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• W1971467040 endingPage "e1002429" @default.
• W1971467040 startingPage "e1002429" @default.
• W1971467040 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." @default.
• W1971467040 created "2016-06-24" @default.
• W1971467040 creator A5017097104 @default.
• W1971467040 creator A5022755409 @default.
• W1971467040 creator A5039838426 @default.
• W1971467040 date "2012-03-08" @default.
• W1971467040 modified "2023-10-16" @default.
• W1971467040 title "Beyond the Binding Site: The Role of the β2 – β3 Loop and Extra-Domain Structures in PDZ Domains" @default.
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• W1971467040 doi "https://doi.org/10.1371/journal.pcbi.1002429" @default.
• W1971467040 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3297566" @default.
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• W1971467040 hasPublicationYear "2012" @default.
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