Allosteric and energetic remodeling of a PDZ domain by protein domain extensions

Many functions of proteins are performed by independently folding structural units called domains. These domains are structurally conserved but not identical in different proteins. Here, to understand the consequences for regulation and evolvability of domain extensions, we quantify the energetic effects of two extensions in a model protein domain. Quantifying abundance and ligand binding for >190,000 protein variants allows us to measure the free energy changes for mutations throughout a PDZ domain and ~7000 energetic couplings between these mutations and two domain extensions. Both a structured extension and a more dynamic extension substantially but specifically re-shape the energy landscape. In particular, deleting an ɑ-helix alters the energetic consequences of >400 mutations in >50 sites on fold stability or binding energy, and the effects of >300 allosteric mutations, including at solvent-accessible surface sites. Extending or pruning the domain therefore reshapes its energetic and allosteric landscape, adding and removing opportunities for the allosteric control of protein function. Independently folding domains can be seen as the functional and evolutionary structural units of proteins. Here, the authors assess effects of >7000 mutations in a model PDZ domain, to quantify how two small extensions to a protein domain reshape its energetic and allosteric landscape.