A Workflow for the Prediction of the Effects of Residue Substitution on Protein Stability

The effects of residue substitution in protein can be dramatic and predicting its impact may benefit scientists greatly. Like in many scientific domains there are various methods and tools available to address the potential impact of a mutation on the structure of a protein. The identification of these methods, their availability, the time needed to gain enough familiarity with them and their interface, and the difficulty of integrating their results in a global view where all view points can be visualized often limit their use. In this paper, we present the Structural Prediction for pRotein fOlding UTility System (SPROUTS) workflow and describe our method for designing, documenting, and maintaining the workflow. The focus of the workflow is the thermodynamic contribution to stability, which can be considered as acceptable for small proteins. It compiles the predictions from various sources calculating the ΔΔG upon point mutation, together with a consensus from eight distinct algorithms, with a prediction of the mean number of interacting residues during the process of folding, and a sub domain structural analysis into fragments that may potentially be considered as autonomous folding units, i.e., with similar conformations alone and in the protein body. The workflow is implemented and available online. We illustrate its use with the analysis of the engrailed homeodomain (PDB code 1enh).