Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation

Abstract

The phosphatase and tensin homologue deleted on chromosome 10 (PTEN) tumor suppressor gene encodes a tightly regulated dual-specificity phosphatase that serves as the master regulator of PI3K/AKT/mTOR signaling. The carboxy-terminal tail (CTT) is key to regulation and harbors multiple phosphorylation sites (Ser/Thr residues 380–385). CTT phosphorylation suppresses the phosphatase activity by inducing a stable, closed conformation. However, little is known about the mechanisms of phosphorylation-induced CTT-deactivation dynamics. Using explicit solvent microsecond molecular dynamics simulations, we show that CTT phosphorylation leads to a partially collapsed conformation, which alters the secondary structure of PTEN and induces long-range conformational rearrangements that encompass the active site. The active site rearrangements prevent localization of PTEN to the membrane, precluding lipid phosphatase activity. Notably, we have identified phosphorylation-induced allosteric coupling between the interdomain region and a hydrophobic site neighboring the active site in the phosphatase domain. Collectively, the results provide a mechanistic understanding of CTT phosphorylation dynamics and reveal potential druggable allosteric sites in a previously believed clinically undruggable protein.

Comparative Protein Structural Network Analysis Reveals C-Terminal Tail Phosphorylation Structural Communication Fingerprint in PTEN-Associated Mutations in Autism and Cancer

“…Interestingly, the catalytic triads for the P-M134R and P-R173C RINs both show a marked increase in connectivity and diminished expansion compared to their respective unphosphorylated CTT systems, suggesting CTT phosphorylation mediates rapid signal propagation to a small network of core residues. The distinct differences in connectivity distribution demonstrate that CTT phosphorylation plays a vital role in conformational dynamics and elicits strong network connectivity with active site residues, suggesting a role in phosphorylation-induced allosteric communication as seen in our previous studies. ,, The presence of clinically relevant mutations (Y68H, G132D, M134R, R173C) modulates how the effects of phospho-regulation on the catalytic site, potentially resulting in differences in catalytic activity and regulation.…”

“…Moreover, the study highlights perturbations among global metapaths and community network connections within the active site and inter-domain regions, indicating the significance of these regions in transmitting information across PSN (Figures and , S5). These results are also consistent with regions identified in our previously published work. ,, Notably, our results lend insight into diminutive structural changes which may provide an understanding toward PHTS-associated pathological conformations (“conformational phenotypes”) , and preponderance of disease . While the use of conventional MD simulations is critical to assess the effects of CTT phosphorylation conformational dynamics in PHTS-associated mutations, a possible limitation is that the initial conformations from each of the MD simulations might bias the conformational space.…”

“…For each structure production run, 1000 ns each (1 μs) of unrestrained NPT was performed at 303 K, where bond lengths were constrained using the linear constraint solver (LINCS) algorithm (Table S1, see Supporting Information). Our simulations closely followed the same protocol as in our previous works. ,, Coordinates were saved every 20 ps, leading to 50,000 configurations for each system. Trajectory analyses were conducted using GROMACS utilities, VMD or PyMOL…”

“…Though the initial PTEN X-ray crystal structure lacks the PBD, IDR, and CTT regions (PDB: 1D5R), structural characterizations reveal tight interactions between the phosphatase domain and the C2 domain (Figure A). We recently constructed a full-length PTEN structure that includes the CTT and its phospho-regulatory site (Figure B). , Studies over the past 2 decades provide a valuable framework to further understand PTEN regulation by CTT phosphorylation and its role in stability, as well as PPIs and their implication in disease. − Moreover, biochemical and biophysical studies have revealed that phosphorylation of the serine/threonine cluster (Ser380, Thr382, Thr383, and Ser385) on the PTEN CTT alters the conformational state from an “open” active state to a “closed” autoinhibited state, resulting in reduced membrane localization and phosphatase activity (Figure C,D). This closed conformation precludes productive CTT binding partner interactions, thereby inducing pathological conformations [“conformational phenotypes”] , that further impair activity and disrupt downstream signaling pathways. , Our full-length PTEN structure shows the phospho-tail in the proposed conformationally closed state (Figure B).…”

Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles

“…PRS has been applied to the investigation of the allosteric communication in a wide variety of systems. Here we quote a selection of those studies [34] , [35] , [36] , [92] , [93] , [94] , [95] , [96] , [97] , [98] , [99] , [100] , [101] , [102] , [103] , [104] , [105] , [106] , [107] , [108] , [109] , [110] , [111] .…”