Accuracy of Secondary Structure and Solvent Accessibility Predictions for a Clostridial Neurotoxin C-Fragment

Earlier studies used Rost and Sander's artificial neural network (1993a), J. Mol. Biol. 232, 584–599] to predict the secondary structures Lebeda and Olson (1994), Proteins 20, 293–300] and residue solvent accessibilities Lebeda and Olson (1997), J. Protein Chem. 16, 607–618] of the clostridial neurotoxins. Because the X-ray crystal structure of the 50-kDa C-terminal half of the heavy chain of tetanus toxin was recently determined, this report evaluates the accuracy of these network-derived predictions. For this predominantly -strand-containing fragment, predictions, on a per-residue basis, for both secondary structure and solvent accessibility were about 70% accurate. A more flexible and realistic analysis based on overlapping segments yielded accuracies of over 80% for the three-state secondary structure and for the two-state accessibility predictions. Because the accuracies of these predictions are comparable to those made by Rost and Sander using a dataset of 126 nonhomologous globular proteins, our predictions provide a quantitative foundation for gauging the results when building by homology the structures of related proteins.