FOR the RECORD: Role of loops connecting secondary structure elements in the stabilization of proteins isolated from thermophilic organisms

It has been recently discovered that the connection of secondary structure elements (bb-unit, ba-andab-units) in proteins follows quite stringent principles regarding the chirality and the orientation of the structural units (Koga et al., Nature 2012;491:222-227). By exploiting these rules, a number of protein scaffolds endowedwith a remarkable thermal stability have been designed (Koga et al., Nature 2012;491:222-227). By using structural databases of proteins isolated fromeither mesophilic or thermophilic organisms,we here investigate the influence of supersecondary associations on the thermal stability of natural proteins. Our results suggest that b-hairpins of proteins fromthermophilic organisms are very frequently characterized by shortenings of the loops. Interestingly, this shortening leads to states that display a very strong preference for the most common connectivity of the strands observed in native protein hairpins. The abundance of selective states in these proteins suggests that they may achieve a high stability by adopting a strategy aimed to reduce the possible conformations of the unfolded ensemble. In this scenario, our data indicate that the shortening is effective if it increases the adherence to these rules.We also showthat thismechanismmay operate in the stabilization of well-known protein folds (thioredoxin and RNase A). These findings suggest that future investigations aimed at defining mechanismof protein stabilization should also consider these effects. © 2013 The Protein Society.