There is an increasing recognition of the importance of transient and highly dynamic biomolecular interactions in mediating the specificity of a wide range of biological processes. These ‘fuzzy’ interactions are, by definition, structurally heterogeneous, and as such, their characteriazation by conventional means is challenging.
The monoclonal antibody 6D8 recognises a conserved epitope on the disordered malaria antigen MSP2. Despite the conserved nature of the structurally defined epitope, 6D8 binds the two allelic forms of MSP2 with an approximately 5-fold difference in affinity. This effect is caused by polymorphic residues immediately C-terminal to the epitope proper. Preliminary NMR experiments using peptides that extend the epitope to include these residues have suggested that they engage in fuzzy interactions with the antibody and that these interactions contribute to the strain specificity of 6D8.1 The strain-specificity of 6D8 represents a relatively simple and experimentally tractable model, in which the mechanics of fuzzy interactions can be examined in detail. Here we characterize these interactions in detail using NMR spectroscopy and enhanced-sampling molecular dynamics methods. Together, these approaches define a coherent picture, in which the polymorphic C-terminal extension engages in multiple transient interactions distributed across a broad region of the antibody surface. Differences in these interactions between the two allelic forms of MSP2 are evident, driven by side-chain differences and different intrinsic conformational preferences. These differences in fuzzy interaction appear to account for the unexpected strain-specificity of 6D8.