Multivalent Angiomotin‐like 1 and Yes‐associated protein form a dynamic complex

Abstract

Multivalent complexes formed between the cancer-promoting transcriptional co-activator, Yes-associated protein (YAP), and proteins containing short linear motifs of type PPxY modulate cell proliferation and are attractive therapeutic targets. However, challenges producing PPxY polypeptides containing the full binding domain has limited understanding of the assembly process. Here, we successfully produced a polypeptide containing the complete set of three PPxY binding sites of Angiomotin-like 1 (AMOTL1), a scaffolding protein that regulates the nucleo-cytoplasmic shuttling of YAP via WW-PPxY interactions. Using an array of biophysical techniques including isothermal titration calorimetry, size-exclusion chromatography coupled to multi-angle light scattering, and solution nuclear magnetic resonance spectroscopy, we show that the AMOTL1 polypeptide is partially disordered, and binds the YAP WW domains to form an ensemble of complexes of varying stabilities. The binding process is initiated by the binding of one YAP WW domain to one AMOTL1 PPxY motif and is completed by transient interactions of the second YAP WW domain with a second AMOTL1 PPxY motif to form an equilibrating mixture composed of various species having two YAP sites bound to two conjugate AMOTL1 sites. We rationalize that the transient interactions fine-tune the stability of the complex for rapid assembly and disassembly in response to changes in the local cellular environment.

Predicting the Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins

“…We have reserved nine IDPs for testing SeqDYN (parameterized on the training set of 45 IDPs). The level of disorder in these test proteins also spans the full range, from absence of secondary structures [ChiZ N-terminal region (12), Pdx1 C-terminal region (11), and TIA-1 prion-like domain (17)] to presence of transient short helices [synaptobrevin-2 (7), α-endosulfine (38), YAP (6), angiomotin-like 1 (AMOTL1) (39)] to formation of stable long helices [FtsQ (13) and CAHS-8 (9)]. For eight of the nine test IDPs, the RMSEs of SeqDYN predictions are lower than the experimental values, by an average of 0.62 s −1 .…”

“…However, whereas the two peaks have approximately equal heights in the measured R 2 profile, the predicted peak height around Phe200 is too low. SCSs indicate helix propensity around both R 2 peaks (39). PsiPred also predicts helix in both regions, but only five and two residues, respectively, survive after filtering, which are too short for applying a helix boost.…”

“…SCSs indicate helix propensity around both 𝑅 ! peaks (39). PsiPred also predicts helix in both regions, but only five and two residues, respectively, survive after filtering, which are too short for applying a helix boost.…”

SRY-Box transcription factor 9 triggers YAP nuclear entry via direct interaction in tumors

“…However, when it binds to its partners or undergoes modifications at the binding interface, YAP acquires a more defined structure, facilitating specific interactions. 42 Arginine methylation disperses the charge over more atoms, and subsequently alters its hydrophobic properties, leading to a change in the binding of methylarginine to specific proteins and regulating their functions. 43 Supporting this notion, we found that the asymmetric dimethylation at R124 of YAP (YAP-R124me2a), catalyzed by PRMT1, enhanced the YAP-SOX9 interaction.…”