Structural and ligand-binding analysis of the YAP-binding domain of transcription factor TEAD4

2018 ◽  
Vol 475 (12) ◽  
pp. 2043-2055 ◽  
Author(s):  
Yan Li ◽  
Shuang Liu ◽  
Elizabeth Yihui Ng ◽  
Rong Li ◽  
Anders Poulsen ◽  
...  

The oncoprotein YAP (Yes-associated protein) requires the TEAD family of transcription factors for the up-regulation of genes important for cell proliferation. Disrupting YAP–TEAD interaction is an attractive strategy for cancer therapy. Targeting TEADs using small molecules that either bind to the YAP-binding pocket or the palmitate-binding pocket is proposed to disrupt the YAP–TEAD interaction. There is a need for methodologies to facilitate robust and reliable identification of compounds that occupy either YAP-binding pocket or palmitate-binding pocket. Here, using NMR spectroscopy, we validated compounds that bind to these pockets and also identify the residues in mouse TEAD4 (mTEAD4) that interact with these compounds. Flufenamic acid (FA) was used as a positive control for validation of palmitate-binding pocket-occupying compounds by NMR. Furthermore, we identify a hit from a fragment screen and show that it occupies a site close to YAP-binding pocket on the TEAD surface. Our results also indicate that purified mTEAD4 can catalyze autopalmitoylation. NMR studies on mTEAD4 revealed that exchanges exist in TEAD as NMR signal broadening was observed for residues close to the palmitoylation site. Mutating the palmitoylated cysteine (C360S mutant) abolished palmitoylation, while no significant changes in the NMR spectrum were observed for the mutant which still binds to YAP. We also show that FA inhibits TEAD autopalmitoylation. Our studies highlight the utility of NMR spectroscopy in identifying small molecules that bind to TEAD pockets and reinforce the notion that both palmitate-binding pocket and YAP-binding pocket are targetable.

1987 ◽  
Vol 19 (3-4) ◽  
pp. 159-182 ◽  
Author(s):  
Kevin M. Brindle ◽  
Iain D. Campbell

An exciting aspect of NMR spectroscopy is its ability to monitor, non-invasively, a variety of small molecules in cells and tissues. This leads to the possibility of investigating details of cellular biochemistry previously obscured by separation and purification procedures.


2020 ◽  
Vol 27 ◽  
Author(s):  
Marian Vincenzi ◽  
Flavia Anna Mercurio ◽  
Marilisa Leone

Background: NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. Objective: This review provides a toolkit to investigate peptide conformational properties by NMR. Methods: Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through Pubmed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. Results: The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. Conclusion: NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.


Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 4089
Author(s):  
Katarzyna Betlejewska-Kielak ◽  
Elżbieta Bednarek ◽  
Armand Budzianowski ◽  
Katarzyna Michalska ◽  
Jan K. Maurin

Racemic ketoprofen (KP) and β-cyclodextrin (β-CD) powder samples from co-precipitation (1), evaporation (2), and heating-under-reflux (3) were analysed using X-ray techniques and nuclear magnetic resonance (NMR) spectroscopy. On the basis of NMR studies carried out in an aqueous solution, it was found that in the samples obtained by methods 1 and 2, there were large excesses of β-CD in relation to KP, 10 and 75 times, respectively, while the sample obtained by method 3 contained equimolar amounts of β-CD and KP. NMR results indicated that KP/β-CD inclusion complexes were formed and the estimated binding constants were approximately 2400 M−1, showing that KP is quite strongly associated with β-CD. On the other hand, the X-ray single-crystal technique in the solid state revealed that the (S)-KP/β-CD inclusion complex with a stoichiometry of 2:2 was obtained as a result of heating-under-reflux, for which the crystal and molecular structure were examined. Among the methods used for the preparation of the KP/β-CD complex, only method 3 is suitable.


2001 ◽  
Vol 148 (1) ◽  
pp. 142-146 ◽  
Author(s):  
F.C.L. Almeida ◽  
G.C. Amorim ◽  
V.H. Moreau ◽  
V.O. Sousa ◽  
A.T. Creazola ◽  
...  

2000 ◽  
Vol 78 (3) ◽  
pp. 316-321
Author(s):  
G W Buchanan ◽  
A B Driega ◽  
G PA Yap

The title complex is asymmetric in the crystal due to the spatial orientation of the NCS function. The space group has been determined to be P21 with a = 9.496(3), b = 8.736(3), c = 9.676(3) Å, β = 117.859(5)°, and Z = 2. The solid state 13C NMR spectrum is consistent with the lack of symmetry in the crystal and there is little evidence for large amplitude motion in the macrocycle as determined from the dipolar dephased spectrum.Key words: macrocyclic crown ether, lithium complex.


2017 ◽  
Vol 53 (99) ◽  
pp. 13205-13208 ◽  
Author(s):  
Michael D. Lee ◽  
Matthew L. Dennis ◽  
Bim Graham ◽  
James D. Swarbrick

A new pair of enantiomeric two-armed lanthanide-binding tags have been developed for paramagnetic NMR studies of proteins.


2017 ◽  
Vol 53 (71) ◽  
pp. 9930-9933 ◽  
Author(s):  
Yijue Xu ◽  
Lysiane Champion ◽  
Bulat Gabidullin ◽  
David L. Bryce

In situ 31P solid-state NMR studies of mechanochemical halogen bond formation provide insights into the cocrystallisation process and an estimate of the activation energy.


eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Akira Karasawa ◽  
Toshimitsu Kawate

The P2X7 receptor is a non-selective cation channel activated by extracellular adenosine triphosphate (ATP). Chronic activation of P2X7 underlies many health problems such as pathologic pain, yet we lack effective antagonists due to poorly understood mechanisms of inhibition. Here we present crystal structures of a mammalian P2X7 receptor complexed with five structurally-unrelated antagonists. Unexpectedly, these drugs all bind to an allosteric site distinct from the ATP-binding pocket in a groove formed between two neighboring subunits. This novel drug-binding pocket accommodates a diversity of small molecules mainly through hydrophobic interactions. Functional assays propose that these compounds allosterically prevent narrowing of the drug-binding pocket and the turret-like architecture during channel opening, which is consistent with a site of action distal to the ATP-binding pocket. These novel mechanistic insights will facilitate the development of P2X7-specific drugs for treating human diseases.


Sign in / Sign up

Export Citation Format

Share Document