Two Pathways Mediate Interdomain Allosteric Regulation in Pin1

Abstract

Summary Allostery is an essential means for regulating biomolecular functions and provides unique opportunities for drug design, yet our ability to elucidate allosteric mechanisms remains limited. Here, based on extensive molecular dynamics simulations, we present an atomistic picture of the pathways mediating the allosteric regulation of the PPIase domain of Pin1 by its WW domain. Two pathways jointly propagate the action of substrate-WW binding to produce closure and rigidification of three PPIase catalytic-site loops. One pathway preexists in the apo protein but remains dormant until substrate-WW binding completes the second. The reduction in conformational entropy and preorganization of the catalytic-site loops observed here may explain why substrate-WW binding enhances ligand affinity and catalytic activity of the PPIase domain, and suggest a combination drug therapy for Pin1-related diseases. Whereas the traditional view of allostery has emphasized conformational transition, our study uniquely identifies a distinct role of conformational dynamics in eliciting allostery.

Unidirectional allostery in the regulatory subunit RIα facilitates efficient deactivation of protein kinase A

“…It is worth remarking that the mechanism for unidirectional allostery in the PKA R subunit bears some resemblance to one developed for Pin1 (19). In the latter system, a substrate peptide can bind both to the catalytic site and to an exosite, on a WW domain (a small domain that folds into a three-stranded β-sheet and contains two conserved tryptophans) connected to the catalytic domain by a flexible linker.…”

“…In the absence of dramatic conformational changes, conformational flexibility can provide a sensitive measure of allosteric effects (19). For each system, we calculated the average and standard deviation (SD) of the Cα root-mean-square fluctuations (RMSFs) for each residue over the three replicate runs.…”

“…Previous simulation studies have revealed how unidirectional allosteric communication was achieved in Pin1 (19) and sortase A (20). Several simulation studies have already enriched our knowledge on the conformational properties of RIα, including the conformational space sampled by the tandem CBDs in the apo form (21,22) and cAMP-induced conformational changes of the isolated CBD-A (23,24).…”

“…In the simulations, cAMP releases from the two sites elicited disparate responses in conformational flexibility and chemical shift perturbation, confirming unidirectional allosteric communication. Community analysis, which has achieved successes in the study of other allosteric proteins (19,(25)(26)(27)(28), revealed that central to interdomain communication is a pathway between β-barrel:A and αA:B. The A-site cAMP, through the across-domain π-π stacking with W260, serves as a bridge between these two regions.…”

On protein structure, function and modularity from an evolutionary perspective

“…Binding of shorter peptide substrates and small molecules to Pin1 has been shown to affect interdomain mobility and linker dynamics (Jacobs et al, 2003), and increased affinity and isomerization of phosphorylated peptides binding to Pin1 PPIase has been shown in the presence of PEG-induced transient domain interactions (Matena et al, 2013). Interactions between the two domains have been shown to allosterically affect the isomerization activity by an internal dynamic circuit through the Pin1 PPIase interior (Namanja et al, 2011), as well as through residues in the domain interface (Wilson et al, 2013), both recently supported by molecular simulations (Guo et al, 2015). However, to understand how the dualdomain protein Pin1 acts on its longer, multiply phosphorylated, and often intrinsically disordered substrates , the interaction with such substrates needs to be studied in structural and dynamic detail, but as yet such studies have not been achieved.…”