How do antigens and antibodies bind

Antigen-antibody binding occurs through the recognition and binding of antigens (Ags) presented by MHC molecules by T cells and the recognition of complete antigens by antibodies (Abs) secreted by B cells.


Antibody-mediated immunity is the cornerstone of adaptive immune responses. While there have been many studies on T cell epitopes, 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 have important implications in the fields of biology, biomedicine, disease diagnosis, and treatment. The basic principle of any immunological technique relies on the specific binding of specific antibodies and antigens to form unique antibody-antigen immune complexes. Understanding the role of each part 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, with two antigen-binding regions (Fab) and one crystallizable region (Fc), forming a Y-shaped structure.


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, with its Fab region being unique and capable of specific antigen binding.


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 change (i.e., the difference between different types of antibodies lies in the differences in the constant domains of the heavy chains), while the variable domains of the heavy chains remain unchanged, meaning that the specificity for antigens does not change.


Antibodies induce immune responses against the bound antigens by recruiting immune cells and immune molecules. The binding between the two is completed through the antigen-binding sites (paratopes) on the antibody molecule and the epitopes on the antigen molecule. Antigen epitopes can be continuous amino acid fragments or spatially discontinuous amino acid fragments.


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


Adjacent CDRs form binding sites/surfaces for antigen binding. Due to the different amino acid sequences of CDRs in different antibodies, these surfaces generated by CDRs also differ, resulting in different antigen binding.


This specific binding also depends on the size and shape of the antigen molecule. If it is a small peptide or hapten, binding usually occurs within the groove between the variable domains of the heavy and light chains. If it is a large molecule antigen, the 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 variable domain CDRs of the antibody. The more amino acids involved, the higher the affinity.


Additionally, the amino acid side chains of most or all CDRs are also involved in contact with the antigen, together determining the specificity and affinity of the interaction.


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


In the past, it was generally believed that the variable domain CDRs were responsible for antigen binding, while the constant domains were responsible for effector activation. However, this functional distinction is oversimplified because certain CDR regions are not involved in antigen binding, while certain non-CDR residues play a critical role in antigen binding. Moreover, increasing evidence suggests that the binding of the antibody to the antigen is non-local, and conformational changes may occur, meaning that antigen binding to the antibody may affect the constant domains of the antibody, and vice versa.


In the pharmaceutical industry, it is important to produce high-affinity antibodies, but equally important is whether the antigen-antibody binding will cause conformational changes, including binding sites and the overall conformation of the antibody molecule. The antigen-antibody binding should not lose its original high affinity and should not compromise its effector function.