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A large-scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains

Proteins. 2021-02; 
David Nedrud, Willow Coyote-Maestas, Daniel Schmidt
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Bacterial Expression … Please cite this article as doi: 10.1002/prot.26067© 2021 Wiley Periodicals, Inc. Received: Sep 15, 2020;Revised: Dec 22, 2020;Accepted: Feb 18, 2021 This article is protected by copyright. All rights reserved. Page 2 … frequency in E. coli (obtained from Genscript) (Fig. S1C) … Get A Quote

摘要

Deep mutational scanning (DMS) facilitates data-driven models of protein structure and function. Here, we adapted Saturated Programmable Insertion Engineering (SPINE) as a programmable DMS technique. We validate SPINE with a reference single mutant dataset in the PSD95 PDZ3 domain and then characterize most pairwise double mutants to study epistasis. We observe wide-spread proximal negative epistasis, which we attribute to mutations affecting thermodynamic stability, and strong long-range positive epistasis, which is enriched in an evolutionarily conserved and function-defining network of "sector" and clade-specifying residues. Conditional neutrality of mutations in clade-specifying residues compensates for del... More

关键词

deep mutagenesis, epistasis, protein evolution, protein sector, threshold robustness