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bioRxiv · 10.1101/2023.10.23.563542

Optimization of a deep mutational scanning workflow to improve quantification of mutation effects on protein-protein interactions

Bendel, A. M.·Skendo, K.·Klein, D.·Shimada, K.·Kauneckaite-Griguole, K.·Diss, G.
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Abstract

Deep Mutational Scanning (DMS) assays are powerful tools to study sequence-function relationships by measuring the effects of thousands of sequence variants on protein function. During a DMS experiment, several technical artefacts might distort non-linearly the functional score obtained, potentially biasing the interpretation of the results. We therefore tested several technical parameters in the deepPCA workflow, a DMS assay for protein-protein interactions, in order to identify technical sources of non-linearities. We found that parameters common to many DMS assays such as amount of transformed DNA, timepoint of harvest and library composition can cause non-linearities in the data. Designing experiments in a way to minimize these non-linear effects will improve the quantification and interpretation of mutation effects.

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Bendel, A. M., Skendo, K., Klein, D., Shimada, K., Kauneckaite-Griguole, K., Diss, G.. 2023-10-24. Optimization of a deep mutational scanning workflow to improve quantification of mutation effects on protein-protein interactions. https://doi.org/10.1101/2023.10.23.563542

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