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Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel

As the first potassium channel with an x-ray structure determined, and given its homology to eukaryotic channels, the pH-gated prokaryotic channel KcsA has been extensively studied. Nevertheless, questions related, in particular, to the allosteric coupling between its gates remain open. The many cur...

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Autores principales: Pérez-Conesa, Sergio, Keeler, Eric G., Zhang, Dongyu, Delemotte, Lucie, McDermott, Ann E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: AIP Publishing LLC 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9250420/
https://www.ncbi.nlm.nih.gov/pubmed/33940802
http://dx.doi.org/10.1063/5.0040649
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author Pérez-Conesa, Sergio
Keeler, Eric G.
Zhang, Dongyu
Delemotte, Lucie
McDermott, Ann E.
author_facet Pérez-Conesa, Sergio
Keeler, Eric G.
Zhang, Dongyu
Delemotte, Lucie
McDermott, Ann E.
author_sort Pérez-Conesa, Sergio
collection PubMed
description As the first potassium channel with an x-ray structure determined, and given its homology to eukaryotic channels, the pH-gated prokaryotic channel KcsA has been extensively studied. Nevertheless, questions related, in particular, to the allosteric coupling between its gates remain open. The many currently available x-ray crystallography structures appear to correspond to various stages of activation and inactivation, offering insights into the molecular basis of these mechanisms. Since these studies have required mutations, complexation with antibodies, and substitution of detergents in place of lipids, examining the channel under more native conditions is desirable. Solid-state nuclear magnetic resonance (SSNMR) can be used to study the wild-type protein under activating conditions (low pH), at room temperature, and in bacteriomimetic liposomes. In this work, we sought to structurally assign the activated state present in SSNMR experiments. We used a combination of molecular dynamics (MD) simulations, chemical shift prediction algorithms, and Bayesian inference techniques to determine which of the most plausible x-ray structures resolved to date best represents the activated state captured in SSNMR. We first identified specific nuclei with simulated NMR chemical shifts that differed significantly when comparing partially open vs fully open ensembles from MD simulations. The simulated NMR chemical shifts for those specific nuclei were then compared to experimental ones, revealing that the simulation of the partially open state was in good agreement with the SSNMR data. Nuclei that discriminate effectively between partially and fully open states belong to residues spread over the sequence and provide a molecular level description of the conformational change.
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spelling pubmed-92504202022-07-03 Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel Pérez-Conesa, Sergio Keeler, Eric G. Zhang, Dongyu Delemotte, Lucie McDermott, Ann E. J Chem Phys ARTICLES As the first potassium channel with an x-ray structure determined, and given its homology to eukaryotic channels, the pH-gated prokaryotic channel KcsA has been extensively studied. Nevertheless, questions related, in particular, to the allosteric coupling between its gates remain open. The many currently available x-ray crystallography structures appear to correspond to various stages of activation and inactivation, offering insights into the molecular basis of these mechanisms. Since these studies have required mutations, complexation with antibodies, and substitution of detergents in place of lipids, examining the channel under more native conditions is desirable. Solid-state nuclear magnetic resonance (SSNMR) can be used to study the wild-type protein under activating conditions (low pH), at room temperature, and in bacteriomimetic liposomes. In this work, we sought to structurally assign the activated state present in SSNMR experiments. We used a combination of molecular dynamics (MD) simulations, chemical shift prediction algorithms, and Bayesian inference techniques to determine which of the most plausible x-ray structures resolved to date best represents the activated state captured in SSNMR. We first identified specific nuclei with simulated NMR chemical shifts that differed significantly when comparing partially open vs fully open ensembles from MD simulations. The simulated NMR chemical shifts for those specific nuclei were then compared to experimental ones, revealing that the simulation of the partially open state was in good agreement with the SSNMR data. Nuclei that discriminate effectively between partially and fully open states belong to residues spread over the sequence and provide a molecular level description of the conformational change. AIP Publishing LLC 2021-04-28 2021-04-22 /pmc/articles/PMC9250420/ /pubmed/33940802 http://dx.doi.org/10.1063/5.0040649 Text en © 2021 Author(s). 0021-9606/2021/154(16)/165102/15/$0.00 https://creativecommons.org/licenses/by/4.0/All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle ARTICLES
Pérez-Conesa, Sergio
Keeler, Eric G.
Zhang, Dongyu
Delemotte, Lucie
McDermott, Ann E.
Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel
title Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel
title_full Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel
title_fullStr Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel
title_full_unstemmed Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel
title_short Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel
title_sort informing nmr experiments with molecular dynamics simulations to characterize the dominant activated state of the kcsa ion channel
topic ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9250420/
https://www.ncbi.nlm.nih.gov/pubmed/33940802
http://dx.doi.org/10.1063/5.0040649
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