Crystal Structures of the GluR5 and GluR6 Ligand Binding Cores: Molecular Mechanisms Underlying Kainate Receptor Selectivity

AbstractE1 enzymes function as gatekeepers of ubiquitin (Ub) signaling by catalyzing activation and transfer of Ub to tens of cognate E2 conjugating enzymes in a process called E1–E2 transthioesterification. The molecular mechanisms of transthioesterification and the overall architecture of the E1–E2–Ub complex during catalysis are unknown. Here, we determine the structure of a covalently trapped E1–E2–ubiquitin thioester mimetic. Two distinct architectures of the complex are observed, one in which the Ub thioester (Ub(t)) contacts E1 in an open conformation and another in which Ub(t) instead contacts E2 in a drastically different, closed conformation. Altogether our structural and biochemical data suggest that these two conformational states represent snapshots of the E1–E2–Ub complex pre- and post-thioester transfer, and are consistent with a model in which catalysis is enhanced by a Ub(t)-mediated affinity switch that drives the reaction forward by promoting productive complex formation or product release depending on the conformational state.

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Crystal structures of PI3K-C2α PX domain indicate conformational change associated with ligand binding

BMC Structural Biology ◽

10.1186/1472-6807-8-13 ◽

2008 ◽

Vol 8 (1) ◽

pp. 13 ◽

Cited By ~ 8

Author(s):

Gary N Parkinson ◽

David Vines ◽

Paul C Driscoll ◽

Snezana Djordjevic

Keyword(s):

Ligand Binding ◽

Crystal Structures ◽

Conformational Change ◽

Px Domain

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Transmembrane-truncated αvβ3 integrin retains high affinity for ligand binding: evidence for an ‘inside-out’ suppressor?

Biochemical Journal ◽

10.1042/bj3300861 ◽

1998 ◽

Vol 330 (2) ◽

pp. 861-869 ◽

Cited By ~ 59

Author(s):

J. Raj MEHTA ◽

Beate DIEFENBACH ◽

Alex BROWN ◽

Eilish CULLEN ◽

Alfred JONCZYK ◽

...

Keyword(s):

Ligand Binding ◽

Wound Repair ◽

Molecular Mechanisms ◽

Full Length ◽

Αvβ3 Integrin ◽

Cytoplasmic Domains ◽

Bivalent Cation ◽

High Affinity ◽

Cellular Environment

The molecular mechanisms of αvβ3 integrin affinity regulation have important biological implications in tumour development, wound repair and angiogenesis. We expressed, purified and characterized recombinant forms of human αvβ3 (r-αvβ3) and compared the activation state of these with αvβ3 in its cellular environment. The ligand specificity and selectivity of recombinant full-length and double transmembrane truncations of r-αvβ3 cloned in BacPAK6 vectors and expressed in Sf9 and High Five insect cells were compared with those of native placental αvβ3 and the receptor in situ on the cell surface. r-αvβ3 integrins were purified by affinity chromatography from detergent extracts of cells (full-length), and from the culture medium of cells expressing double-truncated r-αvβ3. r-αvβ3 had the same epitopes, ligand-binding specificities, bivalent cation requirements and susceptibility to RGD-containing peptides as native αvβ3. On M21-L4 melanoma cells, αvβ3 mediated binding to vitronectin, but not to fibrinogen unless activated with Mn2+. Non-activated αIIbβ3 integrin as control in M21-L-IIb cells had the opposite profile, mediating binding to fibrinogen, but not to vitronectin unless activated with Mn2+. Thus these receptors had moderate to low ligand affinity. In marked contrast, purified αvβ3 receptors, with or without transmembrane and cytoplasmic domains, were constitutively of high affinity and able to bind strongly to vitronectin, fibronectin and fibrinogen under physiological conditions. Our data suggest that, in contrast with the positive regulation of αIIbβ3 in situ, intracellular controls lower the affinity of αvβ3, and the cytoplasmic domains may act as a target for negative regulators of αvβ3 activity.

