Comprehensive analysis of all evolutionary paths between two divergent PDZ domain specificities

AbstractTo understand the molecular evolution of functional diversity in protein families, we comprehensively investigated the consequences of all possible mutation combinations separating two peptide ‐binding domains with highly divergent specificities. We analyzed the Erbin PDZ domain (Erbin‐PDZ), which exhibits canonical type I specificity, and a synthetic Erbin‐PDZ variant (E‐14) that differs at six positions and exhibits an atypical specificity that closely resembles that of the natu ral Pdlim4 PDZ domain (Pdlim4‐PDZ). We constructed a panel of 64 PDZ domains covering all possible transitions between Erbin‐PDZ and E‐14 (i.e. the panel contained variants with all possible combinations of either the Erbin ‐PDZ or E‐14 sequence at the six differing positions). We assessed the specificity profiles of the 64 PDZ domains using a C‐terminal phage‐displayed peptide library containing all possible genetically encoded heptapeptides. The specificity profiles clustered into six distinct groups, showing that intermediate domains can be nodes for the evolution of divergent functions. Remarkably, three substitutions were sufficient to convert the specificity of Erbin‐PDZ to that of Pdlim4‐PDZ, whereas Pdlim4‐PDZ contains 71 differences relative to Erbin‐PDZ. X‐ray crystallography revealed the structural basis for specificity transition: a single substitution in the center of the binding site, supported by contributions from auxiliary substitutions, alter...
Source: Protein Science - Category: Biochemistry Authors: Tags: Article Source Type: research