Transient antibody-antigen interactions mediate the strain-specific recognition of a conserved malaria epitope

Abstract

Transient interactions in which binding partners retain substantial conformational disorder play an essential role in regulating biological networks, challenging the expectation that specificity demands structurally defined and unambiguous molecular interactions. The monoclonal antibody 6D8 recognises a completely conserved continuous nine-residue epitope within the intrinsically disordered malaria antigen, MSP2, yet it has different affinities for the two allelic forms of this antigen. NMR chemical shift perturbations, relaxation rates and paramagnetic relaxation enhancements reveal the presence of transient interactions involving polymorphic residues immediately C-terminal to the structurally defined epitope. A combination of these experimental data with molecular dynamics simulations shows clearly that the polymorphic C-terminal extension engages in multiple transient interactions distributed across much of the accessible antibody surface. These interactions are determined more by topographical features of the antibody surface than by sequence-specific interactions. Thus, specificity arises as a consequence of subtle differences in what are highly dynamic and essentially non-specific interactions.

Disordered epitopes as peptide vaccines

“…NMR experiments provide evidence of transient interactions that are not resolved in the crystal structure and which involve variable residues that are distal to the structurally defined epitope. These transient or fuzzy interactions thus appear to modulate the specificity of 6D8, rendering the antibody somewhat strain‐specific in spite of the conserved nature of its epitope . Although the generality of this effect remains to be established, it appears to originate from largely non‐specific interactions that occur, almost inevitably, as a result of the high effective concentration of the disordered regions that immediately flank the structurally defined epitope .…”

“…These transient or fuzzy interactions thus appear to modulate the specificity of 6D8, rendering the antibody somewhat strain‐specific in spite of the conserved nature of its epitope . Although the generality of this effect remains to be established, it appears to originate from largely non‐specific interactions that occur, almost inevitably, as a result of the high effective concentration of the disordered regions that immediately flank the structurally defined epitope . As such, it is expected that similar fuzzy interactions may contribute to antibody recognition of many disordered antigens.…”

Aggregation and the Intrinsic Structural Disorder of Dipeptide Repeat Peptides of C9orf72-Related Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Characterized by NMR

“…Additionally, because of a time-dependent structural transition (self-assembly), structural disorder, and heterogeneity, these systems are not suitable for characterization by X-ray crystallography and cryo-electron microscopy. Moreover, on the one hand, the exceptionally flexible DPRs and the repeat sequences within the intrinsically disordered proteins (IDPs) are challenging to study. , On the other hand, the complementary and versatile structural technique, NMR spectroscopy, can visualize the IDPs and sequence repeats at their molecular level. , NMR spectroscopy also makes it feasible to probe the atomic-level transient interactions by IDPs/peptides with their binding partners. , The structural details of IDPs can be obtained label-free, thus avoiding complications in data interpretation due to the addition of reagents such as ThT and uranyl acetate used for fluorescence and TEM experiments.…”

“…35,36 NMR spectroscopy also makes it feasible to probe the atomic-level transient interactions by IDPs/peptides with their binding partners. 37,38 The structural details of IDPs can be obtained label-free, thus avoiding complications in data interpretation due to the addition of reagents such as ThT and uranyl acetate used for fluorescence and TEM experiments.…”

Structural Biology, ASB/ABA meeting, Melbourne

“…The multiple transient interactions, which were observed via NMR chemical shift perturbations, relaxation rates, paramagnetic relaxation enhancement, and molecular dynamic simulations, were modulated by topological features rather than sequence-specific interactions. Understanding the non-specific antigen-antibody interactions could enable the design of new vaccine formulations based on disordered antigens (Krishnarjuna et al 2018).…”