scholarly journals Quantifying the cooperative subunit action in a multimeric membrane receptor

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Nisa Wongsamitkul ◽  
Vasilica Nache ◽  
Thomas Eick ◽  
Sabine Hummert ◽  
Eckhard Schulz ◽  
...  
Keyword(s):  
Ion Channels ◽  
Ligand Binding ◽  
Cyclic Nucleotide ◽  
Binding Sites ◽  
Membrane Receptor ◽  
Membrane Receptors ◽  
Cooperative Action ◽  
The Individual ◽  
Insight Into

Abstract In multimeric membrane receptors the cooperative action of the subunits prevents exact knowledge about the operation and the interaction of the individual subunits. We propose a method that permits quantification of ligand binding to and activation effects of the individual binding sites in a multimeric membrane receptor. The power of this method is demonstrated by gaining detailed insight into the subunit action in olfactory cyclic nucleotide-gated CNGA2 ion channels.

scholarly journals Putative ligand binding sites of two functionally characterized bark beetle odorant receptors

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jothi K. Yuvaraj ◽  
Rebecca E. Roberts ◽  
Yonathan Sonntag ◽  
Xiao-Qing Hou ◽  
Ewald Grosse-Wilde ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Bark Beetle ◽  
Pest Control ◽  
Binding Sites ◽  
Functional Characterization ◽  
Site Directed Mutagenesis ◽  
Odorant Receptors ◽  
Functional Evolution ◽  
General Importance ◽  
Insight Into

Abstract Background Bark beetles are major pests of conifer forests, and their behavior is primarily mediated via olfaction. Targeting the odorant receptors (ORs) may thus provide avenues towards improved pest control. Such an approach requires information on the function of ORs and their interactions with ligands, which is also essential for understanding the functional evolution of these receptors. Hence, we aimed to identify a high-quality complement of ORs from the destructive spruce bark beetle Ips typographus (Coleoptera, Curculionidae, Scolytinae) and analyze their antennal expression and phylogenetic relationships with ORs from other beetles. Using 68 biologically relevant test compounds, we next aimed to functionally characterize ecologically important ORs, using two systems for heterologous expression. Our final aim was to gain insight into the ligand-OR interaction of the functionally characterized ORs, using a combination of computational and experimental methods. Results We annotated 73 ORs from an antennal transcriptome of I. typographus and report the functional characterization of two ORs (ItypOR46 and ItypOR49), which are responsive to single enantiomers of the common bark beetle pheromone compounds ipsenol and ipsdienol, respectively. Their responses and antennal expression correlate with the specificities, localizations, and/or abundances of olfactory sensory neurons detecting these enantiomers. We use homology modeling and molecular docking to predict their binding sites. Our models reveal a likely binding cleft lined with residues that previously have been shown to affect the responses of insect ORs. Within this cleft, the active ligands are predicted to specifically interact with residues Tyr84 and Thr205 in ItypOR46. The suggested importance of these residues in the activation by ipsenol is experimentally supported through site-directed mutagenesis and functional testing, and hydrogen bonding appears key in pheromone binding. Conclusions The emerging insight into ligand binding in the two characterized ItypORs has a general importance for our understanding of the molecular and functional evolution of the insect OR gene family. Due to the ecological importance of the characterized receptors and widespread use of ipsenol and ipsdienol in bark beetle chemical communication, these ORs should be evaluated for their potential use in pest control and biosensors to detect bark beetle infestations.

Mapping of ligand binding sites provides insight into the function of factor H-related protein 5

2017 ◽  
Vol 89 ◽  
pp. 145
Author(s):  
Alexandra Papp ◽  
Marcell Cserhalmi ◽  
Ádám I. Csincsi ◽  
Barbara Uzonyi ◽  
David Ermert ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Sites ◽  
Factor H ◽  
Related Protein ◽  
Ligand Binding Sites ◽  
Insight Into

scholarly journals Identifying and quantifying two ligand-binding sites while imaging native human membrane receptors by AFM

