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

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...

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Veröffentlicht in:BMC genomics 2024-06, Vol.25 (1), p.630-16, Article 630
Hauptverfasser: Bendel, Alexandra M, Skendo, Kristjana, Klein, Dominique, Shimada, Kenji, Kauneckaite-Griguole, Kotryna, Diss, Guillaume
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Sprache:eng
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Zusammenfassung: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.
ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-024-10524-7