scholarly journals Ligand binding and structural rearrangements of quadruplexes containing human telomeric sequences

2008 ◽  
Vol 64 (a1) ◽  
pp. C156-C156
Author(s):  
G.N. Parkinson ◽  
S. Neidle ◽  
N.H. Campbell
2014 ◽  
Vol 167 (2) ◽  
pp. 428-433 ◽  
Author(s):  
Jonathan Lévy ◽  
Aline Receveur ◽  
Guillaume Jedraszak ◽  
Sandra Chantot-Bastaraud ◽  
Florence Renaldo ◽  
...  

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Nandish Khanra ◽  
Patricia MGE Brown ◽  
Amanda M Perozzo ◽  
Derek Bowie ◽  
Joel Meyerson

Kainate receptors (KARs) are L-glutamate-gated ion channels that regulate synaptic transmission and modulate neuronal circuits. KARs have strict assembly rules and primarily function as heteromeric receptors in the brain. A longstanding question is how KAR heteromer subunits organize and coordinate together to fulfill their signature physiological roles. Here we report structures of the GluK2/GluK5 heteromer in apo, antagonist-bound, and desensitized states. The receptor assembles with two copies of each subunit, ligand binding domains arranged as two heterodimers, and GluK5 subunits proximal to the channel. Strikingly, during desensitization GluK2 but not GluK5 subunits undergo major structural rearrangements to facilitate channel closure. We show how the large conformational differences between antagonist-bound and desensitized states are mediated by the linkers connecting the pore helices to the ligand-binding domains. This work presents the first KAR heteromer structure, reveals how its subunits are organized, and resolves how the heteromer can accommodate functionally-distinct closed channel structures.


2019 ◽  
Author(s):  
Dababrata Paul ◽  
Adrien Marchand ◽  
Daniela Verga ◽  
Marie-Paule Teulade-Fichou ◽  
Sophie Bombard ◽  
...  

ABSTRACTMass spectrometry provides exquisite detail on ligand and cation binding stoichiometries with a DNA target. The next important step is to develop reliable methods to determine the cation and ligand binding sites in each complex separated by the mass spectrometer. To circumvent the caveat of ligand derivatization for cross-linking, which may alter the ligand binding mode, we explored a tandem mass spectrometry (MS/MS) method that does not require ligand derivatization, and is therefore also applicable to localize metal cations. By obtaining more negative charge states for the complexes using supercharging agents, and by creating radical ions by electron photodetachment, oligonucleotide bonds become weaker than the DNA-cation or DNA-ligand noncovalent bonds upon collision-induced dissociation of the radicals. This electron photodetachment (EPD) method allows to locate the binding regions of cations and ligands by top-down sequencing of the oligonucleotide target. The very potent G-quadruplex ligands 360A and PhenDC3 were found to replace a potassium cation and bind close to the central loop of 4-repeat human telomeric sequences.


2020 ◽  
Author(s):  
Tushar Raskar ◽  
Stephan Niebling ◽  
Juliette M. Devos ◽  
Briony A. Yorke ◽  
Michael Härtlein ◽  
...  

AbstractIncoherent neutron spectroscopy, in combination with dynamic light scattering was used to investigate the effect of ligand binding on the center-of-mass self-diffusion and internal diffusive dynamics of E.coli aspartate α-decarboxylase (ADC). The X-ray crystal structure of the D-serine inhibitor complex with ADC was also determined, and molecular dynamics simulations used to further probe the structural rearrangements that occur as a result of ligand binding. These experiments reveal the existence of higher order oligomers of the ADC tetramer on ns-ms time-scales, and also show that ligand binding both affects the ADC internal diffusive dynamics and appears to further increase the size of the higher order oligomers.


2020 ◽  
Vol 21 (21) ◽  
pp. 8348
Author(s):  
Dániel Dudola ◽  
Anett Hinsenkamp ◽  
Zoltán Gáspári

PDZ domains are abundant interaction hubs found in a number of different proteins and they exhibit characteristic differences in their structure and ligand specificity. Their internal dynamics have been proposed to contribute to their biological activity via changes in conformational entropy upon ligand binding and allosteric modulation. Here we investigate dynamic structural ensembles of PDZ3 of the postsynaptic protein PSD-95, calculated based on previously published backbone and side-chain S2 order parameters. We show that there are distinct but interdependent structural rearrangements in PDZ3 upon ligand binding and the presence of the intramolecular allosteric modulator helix α3. We have also compared these rearrangements in PDZ1-2 of PSD-95 and the conformational diversity of an extended set of PDZ domains available in the PDB database. We conclude that although the opening-closing rearrangement, occurring upon ligand binding, is likely a general feature for all PDZ domains, the conformer redistribution upon ligand binding along this mode is domain-dependent. Our findings suggest that the structural and functional diversity of PDZ domains is accompanied by a diversity of internal motional modes and their interdependence.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1848-1848
Author(s):  
Jun Yamanouchi ◽  
Takaaki Hato ◽  
Hiroshi Fujiwara ◽  
Yoshihiro Yakushijin ◽  
Masaki Yasukawa