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Moritz Pfreundschuh ◽  
David Alsteens ◽  
Ralph Wieneke ◽  
Cheng Zhang ◽  
Shaun R. Coughlin ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Sites ◽  
Membrane Receptors ◽  
Ligand Binding Sites

scholarly journals Thermodynamic profile of mutual subunit control in a heteromeric receptor

2021 ◽  
Vol 118 (30) ◽  
pp. e2100469118
Author(s):  
Jana Schirmeyer ◽  
Sabine Hummert ◽  
Thomas Eick ◽  
Eckhard Schulz ◽  
Tina Schwabe ◽  
...  
Keyword(s):  
Cyclic Nucleotide ◽  
Equilibrium Constants ◽  
Membrane Receptors ◽  
Nucleotide Binding Domain ◽  
Closed Channel ◽  
Olfactory Neurons ◽  
Channel Opening ◽  
Cng Channel ◽  
Complete Set ◽  
The Individual

Cyclic nucleotide-gated (CNG) ion channels of olfactory neurons are tetrameric membrane receptors that are composed of two A2 subunits, one A4 subunit, and one B1b subunit. Each subunit carries a cyclic nucleotide-binding domain in the carboxyl terminus, and the channels are activated by the binding of cyclic nucleotides. The mechanism of cooperative channel activation is still elusive. Using a complete set of engineered concatenated olfactory CNG channels, with all combinations of disabled binding sites and fit analyses with systems of allosteric models, the thermodynamics of microscopic cooperativity for ligand binding was subunit- and state-specifically quantified. We show, for the closed channel, that preoccupation of each of the single subunits increases the affinity of each other subunit with a Gibbs free energy (ΔΔG) of ∼−3.5 to ∼−5.5 kJ ⋅ mol−1, depending on the subunit type, with the only exception that a preoccupied opposite A2 subunit has no effect on the other A2 subunit. Preoccupation of two neighbor subunits of a given subunit causes the maximum affinity increase with ΔΔG of ∼−9.6 to ∼−9.9 kJ ⋅ mol−1. Surprisingly, triple preoccupation leads to fewer negative ΔΔG values for a given subunit as compared to double preoccupation. Channel opening increases the affinity of all subunits. The equilibrium constants of closed–open isomerizations systematically increase with progressive liganding. This work demonstrates, on the example of the heterotetrameric olfactory CNG channel, a strategy to derive detailed insights into the specific mutual control of the individual subunits in a multisubunit membrane receptor.

Mapping of ligand binding sites gives further insight into FHR-4 function

2007 ◽  
Vol 44 (16) ◽  
pp. 3984
Author(s):  
Mario Hebecker ◽  
Michael Mihlan ◽  
Peter F. Zipfel ◽  
Mihály Józsi
Keyword(s):  
Ligand Binding ◽  
Binding Sites ◽  
Ligand Binding Sites ◽  
Insight Into

Locating GABA in GABA receptor binding sites

2009 ◽  
Vol 37 (6) ◽  
pp. 1343-1346 ◽  
Author(s):  
Sarah C.R. Lummis
Keyword(s):  
Ion Channels ◽  
Ligand Binding ◽  
Binding Site ◽  
Receptor Binding ◽  
Functional Data ◽  
Binding Sites ◽  
Gaba Receptor ◽  
Aminobutyric Acid ◽  
Specific Interactions ◽  
Gabac Receptors

The Cys-loop family of ligand-gated ion channels contains both vertebrate and invertebrate members that are activated by GABA (γ-aminobutyric acid). Many of the residues that are critical for ligand binding have been identified in vertebrate GABAA and GABAC receptors, and specific interactions between GABA and some of these residues have been determined. In the present paper, I show how a cation–π interaction for one of the binding site residues has allowed the production of models of GABA docked into the binding site, and these orientations are supported by mutagenesis and functional data. Surprisingly, however, the residue that forms the cation–π interaction is not conserved, suggesting that GABA occupies subtly different locations even in such closely related receptors.

scholarly journals Polarization of endocytosis and receptor topography on cultured macrophages.

