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Prediction of mutation effects

RH Rafał Hołubowicz
AO Andrzej Ożyhar
PD Piotr Dobryszycki
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Natural and designed mutants were assessed using online tools to predict their effects on protein structure and function. Data for the natural E470A SNP accompanied a respective entry in the Ensembl database, from which the results for SIFT (https://sift.bii.a-star.edu.sg/)62 and PolyPhen2 (http://genetics.bwh.harvard.edu/pph2/)63 tools were chosen for comparisons, as these tools were also useful to predict the effects of artificial mutations for both hOtolC1q and dOtolC1q. Additionally, for all investigated mutations, the SNP MuSiC (https://soft.dezyme.com/) tool was used to predict the effects on protein stability64. Models of gC1q trimers, which were used as a template, were based on already published EOM analysis conducted on the basis of SAXS data33. Default parameters were used in all predictions. The structure model was visualized using VMD software (University of Illinois, https://www.ks.uiuc.edu/Research/vmd/)65. Sequences of otolin-1 from selected fish, birds and mammals were aligned using Clustal X66 and visualized using Jalview67.

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