CPred: a web server for predicting viable circular permutations in proteins

Abstract

Circular permutation (CP) is a protein structural rearrangement phenomenon, through which nature allows structural homologs to have different locations of termini and thus varied activities, stabilities and functional properties. It can be applied in many fields of protein research and bioengineering. The limitation of applying CP lies in its technical complexity, high cost and uncertainty of the viability of the resulting protein variants. Not every position in a protein can be used to create a viable circular permutant, but there is still a lack of practical computational tools for evaluating the positional feasibility of CP before costly experiments are carried out. We have previously designed a comprehensive method for predicting viable CP cleavage sites in proteins. In this work, we implement that method into an efficient and user-friendly web server named CPred (CP site predictor), which is supposed to be helpful to promote fundamental researches and biotechnological applications of CP. The CPred is accessible at http://sarst.life.nthu.edu.tw/CPred.

The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation

“…In addition, we provide evidence that the tolerance of a thermophilic phosphotransferase to circular permutation correlates strongest with three parameters, including: (i) the distance between the backbone fission and AK phosphotransfer site, (ii) AK family sequence variability at residues near the fission site, and (iii) root mean square deviation (RMSD) of residues near the fission site in superimposed AK structures. Among the structure-derived metrics analyzed, these three structure-derived metrics correlated with functional conservation to the greatest extent, while no significant correlation was observed using CPred 27,28 .…”

“…These studies have revealed that polypeptides involved in early folding events and stability display a low tolerance to backbone fission arising from permutation 8,9 . Structure-derived parameters extracted from these studies have been used to develop an algorithm (CP site predictor, CPred), which scores the likelihood that proteins fold and function upon circular permutation 27,28 . To date, the quality of CPred predictions has not been tested with a thermophilic protein, and it remains unclear how well CPred anticipates the results of a combinatorial experiment involving proteins with extreme stability.…”

Clostridium thermocellum thermostable lichenase with circular permutations and modifications in the N-terminal region retains its activity and thermostability

“…Involvement of in silico analysis into CP prediction helped in the selection of circular permutations in lichenase sequence [10,30,41]. New open termini in two CP lichenase variants (CN-53 and CN-99) had no effect on both the activity and thermal tolerance unlike another CP variant, CN-140, which displayed a dramatic decrease in the activity and thermostability, presumably associated with a loss in stability at a high temperature ( Fig.…”

“…The circularly permutated lichenase homologs were searched for using iSARST web server [29] and the Blast software in PDB [26]. Potential CP sites in proteins were predicted using the CPred web server [30].…”

“…The next stage of in silico analysis was conducted with the help of the CPred server, providing prediction of potential CP sites in the proteins with a known PDB structure [30]. For this purpose, we selected the 3I4I protein, displaying the maximal linear homology to LicBM3 ( Table 1).…”