Static accessibility model of protein antigenicity: the case of scorpion neurotoxin

Scorpion neurotoxins are a family of homologous, 64 to 65 residue containing proteins with four invariant disulfide bridges. Previous experimental work established four antigenic epitopes in the Androctonus australis neurotoxin and localized them in the amino acid sequence. Using crystallographic coordinates of the Centruroides sculpturatus neurotoxin and computing its large sphere (radius 1 nm or 10 A) accessibility profiles, we identified six antigenic sites clustered into four surface regions. Three of four computed sites coincided with the epitopes identified and localized experimentally in the A. australis neurotoxin, while two of the computed sites partially overlapped the fourth epitope. To investigate the relationship between antigenicity and segmental flexibility, 8-ps molecular dynamics simulations were performed on the C. sculpturatus structure, average backbone temperature factors computed from the simulation, and results compared with the X-ray-derived B values. Most of the neurotoxin structure and, in particular, three of the four antigenic sites were found inflexible, as judged by the computed and/or crystallographic temperature factors. The remaining epitope was associated with only marginal above-average maxima of backbone B values, corresponding to root mean square atomic displacements of 0.5 A (50 pm). We conclude that neurotoxin antigenicity is determined by an exceptional surface exposure of relatively short loop segments and that segmental flexibility is not an essential component of antigenicity.