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

Abstract

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).

Protein intrachain contact prediction with most interacting residues (MIR)

“…It then gives a precise idea of positions where a mutation that would change the hydrophobicity of the side chain is likely to have important consequences on the structure. MIR and its extension SMIR are also integrated in the whole SPROUTS analysis system, where the results can be compared to stability analyses [10,38,39]. MIR is listed as a service of the Mobyle portal for bioinformatics analyses (http://mobyle.rpbs.univparis-diderot.fr/), developed joint ly by the Institut Pasteur Biology IT Center and RPBS that supports linear workflows integrating various services and databanks [40].…”

“…We will explore how MIR can be used as an index to guide the alignment of proteins, therefore identifying areas of similarities that typically are not captured by traditional alignment methods [44]. A second promising area resides in integrating MIR with stability analyses to better predict the impact of mutations on protein structure [10,38,39]. We will investigate how the consensus method consisting of the average of various stability analyses currently made available in SPROUTS [12] can be improved for the prediction of the dramatic impact of mutation of protein structures with MIR.…”