Antigen–Antibody Binding


Antibodies are a family of glycoproteins that bind specifically to target molecules (antigens). The antibody‐binding sites are formed by six segments of variable structure (CDRs) supported by a scaffold of essentially invariant architecture (framework regions). Shape complementarity between the contact surfaces (in the case of protein antigens) or close interactions with small antigens (hapten, peptide or others), together with complementation of water molecules, are important to achieve high affinity and specificity. The binding of an antigen to an antibody takes place by the formation of multiple noncovalent bonds between the antigen and the amino acids of the binding site. The increase in van der Waals contacts and/or buried surfaces upon complexation generally correlates well with the binding strength. Hydrogen bonds are in most cases critical to achieve high specificity and affinity for the antigen target. Importantly, antibodies have at least two antigen binding sites, boosting the effective affinity of the antibody for its target by a mechanism termed avidity.

Key Concepts

  • The binding between antibodies and antigens is characterised by high specificity and affinity resulting from distinct structural and energetic features.
  • Non‐covalent forces dominate antibody‐antigen interactions.
  • Generally, the recognition of an antigen is driven by the favorable change of enthalpy, and opposed by the entropy term.
  • Multivalency is an important property of antibodies that govern their interaction with antigens in a biological setting.
  • Progress in the fundamental understanding of antigen‐antibody interactions will lead to the rational design of more efficient and potent therapeutic antibodies.

Keywords: antibody; specificity; affinity; avidity; complementarity‐determining region

Figure 1. Structure of immunoglobulin G (IgG). (a) Schematic representation of a typical IgG. The L and H chains are shown in light orange and gray, respectively. Intermolecular disulfide bonds (S–S bonds) at the hinge region between two different heavy chains (green) or between the heavy and the light chains (magenta) are shown. (b) Three‐dimensional structure of murine IgG (PDB entry 1igy) (Harris et al., ). The residues in green correspond to S–S bonds at the hinge region. The attached carbohydrates in the Fc fragment are shown as sticks. The figure was prepared with CHIMERA.
Figure 2. The immunoglobulin fold. The variable domain of a heavy chain is shown. The stabilising intramolecular S–S bond between two Cys residues is shown with sticks. The figure was prepared with CHIMERA.
Figure 3. Structure of complementarity‐determining regions (CDRs). (a) Variable domains of a murine immunoglobulin G (composed of heavy chain and light chain) are shown (PDB entry 2e27) (Tsumoto et al., ). The hypervariable regions, CDRs comprising the antigen‐binding site, are depicted in red, green, and magenta. These are located at the one edge of the β‐barrel structure. The antigen (hapten) is shown with sticks. (b) Fab fragment of 10C9 complexed with the antigen 10C9‐ABCDE (PDB entry 2Z92) (Ui et al., ) showing the location of water molecules (red spheres). The figure was prepared with CHIMERA.
Figure 4. Molecular basis for antibody diversity. The figure illustrates an example for the heavy chain. In the human genome, one of the about 80 VH genes (in mouse, about 100) recombines with one of the 30 D segments (in mouse, about 10), and one of the 6 JH segments (in mouse, 4), producing the functional V–D–J gene in an immune B cell. The recombined DNA (deoxyribonucleic acid) is transcribed, spliced and translated into a polypeptide chain. Half of the VH genes in human B cell seem to be pseudo‐genes.


Akiba H and Tsumoto K (2015) Thermodynamics of antibody‐antigen interaction revealed by mutation analysis of antibody variable regions. Journal of Biochemistry 158: 1–13.

Arevalo JH, Taussig MJ and Wilson IA (1993) Molecular basis of crossreactivity and the limits of antibody‐antigen complementarity. Nature 365: 859–863.

Bhat TN, Bentley GA, Boulot G, et al. (1994) Bound water‐molecules and conformational stabilization help mediate an antigen‐antibody association. Proceedings of the National Academy of Sciences of the United States of America 91: 1089–1093.

Birtalan S, Zhang YN, Fellouse FA, et al. (2008) The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies. Journal of Molecular Biology 377: 1518–1528.

Bostrom J, Yu SF, Kan D, et al. (2009) Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site. Science 323: 1610–1614.

Chitarra V, Alzari PM, Bentley GA, et al. (1993) 3‐Dimensional structure of a heteroclitic antigen‐antibody cross‐reaction complex. Proceedings of the National Academy of Sciences of the United States of America 90: 7711–7715.

Chothia C, Lesk AM, Tramontano A, et al. (1989) Conformations of immunoglobulin hypervariable regions. Nature 342: 877–883.

Dall'Acqua W, Goldman ER, Lin WH, et al. (1998) A mutational analysis of binding interactions in an antigen‐antibody protein‐protein complex. Biochemistry 37: 7981–7991.

Davies DR, Padlan EA and Sheriff S (1990) Antibody‐antigen complexes. Annual Review of Biochemistry 59: 439–473.

