beyond the binding site the role of the β2 – β3 loop and extra-domain structures in pdz domains除了结合位点的作用β2u2014u2014β3循环和extra-domain在pdz结构域.pdfVIP

Beyond the Binding Site: The Role of the b2 – b3 Loop and Extra-Domain Structures in PDZ Domains 1 2 1 Stefano Mostarda , David Gfeller , Francesco Rao * 1 Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany, 2 Molecular Modeling, Swiss Institute of Bioinformatics, Lausanne, Switzerland 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 b2 {b3 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 b2 {b3 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. Citation: Mostarda S, Gfeller D,