Exploration of novel αβ-protein folds through de novo design

Here the authors carry out a systematic de novo protein design exploration of novel & alpha;& beta;-folds predicted under a defined set of rules for & beta;-sheet topology, in an effort to find out the extent to which all possible & alpha;& beta;-folds are already sampled in nature. A fundamental question in protein evolution is whether nature has exhaustively sampled nearly all possible protein folds throughout evolution, or whether a large fraction of the possible folds remains unexplored. To address this question, we defined a set of rules for & beta;-sheet topology to predict novel & alpha;& beta;-folds and carried out a systematic de novo protein design exploration of the novel & alpha;& beta;-folds predicted by the rules. The designs for all eight of the predicted novel & alpha;& beta;-folds with a four-stranded & beta;-sheet, including a knot-forming one, folded into structures close to the design models. Further, the rules predicted more than 10,000 novel & alpha;& beta;-folds with five- to eight-stranded & beta;-sheets; this number far exceeds the number of & alpha;& beta;-folds observed in nature so far. This result suggests that a vast number of & alpha;& beta;-folds are possible, but have not emerged or have become extinct due to evolutionary bias.