SODA: prediction of protein solubility from disorder and aggregation propensity

Nucleic Acids Research
Lisanna PaladinSilvio C E Tosatto

Abstract

Solubility is an important, albeit not well understood, feature determining protein behavior. It is of paramount importance in protein engineering, where similar folded proteins may behave in very different ways in solution. Here we present SODA, a novel method to predict the changes of protein solubility based on several physico-chemical properties of the protein. SODA uses the propensity of the protein sequence to aggregate as well as intrinsic disorder, plus hydrophobicity and secondary structure preferences to estimate changes in solubility. It has been trained and benchmarked on two different datasets. The comparison to other recently published methods shows that SODA has state-of-the-art performance and is particularly well suited to predict mutations decreasing solubility. The method is fast, returning results for single mutations in seconds. A usage example estimating the full repertoire of mutations for a human germline antibody highlights several solubility hotspots on the surface. The web server, complete with RESTful interface and extensive help, can be accessed from URL: http://protein.bio.unipd.it/soda.

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Citations

Jul 18, 2018·International Journal of Molecular Sciences·Mengting NiuKe Han
Oct 26, 2018·FEMS Microbiology Reviews·Ario de MarcoAntonio Villaverde
May 1, 2020·PLoS Computational Biology·Daniele RaimondiYves Moreau
Jun 28, 2019·Frontiers in Molecular Biosciences·Mohd AmirMd Imtaiyaz Hassan
Jan 30, 2021·Biotechnology Advances·Joan Planas-IglesiasDavid Bednar
Apr 13, 2021·Journal of Biomolecular Structure & Dynamics·Mansoureh Shahbazi DastjerdehMajid Golkar
May 14, 2021·Journal of Biomolecular Structure & Dynamics·Insan HabibMd Imtaiyaz Hassan
Jun 3, 2021·International Journal of Molecular Sciences·Magdalena Ptak-KaczorIrena Roterman
Aug 8, 2021·International Journal of Molecular Sciences·Yang YangMauno Vihinen
Dec 2, 2021·Bioinformatics·Vineet ThumuluriAlexander R Johansen

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