How do antigens and antibodies bind together?

Adaptive immunity mainly involves T cells and B cells. T cells can recognize antigen (Ag) fragments presented by MHC molecules, while antibodies (Abs) secreted by B cells can recognize complete antigens.

Antibody-mediated immunity is the cornerstone of adaptive immune responses. There has been extensive research on T cell epitopes, and we can now successfully predict T cell epitopes on antigens. However, the mutual recognition and binding between antigens and antibodies are not yet fully understood. The specificity and affinity of antigen-antibody binding not only determine the immune response itself but also play an important role in the fields of biology, biomedicine, disease diagnosis, and treatment. The basic principle of any immunological technique relies on the specific binding of antibodies and antigens, forming unique antibody-antigen immune complexes. Understanding the role of each component of the antibody structure in antigen recognition can lead to a better understanding of their mutual recognition and binding.

An antibody molecule consists of two heavy chains and two light chains, forming a Y-shaped structure with two antigen-binding regions (Fragment antigen binding region, Fab) and one crystallizable region (Fragment crystallizable region), also known as the Fc region.

The Fab region, also known as the variable domain, is responsible for antigen recognition and binding, while the Fc region, also known as the constant domain, is responsible for effector functions. Each type of antibody molecule has a unique structure, and its Fab region is unique, allowing for specific binding to an antigen.

Plasma cells produce different types of antibodies through class switching, such as from IgM to IgG1, IgG4, IgE, or any other antibody type. During class switching, the constant domains of the heavy chains undergo changes (i.e., the differences between different types of antibodies lie in the variations in the constant domains of the heavy chains), while the variable domains of the heavy chains remain unchanged, meaning the specificity for antigens remains the same.

Antibodies induce immune responses against the bound antigens by recruiting immune cells and immune molecules. The binding between the two is accomplished through the antibody's antigen-binding sites (paratopes) and the antigen's epitopes. Antigen epitopes can be continuous amino acid sequences or non-contiguous amino acid sequences in space.

The Fab region of the antibody has six highly variable loops, commonly known as complementarity-determining regions (CDRs), which determine the specificity of the antigen. The amino acids on the surface of the CDRs bind to the antigen.

Adjacent CDRs form binding sites/surfaces for the antigen. Clearly, due to the different amino acid sequences of the CDRs in different antibodies, the surfaces generated by these CDRs are diverse, resulting in different antigen bindings.

The specificity of this binding also depends on the size and shape of the antigen molecule. If it is a small peptide or hapten, the binding usually occurs in a groove between the variable domains of the heavy and light chains. For large molecule antigens, this binding may involve all CDRs, and even other parts of the framework regions, and the binding surface may not necessarily be concave but can be flat, undulating, or convex.

The affinity of antigen-antibody binding largely depends on the number and types of amino acids in the CDRs of the antibody variable domain. The more amino acids involved, the higher the affinity.

Furthermore, the side chains of most or all CDRs also participate in contacting the antigen, collectively determining the specificity and affinity of the interaction.

The binding between antigen epitopes and antibody paratopes occurs through non-covalent bonds, which determine the binding affinity. The antigen-antibody binding can be disrupted by high salt concentrations, extreme pH values, detergents, etc. It can also be influenced by competition from other higher concentration epitopes.

In the past, it was generally believed that the variable domain CDRs were responsible for antigen binding, while the constant domain mediated effector activation. However, this functional distinction was oversimplified because certain CDR regions are not involved in antigen binding, while some non-CDR residues play crucial roles in antigen binding. Moreover, increasing evidence suggests that antigen-antibody binding is non-local and can even induce conformational changes, affecting both the antigen-binding site and the constant domain of the antibody.

For the pharmaceutical industry, it is essential to produce antibodies with high affinity, but equally important is whether antigen-antibody binding will lead to conformational changes, including the binding site and the overall conformation of the antibody molecule. Antigen-antibody binding should not compromise the original high affinity or effector functions.