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Directed evolution of anti-HER2 DARPins by SNAP display reveals stability/function trade-offs in the selection process.

ABSTRACT: In vitro display technologies have proved to be powerful tools for obtaining high-affinity protein binders. We recently described SNAP display, an entirely in vitro DNA display system that uses the SNAP-tag to link protein with its encoding DNA in water-in-oil emulsions. Here, we apply SNAP display for the affinity maturation of a designed ankyrin repeat proteins (DARPin) that binds to the extracellular domain of HER2 previously isolated by ribosome display. After four SNAP display selection cycles, proteins that bound specifically to HER2 in vitro, with dissociation constants in the low- to sub-nanomolar range, were isolated. In vitro affinities of the panel of evolved DARPins directly correlated with the fluorescence intensities of evolved DARPins bound to HER2 on a breast cancer cell line. A stability trade-off is observed as the most improved DARPins have decreased thermostability, when compared with the parent DARPin used as a starting point for affinity maturation. Dissection of the framework mutations of the highest affinity variant, DARPin F1, shows that functionally destabilising and compensatory mutations accumulated throughout the four rounds of evolution.

SUBMITTER: Houlihan G

PROVIDER: S-EPMC4550541 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Directed evolution of anti-HER2 DARPins by SNAP display reveals stability/function trade-offs in the selection process.

Houlihan Gillian G Gatti-Lafranconi Pietro P Lowe David D Hollfelder Florian F

Protein engineering, design & selection : PEDS 20150630 9

In vitro display technologies have proved to be powerful tools for obtaining high-affinity protein binders. We recently described SNAP display, an entirely in vitro DNA display system that uses the SNAP-tag to link protein with its encoding DNA in water-in-oil emulsions. Here, we apply SNAP display for the affinity maturation of a designed ankyrin repeat proteins (DARPin) that binds to the extracellular domain of HER2 previously isolated by ribosome display. After four SNAP display selection cyc ...[more]

PMID: 26134501

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Project description:Animals select resources to maximize fitness but associated costs and benefits are spatially and temporally variable. Differences in wetland management influence resource availability for ducks and mortality risk from duck hunting. The local distribution of the Mallard (Anas platyrhynchos) is affected by this resource heterogeneity and variable risk from hunting. Regional conservation strategies primarily focus on how waterfowl distributions are affected by food resources during the nonbreeding season. To test if Mallard resource selection was related to the abundance of resources, risks, or a combination, we studied resource selection of adult female Mallards during autumn and winter. We developed a digital spatial layer for Lake St. Clair, Ontario, Canada, that classified resources important to Mallards and assigned these resources a risk level based on ownership type and presumed disturbance from hunting. We monitored 59 individuals with GPS back-pack transmitters prior to, during, and after the hunting season and used discrete choice modeling to generate diurnal and nocturnal resource selection estimates. The model that classified available resources and presumed risk best explained Mallard resource selection strategies. Resource selection varied within and among seasons. Ducks selected for federal, state and private managed wetland complexes that provided an intermediate or relatively greater amount of refuge and foraging options than public hunting areas. Across all diel periods and seasons, there was selection for federally managed marshes and private supplemental feeding refuges that prohibited hunting. Mallard resource selection demonstrated trade-offs related to the management of mortality risk, anthropogenic disturbances, and foraging opportunities. Understanding how waterfowl respond to heterogeneous landscapes of resources and risks can inform regional conservation strategies related to waterfowl distribution during the nonbreeding season.

Dataset Information

Directed evolution of anti-HER2 DARPins by SNAP display reveals stability/function trade-offs in the selection process.

Publications

Directed evolution of anti-HER2 DARPins by SNAP display reveals stability/function trade-offs in the selection process.

Similar Datasets

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