circular permutation prediction reveals a viable backbone disconnection for split proteins an approach in identifying a new functional split intein圆形排列预测显示一个可行的骨干断开分离蛋白质的方法确定一个新的功能intein分裂.pdfVIP

Circular Permutation Prediction Reveals a Viable Backbone Disconnection for Split Proteins: An Approach in Identifying a New Functional Split Intein 1 1 1,4 1,3 1,2 Yun-Tzai Lee , Tz-Hsiang Su , Wei-Cheng Lo , Ping-Chiang Lyu *, Shih-Che Sue * 1 Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, 2 Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, 3 Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, 4 Institute of Bioinformatics and Structural Biology, National Chiao Tung University, Hsinchu, Taiwan Abstract Split-protein systems have emerged as a powerful tool for detecting biomolecular interactions and reporting biological reactions. However, reliable methods for identifying viable split sites are still unavailable. In this study, we demonstrated the feasibility that valid circular permutation (CP) sites in proteins have the potential to act as split sites and that CP prediction can be used to search for internal permissive sites for creating new split proteins. Using a protein ligase, intein, as a model, CP predictor facilitated the creation of circular permutants in which backbone opening imposes the least detrimental effects on intein folding. We screened a series of predicted intein CPs and identified stable and native-fold CPs. When the valid CP sites were introduced as split sites, there was a reduction in folding enthalpy caused by the new backbone opening; however, the coincident loss in entropy was sufficient to be compensated, yielding a favorable free energy for self- association. Since split intein is exploited in protein semi-synthesi