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Fig. 3 | Genome Biology

Fig. 3

From: DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

Fig. 3

Variable-length indel scanning of Kir2.1 membrane trafficking. A Cartoon schematic of Kir architecture: the monomeric structure and overall tetrameric assembly are shown with the crystal structure of Kir2.2 (3SPI). Boundaries of the lipid membrane are indicated with lines, the crystallographic potassium are shown in purple, and locations of the pore highlighted with a cartoon arrow crossing through the channel [29]. B Cartoon workflow for studying how different variant types impact Kir2.1 surface expression. Briefly, we use DIMPLE to generate a library including insertion, missense, synonymous, and deletion variants at all positions of Kir2.1, we generate stable HEK293 cell lines, sort these cells based on surface-expression using FACS, perform deep sequencing of these subpopulations, and calculate surface expression fitness scores using Enrich2. C The distribution of fitness effects on surface expression of Kir2.1 is displayed as a kernel density estimate. Negative scores indicate decreased trafficking relative to WT Kir2.1. Deletions are the most disruptive perturbation, followed by insertion, missense, and synonymous mutations, respectively. D–F Mapping the average fitness effects of deletions, substitutions, and insertions across homologous positions in Kir2.2 shows global similarities but local differences between perturbation types. These are plotted from red-white-blue based on surface fitness scores. In general, the structured regions of Kir2.1 are more sensitive to all mutation types

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