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  In silico assessment of the conduction mechanism of the ryanodine receptor 1 reveals previously unknown exit pathways.

Heinz, L. P., Kopec, W., de Groot, B. L., & Fink, R. H. A. (2018). In silico assessment of the conduction mechanism of the ryanodine receptor 1 reveals previously unknown exit pathways. Scientific Reports, 8: 6886. doi:10.1038/s41598-018-25061-z.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0001-44D3-4 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-649C-D
Genre: Journal Article

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 Creators:
Heinz, L. P.1, Author              
Kopec, W.2, Author              
de Groot, B. L.2, Author              
Fink, R. H. A., Author
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for Biophysical Chemistry, Max Planck Society, ou_578631              
2Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578573              

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 Abstract: The ryanodine receptor 1 is a large calcium ion channel found in mammalian skeletal muscle. The ion channel gained a lot of attention recently, after multiple independent authors published near-atomic cryo electron microscopy data. Taking advantage of the unprecedented quality of structural data, we performed molecular dynamics simulations on the entire ion channel as well as on a reduced model. We calculated potentials of mean force for Ba2+, Ca2+, Mg2+, K+, Na+ and Cl- ions using umbrella sampling to identify the key residues involved in ion permeation. We found two main binding sites for the cations, whereas the channel is strongly repulsive for chloride ions. Furthermore, the data is consistent with the model that the receptor achieves its ion selectivity by over-affinity for divalent cations in a calcium-block-like fashion. We reproduced the experimental conductance for potassium ions in permeation simulations with applied voltage. The analysis of the permeation paths shows that ions exit the pore via multiple pathways, which we suggest to be related to the experimental observation of different subconducting states.

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Language(s): eng - English
 Dates: 2018-05-02
 Publication Status: Published online
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 Rev. Method: Peer
 Identifiers: DOI: 10.1038/s41598-018-25061-z.
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Title: Scientific Reports
Source Genre: Journal
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Pages: 12 Volume / Issue: 8 Sequence Number: 6886 Start / End Page: - Identifier: -