Abstract Integrin αIIbβ3 exists in a low affinity state in resting platelets and requires activation for high affinity binding with soluble ligands. Activation of αIIbβ3 is tightly linked to structural rearrangements of the αIIbβ3 molecule that is initiated from the cytoplasmic tails of the αIIb and β3 subunits. The β3 membrane-distal region has been shown to interact with many signaling and cytoskeletal molecules, and considered as a trigger point of integrin activation. The interaction of the β3 tail with a cytoplasmic protein, talin, largely contributes to integrin activation. In view of the link between integrin activation and allosteric structural rearrangements of integrins, one would expect that structural changes in the β3 membrane-distal region containing binding sites for intracellular proteins would be relayed to the membrane-proximal region, leading to αIIbβ3 activation. However, there has been no evidence that structural rearrangement of the β3 membrane-distal region is directly linked to integrin activation. No activating mutation has so far been reported in the β3 membrane-distal region despite numerous reports of loss-of-function mutants in this region. In this context, a previously reported αIIbβ3 mutant in which the β3 tail was replaced by the β1 tail was noteworthy. This chimeric integrin, αIIbβ3/β1, was constitutively active. Because the β1 and β3 subunits have relatively high sequence homology in their membrane-proximal regions, we reasoned that the residues differing between the β1 and β3 membrane-distal regions may be responsible for αIIbβ3 activation. To identify such residues, we produced 13 αIIbβ3 mutants in which the individual or group residues in the β3 tail were substituted with the corresponding β1 tail residues. The αIIbβ3 mutants were expressed on the surface of CHO cells by cotransfection of mutant β3 and wild-type αIIb cDNAs, and were tested for binding of fibrinogen and PAC1, a ligand-mimetic anti-αIIbβ3 antibody. Among them, only β3I719M and E749S mutants bound significant PAC1 and fibrinogen binding without any stimulation and the RGDS peptide abolished binding of these ligands, indicating a constitutively active state. The similar effect was observed with I719A and E749A mutants. Moreover, the I719M/E749S double mutant showed more PAC1 binding than the single mutants, reaching the same ligand binding activity as αIIbβ3/β1. These β3 mutations also induced αVβ3 activation. Conversely, substitution of M719 or S749 in the β1 tail with the corresponding β3 tail residue (M719I or S749E) inhibited αIIbβ3/β1 activation, and the M719I/S749E double mutant inhibited ligand binding to a level comparable with that of the wild-type αIIbβ3. Knock down of talin by short hairpin RNA inhibited the I719M- and E749S-induced αIIbβ3 activation, indicating talin-mediated activation of mutant integrins. Since I719 is located at the β3 membrane-proximal region, it is likely that the I719 mutation disrupts the well-known membrane-proximal clasp to maintain integrins at a low affinity state. On the other hand, E749 is located at the β3 membrane-distal region. This result provides experimental evidence that structural perturbation of the β3 membrane-distal region is linked to integrin activation. Moreover, our result showed that the mutational effects of the membrane-proximal I719 and the membrane-distal E749 residues were additive and talin-dependent, suggesting that the β3 membrane-proximal and –distal regions cooperatively regulate talin-mediated αIIbβ3 activation. This finding is consistent with a recent model of talin-induced αIIbβ3 activation in which talin cooperatively interacts with the β3 membrane-proximal and distal regions.


eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Yihe Huang ◽  
Becca Roth ◽  
Wei Lü ◽  
Juan Du

TRPM2 is critically involved in diverse physiological processes including core temperature sensing, apoptosis, and immune response. TRPM2’s activation by Ca2+ and ADP ribose (ADPR), an NAD+-metabolite produced under oxidative stress and neurodegenerative conditions, suggests a role in neurological disorders. We provide a central concept between triple-site ligand binding and the channel gating of human TRPM2. We show consecutive structural rearrangements and channel activation of TRPM2 induced by binding of ADPR in two indispensable locations, and the binding of Ca2+ in the transmembrane domain. The 8-Br-cADPR—an antagonist of cADPR—binds only to the MHR1/2 domain and inhibits TRPM2 by stabilizing the channel in an apo-like conformation. We conclude that MHR1/2 acts as a orthostatic ligand-binding site for TRPM2. The NUDT9-H domain binds to a second ADPR to assist channel activation in vertebrates, but not necessary in invertebrates. Our work provides insights into the gating mechanism of human TRPM2 and its pharmacology.


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