two heavy chains.
Proteolytic enzymes (proteases) were an important tool in early studies of antibody structure, and it is valuable to review the terminology they generated. Limited digestion with the protease papain cleaves antibody molecules into three fragments (Fig. 4.4). Papain cuts the antibody molecule on the amino-terminal side of the disulfide bonds that link the two heavy chains, releasing the two arms of the antibody molecule as two identical fragments that contain the antigen-binding activity. These are called the Fab fragments, for fragment antigen binding. The other fragment contains no antigen-binding activity, but because it crystallized readily, it was named the Fc fragment (fragment crystallizable). It corresponds to the paired CH2 and CH3 domains. The Fc fragment is the part of the antibody molecule that does not interact with antigen, but rather interacts with effector molecules and cells, and it differs between heavy-chain isotypes. Another protease, pepsin, cuts on the carboxy-terminal side of the disulfide bonds (see Fig. 4.4). This produces a fragment, the F(abʹ)2 fragment, in which the two antigen-binding arms of the antibody molecule remain linked. Pepsin cuts the remaining part of the heavy chain into several small fragments. The F(abʹ)2 fragment has exactly the same antigen-binding characteristics as the original antibody but is unable to interact with any effector molecule, such as C1q or Fc receptors, and can be used experimentally to separate the antigen-binding functions from the antibody’s other effector functions.
Many antibody-related molecules can be constructed using genetic engineering techniques, and many antibodies and antibody-related molecules are being used therapeutically to treat a variety of diseases. We will return to this topic in Chapter 16, where we discuss the various therapeutic uses of antibodies that have been developed over the last two decades.