Abstract
A general paradigm to understand protein function is to look at properties of isolated well conserved domains, such as SH3 or PDZ domains. While common features of domain families are well understood, the role of subtle differences among members of these families is less clear. Here, molecular dynamics simulations indicate that the binding mechanism in PSD95-PDZ3 is critically regulated via interactions outside the canonical binding site, involving both the poorly conserved loop and an extra-domain helix. Using the CRIPT peptide as a prototypical ligand, our simulations suggest that a network of salt-bridges between the ligand and this loop is necessary for binding. These contacts interconvert between each other on a time scale of a few tens of nanoseconds, making them elusive to X-ray crystallography. The loop is stabilized by an extra-domain helix. The latter influences the global dynamics of the domain, considerably increasing binding affinity. We found that two key contacts between the helix and the domain, one involving the loop, provide an atomistic interpretation of the increased affinity. Our analysis indicates that both extra-domain segments and loosely conserved regions play critical roles in PDZ binding affinity and specificity.
Highlights
PDZ domains are modular protein interaction domains specialized in binding short linear motifs at the C-terminus of their cognate protein partners [1,2]
It is known that most PDZ domains mediate protein interactions by binding to the C-terminus of other proteins
Using detailed molecular dynamics simulations in conjunction with statistical analysis, we predict that contacts outside of the canonical binding site play important roles in regulating protein interactions
Summary
PDZ domains are modular protein interaction domains specialized in binding short linear motifs at the C-terminus of their cognate protein partners [1,2]. Studies organized binding specificity in three canonical classes: class-I involving C-terminal motifs of the type [X–(S/T)–X–(V/I)COOH], class-II [x{W{x{WCOOH] and class-III [X– (D/E)–X–WCOOH], where W is a hydrophobic residue and x any amino acid [2,4]. This classification, though consistent with the highly conserved binding groove [2], does not explain the large selectivity observed both in naturally occurring C-terminal peptides and synthetic peptide library screening [5,6,7,8]. The solution structure of the second domain of the hPTP1E protein showed that this loop interacts with the sixth amino acid from the peptide C-terminus [10], while possible electrostatic contacts between the loop and peptide amino acids up to position eight were found in the Par PDZ3-VE-Cad domain [14,15]
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