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Defining epitopes: It's not as easy as it seems

Nature Biotechnology volume 17, pages 936–937 (1999)Cite this article

A major theme in biomedical research and biotechnology is the definition of sites involved in noncovalent interactions, often generically referred to as epitopes. Characterization of epitopes and the sites with which they interact (paratopes) contributes to the understanding, at the level of molecules and physical forces, of such important and diverse phenomena as immune recognition mediated by antibodies or T lymphocytes, hormonal regulation of physiological processes, regulation of gene expression by transcription factors, signal transduction, and the pharmacologic effects of drugs.

One approach to defining such sites relies on determination of 3D structure, most often through the application of X-ray crystallography, for a complex composed of the molecules containing, respectively, epitope and paratope. A popular alternative method for identifying the structural elements of such sites is systematic mutation of amino acids to alanine, known as alanine scanning mutagenesis. We explore here the critical assumptions of alanine scanning mutagenesis (ASM) and consider the logic by which such analyses should be interpreted. In addition, we examine the complexity of epitopes as reflected in the different aspects that are captured by structural versus mutational methods.

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Figure 1: Surface of human thrombin (white) bound to a fragment of the fibrinogen Aa chain (stick model), according to the crystal structure5.
Figure 2: Venn diagrams depicting two conceivable extremes in the relationships among the structural correlates of intermolecular contact, affinity, and specificity.

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Acknowledgements

We thank Dr. Thierry Rose for Figure 1, and Dr. David Kaplan for critical review of the manuscript. This work was supported by NIH grants HL49413 and HL58141 to E.D.C. and AI41657 to N.S.G.

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Authors and Affiliations

  1. Case Western Reserve University, Cleveland, 44106, OH

    Neil S. Greenspan

  2. Washington University School of Medicine, St. Louis, 63110, MO

    Enrico Di Cera

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  1. Neil S. Greenspan
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  2. Enrico Di Cera
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Greenspan, N., Di Cera, E. Defining epitopes: It's not as easy as it seems. Nat Biotechnol 17, 936–937 (1999). https://doi.org/10.1038/13590

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