1980 ◽  
Vol 86 (1) ◽  
pp. 199-211 ◽  
Author(s):  
R J Walter ◽  
R D Berlin ◽  
J R Pfeiffer ◽  
J M Oliver
Keyword(s):  
Concanavalin A ◽  
Binding Sites ◽  
Membrane Receptors ◽  
Macrophage Cell ◽  
Oil Emulsion ◽  
Opsonized Zymosan ◽  
Membrane Topography ◽  
Polarized Epithelia ◽  
Endocytic Activity ◽  
Insight Into

In the 1774.2 macrophage cell line, microtubule disassembly by colchicine causes the polarization of membrane functions ane structure. Colchicine-treated cells develop a bulge or protuberance that is bordered by microvillous membrane. The protuberance is the site of concanavalin A cap formation. The fluid pinocytosis of horseradish peroxidase and of fluorescein- and rhodamine-conjugated high molecular-weight dextrans, the adsorptive pinocytosis of concanavalin A, and the concentration and phagocytosis at 37 degrees C of a range of phagocytic particles (IgG- and complement-opsonized erythrocytes, complement-opsonized zymosan, latex shpres, albumin-stabilized oil droplets) are all similarly restricted to the protuberance. A reduction in the rate of dextran pinocytosis, determined by fluorimetry, and reductions in phagocytic rates for oil emulsion and IgG-opsonized erythrocytes accompany the polarization of endocytic activity in colchicine-trated 1774.2 macrophages. Membrane receptors for phagocytic particles are not confined to the protuberance but rather may display their own unique topographical asymmetry. The inherent topography of receptors was inferred from particle distribution under conditions that limit particle-receptor redistribution (after labeling at 4 degrees C or a very brief incubation at 37 degrees C). Under these restrictive conditions, latex binding sites were detected over the whole membrane whereas receptors for IgG-opsonized erythrocytes, aggregated IgG, complement-opsonized erythrocytes, and complement-opsonized zymosan were excluded from the protuberance. Thus, functional (endocytosis) and structural (inherent receptor distribution) analyses of membrane topography define different patterns of asymmetry in protuberant cells. The asymmetry induced in 1774.2 macrophages by colchicine is highly analogous to the functional and structural polarity of epithelial cells. Exploration of this analogy may provide insight into the development of polarized epithelia and, more generally, into mechanisms by which specialized areas of membrane are established.

AN IMPROVED METHOD FOR THE ASSAY OF PROGESTERONE BY COMPETITIVE PROTEIN BINDING

1970 ◽  
Vol 63 (2) ◽  
pp. 225-241 ◽  
Author(s):  
B. D. Reeves ◽  
M. L. A. de Souza ◽  
I. E. Thompson ◽  
E. Diczfalusy
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Entire Range ◽  
Improved Method ◽  
Plasma Progesterone ◽  
Extraction And Purification ◽  
Corticosteroid Binding Globulin ◽  
Competitive Protein Binding ◽  
The Individual ◽  
Range Of Values

ABSTRACT An improved method for the assay of plasma progesterone by competitive protein binding is described. The improvement is based upon rigorous control of the variables, the compensation for and standardisation of interfering factors inherent in the method and the use of a human corticosteroid binding globulin, that meets the requirements for sensitivity at levels of 1.0 ng of progesterone and below. The assessment of the reliability of the individual steps in the method as well as that of the complete method is presented. The sensitivity of the method is around 0.2 ng progesterone per ml plasma. Accuracy was measured by adding progesterone in amounts ranging from 0.0 to 1.0 ng to 1.0 ml plasma. There was a linear relationship between the progesterone added and recovered throughout the entire range of values, with a coefficient of correlation (r) of 0.94. Of 52 related steroids tested, none was found which would remain associated with progesterone following extraction and purification and which would also compete with progesterone for binding sites.

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

2020 ◽  
Author(s):  
Samuel C. Gill ◽  
David Mobley
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Sites ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Hiv Integrase ◽  
Binding Modes ◽  
System A ◽  
Multiple Binding ◽  
Internal Degrees Of Freedom

<div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div>

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