Davies DR and Chacko S (1993) Antibody structure. Accounts of Chemical Research 26: 421–427.

Davies DR and Cohen GH (1996) Interactions of protein antigens with antibodies. Proceedings of the National Academy of Sciences of the United States of America 93: 7–12.

Harris LJ, Larson SB, Hasel KW, et al. (1992) The 3‐dimensional structure of an intact monoclonal‐antibody for canine lymphoma. Nature 360: 369–372.

Kiyoshi M, Caaveiro JMM, Miura E, et al. (2014) Affinity improvement of a therapeutic antibody by structure‐based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody‐antigen complex. Plos One 9 (1): e87099.

Lippow SM, Wittrup KD and Tidor B (2007) Computational design of antibody‐affinity improvement beyond in vivo maturation. Nature Biotechnology 25: 1171–1176.

Mian IS, Bradwell AR and Olson AJ (1991) Structure, function and properties of antibody‐binding sites. Journal of Molecular Biology 217: 133–151.

Padlan EA (1994) Anatomy of the antibody molecule. Molecular Immunology 31: 169–217.

Peng HP, Lee KH, Jian JW, et al. (2014) Origins of specificity and affinity in antibody‐protein interactions. Proceedings of the National Academy of Sciences of the United States of America 111: E2656–E2665.

Pons J, Rajpal A and Kirsch JF (1999) Energetic analysis of an antigen/antibody interface: alanine scanning mutagenesis and double mutant cycles on the HyHEL‐10/lysozyme interaction. Protein Science 8: 958–968.

Saphire EO, Parren PWHI, Pantophlet R, et al. (2001) Crystal structure of a neutralizing human IgG against HIV‐1: a template for vaccine design. Science 293: 1155–1159.

Shiroishi M, Tsumoto K, Tanaka Y, et al. (2007) Structural consequences of mutations in interfacial Tyr residues of a protein antigen‐anti body complex ‐ the case of HyHEL‐10‐HEL. Journal of Biological Chemistry 282: 6783–6791.

Sinha N, Mohan S, Lipschultz CA, et al. (2002) Differences in electrostatic properties at antibody‐antigen binding sites: implications for specificity and cross‐reactivity. Biophysical Journal 83: 2946–2968.

Sundberg EJ, Urrutia M, Braden BC, et al. (2000) Estimation of the hydrophobic effect in an antigen‐antibody protein‐protein interface. Biochemistry 39: 15375–15387.

Sundberg EJ and Mariuzza RA (2003) Molecular recognition in antibody‐antigen complexes. Advances in Protein Chemistry 61: 119–160.

Thorpe IF and Brooks CL (2007) Molecular evolution of affinity and flexibility in the immune system. Proceedings of the National Academy of Sciences of the United States of America 104: 8821–8826.

Tonegawa S (1983) Somatic generation of antibody diversity. Nature 302: 575–581.

Tsumoto K, Ogasahara K, Ueda Y, et al. (1995) Role of Tyr residues in the contact region of antilysozyme monoclonal‐antibody Hyhel10 for antigen‐binding. Journal of Biological Chemistry 270: 18551–18557.

Tsumoto K, Yokota A, Tanaka Y, et al. (2008) Critical contribution of aromatic rings to specific recognition of polyether rings ‐ the case of ciguatoxin CTX3C‐ABC and its specific antibody 1C49. Journal of Biological Chemistry 283: 12259–12266.

Ui M, Tanaka Y, Tsumuraya T, et al. (2008) How protein recognizes ladder‐like polycyclic ethers ‐ interactions between ciguatoxin (CTX3C) fragments and its specific antibody 10C9. Journal of Biological Chemistry 283: 19440–19447.

Vorup‐Jensen T (2012) On the roles of polyvalent binding in immune recognition: perspectives in the nanoscience of immunology and the immune response to nanomedicines. Advanced Drug Delivery Reviews 64: 1759–1781.

Wedemayer GJ, Patten PA, Wang LH, et al. (1997) Structural insights into the evolution of an antibody combining site. Science 276: 1665–1669.

Yokota A, Tsumoto K, Shiroishi M, et al. (2003) The role of hydrogen bonding via interfacial water molecules in antigen‐antibody complexation ‐ the HyHEL‐10‐HEL interaction. Journal of Biological Chemistry 278: 5410–5418.

Further Reading

Branden C and Branden J (1999) Introduction to Protein Structure, 2nd edn. New York: Garland Publishing.

Delves P, Martin S, Burton D and Roitt I (2007) Essential Immunology, 11th edn. London: John Wiley & Sons, Ltd.

Paul WE (2013) Fundamental Immunology, 7th edn. Philadelphia: Lippincott Williams & Wilkins.

Roitt I, Brostoff J and Male D (1996) Immunology, 3rd edn. London: Mosby Year Book.

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Tsumoto, Kouhei, and Caaveiro, Jose MM(Dec 2016) Antigen–Antibody Binding. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001117.pub3]