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PACS-DMS.v38.pdf (7.27 MB)
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A Phage-Assisted Continuous Selection Approach for Deep Mutational Scanning of Protein-Protein Interactions

preprint
submitted on 18.08.2019 and posted on 19.08.2019 by Julia Zinkus-Boltz, Craig Devalk, Bryan Dickinson
Protein-protein interactions (PPIs) are critical for organizing molecules in a cell and mediating signaling pathways. Dysregulation of PPIs are often key drivers of disease. To better understand the biophysical basis of such disease processes – and to potentially target them - it is critical to understand the molecular determinants of PPIs. Deep mutational scanning (DMS) facilitates the acquisition of large amounts of biochemical data by coupling selection with high throughput sequencing (HTS). The challenging and labor-intensive design and optimization of a relevant selection platform for DMS, however, limits the use of powerful directed evolution and selection approaches. To address this limitation, we designed a versatile new phage assisted continuous selection (PACS) system using our proximity-dependent split RNA polymerase (RNAP) biosensors with the aim of greatly simplifying and streamlining the design of a new selection platform for PPIs. After characterization and validation using the model KRAS/RAF PPI, we generated a library of RAF variants and subjected them to PACS and DMS. Our HTS data revealed that amino acid (aa) positions 66, 84, and 89 on RAF, key residues in the KRAS/RAF PPI, are intolerant to mutations. We also identified a subset of residues with broad aa substitution tolerance, aa positions 52, 55, 76, and 79. Due to the plug and play nature of RNAP biosensors, this method can easily be extended to other PPIs. More broadly, this, and other methods under development, supports the application of evolutionary and high-throughput approaches to bear on biochemical problems, moving towards a more comprehensive understanding of sequence-function relationships in proteins.

Funding

rePPI-i: A system for the rapid continuous evolution of protein-protein interaction inhibitors

National Cancer Institute

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CAREER: Rapid continuous molecular evolution to create and probe protein-protein interactions

Directorate for Biological Sciences

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History

Email Address of Submitting Author

dickinson@uchicago.edu

Institution

University of Chicago

Country

USA

ORCID For Submitting Author

0000-0002-9616-1911

Declaration of Conflict of Interest

None

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