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Structure And Stability Of Ligand Binding Core Dimer Assembly Controls Desensitization In A Kainate Receptor

Biophysical Journal ◽

10.1016/j.bpj.2008.12.2537 ◽

2009 ◽

Vol 96 (3) ◽

pp. 491a

Author(s):

Charu Chaudhry ◽

Matthew C. Weston ◽

Peter Schuck ◽

Christian Rosenmund ◽

Mark L. Mayer

Keyword(s):

Ligand Binding ◽

Kainate Receptor ◽

Structure And Stability ◽

Binding Core

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Crystal Structures of Potent Dimeric Positive Allosteric Modulators at the Ligand-Binding Domain of the GluA2 Receptor

ACS Medicinal Chemistry Letters ◽

10.1021/acsmedchemlett.8b00369 ◽

2018 ◽

Vol 10 (3) ◽

pp. 243-247

Author(s):

Saara Laulumaa ◽

Kathrine Voigt Hansen ◽

Magdalena Masternak ◽

Thomas Drapier ◽

Pierre Francotte ◽

...

Keyword(s):

Ligand Binding ◽

Crystal Structures ◽

Binding Domain ◽

Ligand Binding Domain ◽

Allosteric Modulators ◽

Positive Allosteric Modulators

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Assessing The Effects of Ligand-Binding Mutations to AMPA and Kainate Receptor Kinetics

Ionotropic Glutamate Receptor Technologies - Neuromethods ◽

10.1007/978-1-4939-2812-5_13 ◽

2016 ◽

pp. 185-203

Author(s):

Mark W. Fleck

Keyword(s):

Ligand Binding ◽

Kainate Receptor ◽

Receptor Kinetics

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Towards comprehensive allosteric control over protein activity

10.1101/384198 ◽

2018 ◽

Author(s):

Enrico Guarnera ◽

Igor N. Berezovsky

Keyword(s):

Ligand Binding ◽

Molecular Mechanisms ◽

Allosteric Regulation ◽

Mode Switching ◽

Contact Network ◽

Protein Activity ◽

Theoretical Understanding ◽

Functional Sites ◽

Allosteric Control ◽

Allosteric Communication

AbstractOn the basis of the perturbation nature of allosteric communication, a computational framework is proposed for estimating the energetics of signaling caused by the ligand binding and mutations. The perturbations are modelled as alterations of the strenght of interactions in the protein contact network in the binding sites and neighborhoods of mutated residues. The combination of protein harmonic modelling with effect of perturbations and the estimate of local partition functions allow one to evaluate the energetics of allosteric communication at single residue level. The potential allosteric effect of a protein residue position, modulation range, is given by the difference between responses to stabilizing and destabilizing mutations. We show a versatility of the approach on three case studies of proteins with different mechanisms of allosteric regulation, testing it on their known regulatory and functional sites. Allosteric Signaling Maps (ASMs) obtained on the basis of residue-by-residue scanning are proposed as a comprehensive tool to explore a relationship between mutations allosterically modulating protein activity and those that mainly affect protein stability. Analysis of ASMs shows distance dependence of the mode switching in allosteric signaling, emphasizing the role of domains/subunits in protein allosteric communication as elements of a percolative system. Finally, ASMs can be used to complement and tune already existing signaling and to design new elements of allosteric regulation.SignificanceUniversality of allosteric signaling in proteins, molecular machines, and receptors and great advantages of prospected allosteric drugs in highly specific, non-competitive, and modulatory nature of their actions call for deeper theoretical understanding of allosteric communication. In the energy landscape paradigm underliying the molecular mechanisms of protein function, allosteric signalling is the result of any perturbation, such as ligand binding, mutations, intermolecular interactions etc. We present a computational model, allowing to tackle the problem of modulating the energetics of protein allosteric communication. Using this method, Allosteric Signaling Maps (ASMs) are proposed as an approach to exhaustively describe allosteric signaling in the protein, making it possible to take protein activity under allosteric control.

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