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A strategy for determining the equilibrium constants for heteromeric ion channels in a complex model
Ligand-gated ion channels are oligomers containing several binding sites for the ligands. However, the signal transmission from the ligand binding site to the pore has not yet been fully elucidated for any of these channels. In heteromeric channels, the situation is even more complex than in homomer...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Rockefeller University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9066054/ https://www.ncbi.nlm.nih.gov/pubmed/35486087 http://dx.doi.org/10.1085/jgp.202113041 |
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author | Benndorf, Klaus Eick, Thomas Sattler, Christian Schmauder, Ralf Schulz, Eckhard |
author_facet | Benndorf, Klaus Eick, Thomas Sattler, Christian Schmauder, Ralf Schulz, Eckhard |
author_sort | Benndorf, Klaus |
collection | PubMed |
description | Ligand-gated ion channels are oligomers containing several binding sites for the ligands. However, the signal transmission from the ligand binding site to the pore has not yet been fully elucidated for any of these channels. In heteromeric channels, the situation is even more complex than in homomeric channels. Using published data for concatamers of heteromeric cyclic nucleotide–gated channels, we show that, on theoretical grounds, multiple functional parameters of the individual subunits can be determined with high precision. The main components of our strategy are (1) the generation of a defined subunit composition by concatenating multiple subunits, (2) the construction of 16 concatameric channels, which differ in systematically permutated binding sites, (3) the determination of respectively differing concentration–activation relationships, and (4) a complex global fit analysis with corresponding intimately coupled Markovian state models. The amount of constraints in this approach is exceedingly high. Furthermore, we propose a stochastic fit analysis with a scaled unitary start vector of identical elements to avoid any bias arising from a specific start vector. Our approach enabled us to determine 23 free parameters, including 4 equilibrium constants for the closed–open isomerizations, 4 disabling factors for the mutations of the different subunits, and 15 virtual equilibrium-association constants in the context of a 4-D hypercube. From the virtual equilibrium-association constants, we could determine 32 equilibrium-association constants of the subunits at different degrees of ligand binding. Our strategy can be generalized and is therefore adaptable to other ion channels. |
format | Online Article Text |
id | pubmed-9066054 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Rockefeller University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-90660542022-12-06 A strategy for determining the equilibrium constants for heteromeric ion channels in a complex model Benndorf, Klaus Eick, Thomas Sattler, Christian Schmauder, Ralf Schulz, Eckhard J Gen Physiol Article Ligand-gated ion channels are oligomers containing several binding sites for the ligands. However, the signal transmission from the ligand binding site to the pore has not yet been fully elucidated for any of these channels. In heteromeric channels, the situation is even more complex than in homomeric channels. Using published data for concatamers of heteromeric cyclic nucleotide–gated channels, we show that, on theoretical grounds, multiple functional parameters of the individual subunits can be determined with high precision. The main components of our strategy are (1) the generation of a defined subunit composition by concatenating multiple subunits, (2) the construction of 16 concatameric channels, which differ in systematically permutated binding sites, (3) the determination of respectively differing concentration–activation relationships, and (4) a complex global fit analysis with corresponding intimately coupled Markovian state models. The amount of constraints in this approach is exceedingly high. Furthermore, we propose a stochastic fit analysis with a scaled unitary start vector of identical elements to avoid any bias arising from a specific start vector. Our approach enabled us to determine 23 free parameters, including 4 equilibrium constants for the closed–open isomerizations, 4 disabling factors for the mutations of the different subunits, and 15 virtual equilibrium-association constants in the context of a 4-D hypercube. From the virtual equilibrium-association constants, we could determine 32 equilibrium-association constants of the subunits at different degrees of ligand binding. Our strategy can be generalized and is therefore adaptable to other ion channels. Rockefeller University Press 2022-04-29 /pmc/articles/PMC9066054/ /pubmed/35486087 http://dx.doi.org/10.1085/jgp.202113041 Text en © 2022 Benndorf et al. https://creativecommons.org/licenses/by-nc-sa/4.0/http://www.rupress.org/terms/This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/). |
spellingShingle | Article Benndorf, Klaus Eick, Thomas Sattler, Christian Schmauder, Ralf Schulz, Eckhard A strategy for determining the equilibrium constants for heteromeric ion channels in a complex model |
title | A strategy for determining the equilibrium constants for heteromeric ion channels in a complex model |
title_full | A strategy for determining the equilibrium constants for heteromeric ion channels in a complex model |
title_fullStr | A strategy for determining the equilibrium constants for heteromeric ion channels in a complex model |
title_full_unstemmed | A strategy for determining the equilibrium constants for heteromeric ion channels in a complex model |
title_short | A strategy for determining the equilibrium constants for heteromeric ion channels in a complex model |
title_sort | strategy for determining the equilibrium constants for heteromeric ion channels in a complex model |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9066054/ https://www.ncbi.nlm.nih.gov/pubmed/35486087 http://dx.doi.org/10.1085/jgp.202113041 |
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