scholarly journals Relating ligand binding to activation gating in P2X2 receptors using a novel fluorescent ATP derivative

2020 ◽  
Vol 154 (3) ◽  
pp. 251-262 ◽  
Author(s):  
Christian Sattler ◽  
Ralf Schmauder ◽  
Tina Schwabe ◽  
Andrea Schweinitz ◽  
Christopher Unzeitig ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Activation Gating

scholarly journals New capsaicin analogs as molecular rulers to define the permissive conformation of the mouse TRPV1 ligand-binding pocket

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Simon Vu ◽  
Vikrant Singh ◽  
Heike Wulff ◽  
Vladimir Yarov-Yarovoy ◽  
Jie Zheng
Keyword(s):  
Ligand Binding ◽  
Conformational Changes ◽  
Binding Pocket ◽  
Functional Tests ◽  
Ligand Binding Pocket ◽  
Ligand Selectivity ◽  
Molecular Rulers ◽  
Activation Gating ◽  
Channel Interactions ◽  
Multiple Ligand

The capsaicin receptor TRPV1 is an outstanding representative of ligand-gated ion channels in ligand selectivity and sensitivity. However, molecular interactions that stabilize the ligand-binding pocket in its permissive conformation, and how many permissive conformations the ligand-binding pocket may adopt, remain unclear. To answer these questions, we designed a pair of novel capsaicin analogs to increase or decrease the ligand size by about 1.5 Å without altering ligand chemistry. Together with capsaicin, these ligands form a set of molecular rulers for investigating ligand-induced conformational changes. Computational modeling and functional tests revealed that structurally these ligands alternate between drastically different binding poses but stabilize the ligand-binding pocket in nearly identical permissive conformations; functionally, they all yielded a stable open state despite varying potencies. Our study suggests the existence of an optimal ligand-binding pocket conformation for capsaicin-mediated TRPV1 activation gating, and reveals multiple ligand-channel interactions that stabilize this permissive conformation.

scholarly journals Ligand Binding and Activation Gating in CNGA2A4B1b Channels

2010 ◽  
Vol 98 (3) ◽  
pp. 706a
Author(s):  
Vasilica Nache ◽  
Jana Kusch ◽  
Christoph Biskup ◽  
Thomas Zimmer ◽  
Eckhard Schulz ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Activation Gating

Relating ligand binding to activation gating in CNGA2 channels

Nature ◽  
2007 ◽  
Vol 446 (7134) ◽  
pp. 440-443 ◽  
Author(s):  
Christoph Biskup ◽  
Jana Kusch ◽  
Eckhard Schulz ◽  
Vasilica Nache ◽  
Frank Schwede ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Activation Gating

scholarly journals Local constraints in either the GluN1 or GluN2 subunit equally impair NMDA receptor pore opening

2011 ◽  
Vol 138 (2) ◽  
pp. 179-194 ◽  
Author(s):  
Iehab Talukder ◽  
Lonnie P. Wollmuth
Keyword(s):  
Nmda Receptor ◽  
Ligand Binding ◽  
Ion Channel ◽  
Nmda Receptors ◽  
Transmembrane Domain ◽  
Conformational Dynamics ◽  
Functional Feature ◽  
Channel Pore ◽  
Activation Gating ◽  
Pore Opening

The defining functional feature of N-methyl-d-aspartate (NMDA) receptors is activation gating, the energetic coupling of ligand binding into opening of the associated ion channel pore. NMDA receptors are obligate heterotetramers typically composed of glycine-binding GluN1 and glutamate-binding GluN2 subunits that gate in a concerted fashion, requiring all four ligands to bind for subsequent opening of the channel pore. In an individual subunit, the extracellular ligand-binding domain, composed of discontinuous polypeptide segments S1 and S2, and the transmembrane channel–forming domain, composed of M1–M4 segments, are connected by three linkers: S1–M1, M3–S2, and S2–M4. To study subunit-specific events during pore opening in NMDA receptors, we impaired activation gating via intrasubunit disulfide bonds connecting the M3–S2 and S2–M4 in either the GluN1 or GluN2A subunit, thereby interfering with the movement of the M3 segment, the major pore-lining and channel-gating element. NMDA receptors with gating impairments in either the GluN1 or GluN2A subunit were dramatically resistant to channel opening, but when they did open, they showed only a single-conductance level indistinguishable from wild type. Importantly, the late gating steps comprising pore opening to its main long-duration open state were equivalently affected regardless of which subunit was constrained. Thus, the NMDA receptor ion channel undergoes a pore-opening mechanism in which the intrasubunit conformational dynamics at the level of the ligand-binding/transmembrane domain (TMD) linkers are tightly coupled across the four subunits. Our results further indicate that conformational freedom of the linkers between the ligand-binding and TMDs is critical to the activation gating process.

CarR, a MarR-family regulator from Corynebacterium glutamicum, modulated antibiotic and aromatic compound resistance

2019 ◽  
Vol 476 (21) ◽  
pp. 3141-3159 ◽  
Author(s):  
Meiru Si ◽  
Can Chen ◽  
Zengfan Wei ◽  
Zhijin Gong ◽  
GuiZhi Li ◽  
...  
Keyword(s):  
Stress Response ◽  
Ligand Binding ◽  
Corynebacterium Glutamicum ◽  
Conformational Changes ◽  
Cysteine Oxidation ◽  
Transcriptional Regulatory ◽  
Ligand Free ◽  
Redox Sensing

Abstract MarR (multiple antibiotic resistance regulator) proteins are a family of transcriptional regulators that is prevalent in Corynebacterium glutamicum. Understanding the physiological and biochemical function of MarR homologs in C. glutamicum has focused on cysteine oxidation-based redox-sensing and substrate metabolism-involving regulators. In this study, we characterized the stress-related ligand-binding functions of the C. glutamicum MarR-type regulator CarR (C. glutamicum antibiotic-responding regulator). We demonstrate that CarR negatively regulates the expression of the carR (ncgl2886)–uspA (ncgl2887) operon and the adjacent, oppositely oriented gene ncgl2885, encoding the hypothetical deacylase DecE. We also show that CarR directly activates transcription of the ncgl2882–ncgl2884 operon, encoding the peptidoglycan synthesis operon (PSO) located upstream of carR in the opposite orientation. The addition of stress-associated ligands such as penicillin and streptomycin induced carR, uspA, decE, and PSO expression in vivo, as well as attenuated binding of CarR to operator DNA in vitro. Importantly, stress response-induced up-regulation of carR, uspA, and PSO gene expression correlated with cell resistance to β-lactam antibiotics and aromatic compounds. Six highly conserved residues in CarR were found to strongly influence its ligand binding and transcriptional regulatory properties. Collectively, the results indicate that the ligand binding of CarR induces its dissociation from the carR–uspA promoter to derepress carR and uspA transcription. Ligand-free CarR also activates PSO expression, which in turn contributes to C. glutamicum stress resistance. The outcomes indicate that the stress response mechanism of CarR in C. glutamicum occurs via ligand-induced conformational changes to the protein, not via cysteine oxidation-based thiol modifications.

TBG MEASUREMENTS BY COMPETITIVE LIGAND BINDING ASSAY (CLBA)

1975 ◽  
Vol 80 (1_Suppla) ◽  
pp. S15
Author(s):  
K. H. Rudorff ◽  
H. J. Kröll ◽  
J. Herrmann
Keyword(s):  
Ligand Binding ◽  
Binding Assay ◽  
Ligand Binding Assay ◽  
Competitive Ligand
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