Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability

Understanding the molecular determinants of protein thermostability is of theoretical and practical importance. While numerous determinants have been suggested, no molecular feature has been judged of paramount importance, with the possible exception of ion-pair networks. The difficulty in identifying the main determinants may have been the limited structural information available on the thermostable proteins. Recently the complete genomes for mesophilic, thermophilic and hyperthermophilic organisms have been sequenced, vastly improving the potential for uncovering general trends in sequence and structure evolution related to thermostability and, thus, for isolating the more important determinants. From a comparative analysis of 20 complete genomes, we find a trend towards shortened thermophilic proteins relative to their mesophilic homologs. Moreover, sequence alignments to proteins of known structure indicate that thermophilic sequences are more likely than their mesophilic homologs to have deletions in exposed loop regions. The new genomes offer enough comparable sequences to compute meaningful statistics that point to loop deletion as a general evolutionary strategy for increasing thermostability.